Merge branch 'develop' of https://github.com/LLNL/spack into features/install_with_phases

Conflicts:
	lib/spack/llnl/util/tty/log.py
	lib/spack/spack/__init__.py
	lib/spack/spack/cmd/install.py
	lib/spack/spack/cmd/setup.py
	lib/spack/spack/package.py
	var/spack/repos/builtin/packages/blitz/package.py
	var/spack/repos/builtin/packages/gmp/package.py
	var/spack/repos/builtin/packages/qhull/package.py
	var/spack/repos/builtin/packages/szip/package.py

770 files changed, 14263 insertions, 4383 deletions

diff --git a/.flake8 b/.flake8
index 286522bc48..b178a2da57 100644
--- a/.flake8
+++ b/.flake8
@@ -19,5 +19,5 @@
 # - F999: name name be undefined or undefined from star imports.
 #
 [flake8]
-ignore = E221,E241,E731,F403,F821,F999,F405
+ignore = E129,E221,E241,E272,E731,F403,F821,F999,F405
 max-line-length = 79
diff --git a/.gitignore b/.gitignore
index 960b5b0035..b1215f0c7e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,5 +1,7 @@
 /var/spack/stage
 /var/spack/cache
+/var/spack/repos/*/index.yaml
+/var/spack/repos/*/lock
 *.pyc
 /opt
 *~
diff --git a/.travis.yml b/.travis.yml
index 904143a00f..b376a33490 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,7 +1,17 @@
 language: python
+
 python:
   - "2.6"
   - "2.7"
+env:
+  - TEST_TYPE=unit
+  - TEST_TYPE=flake8
+
+# Exclude flake8 from python 2.6
+matrix:
+  exclude:
+  - python: "2.6"
+    env: TEST_TYPE=flake8
 
 # Use new Travis infrastructure (Docker can't sudo yet)
 sudo: false
@@ -20,20 +30,13 @@ before_install:
   - git fetch origin develop:develop
 
 script:
-  # Regular spack setup and tests
-  - . share/spack/setup-env.sh
-  - spack compilers
-  - spack config get compilers
-  - spack install -v libdwarf
-
-  # Run unit tests with code coverage
-  - coverage run bin/spack test
-
+  # Run unit tests with code coverage plus install libdwarf
+  - 'if [ "$TEST_TYPE" = "unit" ]; then share/spack/qa/run-unit-tests; fi'
   # Run flake8 code style checks.
-  - share/spack/qa/run-flake8
+  - 'if [ "$TEST_TYPE" = "flake8" ]; then share/spack/qa/run-flake8; fi'
 
 after_success:
-  - coveralls
+  - 'if [ "$TEST_TYPE" = "unit" ] && [ "$TRAVIS_PYTHON_VERSION" = "2.7" ]; then coveralls; fi'
 
 notifications:
   email:
diff --git a/README.md b/README.md
index fe00e2af27..5d5ac7dd39 100644
--- a/README.md
+++ b/README.md
@@ -58,17 +58,24 @@ can join it here:
 
 ### Contributions
 
-At the moment, contributing to Spack is relatively simple.  Just send us
-a [pull request](https://help.github.com/articles/using-pull-requests/).
+Contributing to Spack is relatively.  Just send us a
+[pull request](https://help.github.com/articles/using-pull-requests/).
 When you send your request, make ``develop`` the destination branch on the
 [Spack repository](https://github.com/LLNL/spack).
 
-Your contribution will need to pass all the tests run by the `spack test`
-command, as well as the formatting checks in `share/spack/qa/run-flake8`.
-You should run both of these before submitting your pull request, to
-ensure that the online checks succeed.
+Before you send a PR, your code should pass the following checks:
 
-Spack is using a rough approximation of the [Git
+* Your contribution will need to pass the `spack test` command.
+  Run this before submitting your PR.
+
+* Also run the `share/spack/qa/run-flake8` script to check for PEP8 compliance.
+  To encourage contributions and readability by a broad audience,
+  Spack uses the [PEP8](https://www.python.org/dev/peps/pep-0008/) coding
+  standard with [a few exceptions](https://github.com/LLNL/spack/blob/develop/.flake8).
+
+We enforce these guidelines with [Travis CI](https://travis-ci.org/LLNL/spack).
+
+Spack uses a rough approximation of the [Git
 Flow](http://nvie.com/posts/a-successful-git-branching-model/)
 branching model.  The ``develop`` branch contains the latest
 contributions, and ``master`` is always tagged and points to the
diff --git a/bin/spack b/bin/spack
index e9307d1485..9fed11f33b 100755
--- a/bin/spack
+++ b/bin/spack
@@ -1,4 +1,5 @@
 #!/usr/bin/env python
+# flake8: noqa
 ##############################################################################
 # Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
@@ -24,9 +25,10 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import sys
-if not sys.version_info[:2] >= (2,6):
+if not sys.version_info[:2] >= (2, 6):
     v_info = sys.version_info[:3]
-    sys.exit("Spack requires Python 2.6 or higher.  This is Python %d.%d.%d." % v_info)
+    sys.exit("Spack requires Python 2.6 or higher. "
+             "This is Python %d.%d.%d." % v_info)
 
 import os
 
@@ -62,7 +64,8 @@ for pyc_file in orphaned_pyc_files:
     try:
         os.remove(pyc_file)
     except OSError as e:
-        print "WARNING: Spack may fail mysteriously. Couldn't remove orphaned .pyc file: %s" % pyc_file
+        print ("WARNING: Spack may fail mysteriously. "
+               "Couldn't remove orphaned .pyc file: %s" % pyc_file)
 
 # If there is no working directory, use the spack prefix.
 try:
@@ -128,6 +131,7 @@ if len(sys.argv) == 1:
 # actually parse the args.
 args = parser.parse_args()
 
+
 def main():
     # Set up environment based on args.
     tty.set_verbose(args.verbose)
@@ -148,7 +152,7 @@ def main():
 
     # If the user asked for it, don't check ssl certs.
     if args.insecure:
-        tty.warn("You asked for --insecure, which does not check SSL certificates.")
+        tty.warn("You asked for --insecure. Will NOT check SSL certificates.")
         spack.curl.add_default_arg('-k')
 
     # Try to load the particular command asked for and run it
@@ -167,7 +171,8 @@ def main():
     elif isinstance(return_val, int):
         sys.exit(return_val)
     else:
-        tty.die("Bad return value from command %s: %s" % (args.command, return_val))
+        tty.die("Bad return value from command %s: %s"
+                % (args.command, return_val))
 
 if args.profile:
     import cProfile
diff --git a/lib/spack/docs/basic_usage.rst b/lib/spack/docs/basic_usage.rst
index 50a161a175..a42d941791 100644
--- a/lib/spack/docs/basic_usage.rst
+++ b/lib/spack/docs/basic_usage.rst
@@ -546,7 +546,7 @@ More formally, a spec consists of the following pieces:
   boolean variants
 * ``name=<value>`` Optional compiler flag specifiers. Valid flag names are
   ``cflags``, ``cxxflags``, ``fflags``, ``cppflags``, ``ldflags``, and ``ldlibs``.
-* ``target=<value> os=<value>`` Optional architecture specifier 
+* ``target=<value> os=<value>`` Optional architecture specifier
   (``target=haswell os=CNL10``)
 * ``^`` Dependency specs (``^callpath@1.1``)
 
@@ -764,12 +764,12 @@ words ``target`` and/or ``os`` (``target=x86-64 os=debian7``). You can also
 use the triplet form of platform, operating system and processor.
 
 .. code-block:: sh
-    
+
     spack install libelf arch=cray_xc-CNL10-haswell
 
 Users on non-Cray systems won't have to worry about specifying the architecture.
 Spack will autodetect what kind of operating system is on your machine as well
-as the processor. For more information on how the architecture can be 
+as the processor. For more information on how the architecture can be
 used on Cray machines, check here :ref:`spack-cray`
 
 
@@ -1147,18 +1147,19 @@ packages use RPATH to find their dependencies: this can be true in
 particular for Python extensions, which are currently *not* built with
 RPATH.
 
-Modules may be loaded recursively with the command:
+Modules may be loaded recursively with the ``load`` command's
+``--dependencies`` or ``-r`` argument:
 
 .. code-block:: sh
 
-    $ module load `spack module tcl --dependencies <spec>...
+    $ spack load --dependencies <spec> ...
 
 More than one spec may be placed on the command line here.
 
 Module Commands for Shell Scripts
 ``````````````````````````````````
 
-Although Spack is flexbile, the ``module`` command is much faster.
+Although Spack is flexible, the ``module`` command is much faster.
 This could become an issue when emitting a series of ``spack load``
 commands inside a shell script.  By adding the ``--shell`` flag,
 ``spack module find`` may also be used to generate code that can be
@@ -1793,36 +1794,36 @@ A nicer error message is TBD in future versions of Spack.
 Spack on Cray
 -----------------------------
 
-Spack differs slightly when used on a Cray system. The architecture spec 
+Spack differs slightly when used on a Cray system. The architecture spec
 can differentiate between the front-end and back-end processor and operating system.
-For example, on Edison at NERSC, the back-end target processor 
+For example, on Edison at NERSC, the back-end target processor
 is \"Ivy Bridge\", so you can specify to use the back-end this way:
 
 .. code-block:: sh
-    
+
     spack install zlib target=ivybridge
 
 You can also use the operating system to build against the back-end:
 
 .. code-block:: sh
-    
+
     spack install zlib os=CNL10
 
-Notice that the name includes both the operating system name and the major 
+Notice that the name includes both the operating system name and the major
 version number concatenated together.
 
-Alternatively, if you want to build something for the front-end, 
-you can specify the front-end target processor. The processor for a login node 
+Alternatively, if you want to build something for the front-end,
+you can specify the front-end target processor. The processor for a login node
 on Edison is \"Sandy bridge\" so we specify on the command line like so:
 
 .. code-block:: sh
-    
+
     spack install zlib target=sandybridge
 
 And the front-end operating system is:
 
 .. code-block:: sh
-    
+
     spack install zlib os=SuSE11
 
 
@@ -1830,13 +1831,13 @@ And the front-end operating system is:
 Cray compiler detection
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-Spack can detect compilers using two methods. For the front-end, we treat 
-everything the same. The difference lies in back-end compiler detection. 
-Back-end compiler detection is made via the Tcl module avail command. 
-Once it detects the compiler it writes the appropriate PrgEnv and compiler 
-module name to compilers.yaml and sets the paths to each compiler with Cray\'s 
-compiler wrapper names (i.e. cc, CC, ftn). During build time, Spack will load 
-the correct PrgEnv and compiler module and will call appropriate wrapper. 
+Spack can detect compilers using two methods. For the front-end, we treat
+everything the same. The difference lies in back-end compiler detection.
+Back-end compiler detection is made via the Tcl module avail command.
+Once it detects the compiler it writes the appropriate PrgEnv and compiler
+module name to compilers.yaml and sets the paths to each compiler with Cray\'s
+compiler wrapper names (i.e. cc, CC, ftn). During build time, Spack will load
+the correct PrgEnv and compiler module and will call appropriate wrapper.
 
 The compilers.yaml config file will also differ. There is a
 modules section that is filled with the compiler\'s Programming Environment
@@ -1849,8 +1850,8 @@ and module name. On other systems, this field is empty []::
           - intel/15.0.109
     ...
 
-As mentioned earlier, the compiler paths will look different on a Cray system. 
-Since most compilers are invoked using cc, CC and ftn, the paths for each 
+As mentioned earlier, the compiler paths will look different on a Cray system.
+Since most compilers are invoked using cc, CC and ftn, the paths for each
 compiler are replaced with their respective Cray compiler wrapper names::
 
     ...
@@ -1862,10 +1863,14 @@ compiler are replaced with their respective Cray compiler wrapper names::
     ...
 
 As opposed to an explicit path to the compiler executable. This allows Spack
-to call the Cray compiler wrappers during build time. 
+to call the Cray compiler wrappers during build time.
 
 For more on compiler configuration, check out :ref:`compiler-config`.
 
+Spack sets the default Cray link type to dynamic, to better match other
+other platforms. Individual packages can enable static linking (which is the
+default outside of Spack on cray systems) using the -static flag.
+
 Setting defaults and using Cray modules
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -1885,11 +1890,11 @@ Here\'s an example of an external configuration for cray modules:
 This tells Spack that for whatever package that depends on mpi, load the
 cray-mpich module into the environment. You can then be able to use whatever
 environment variables, libraries, etc, that are brought into the environment
-via module load. 
+via module load.
 
-You can set the default compiler that Spack can use for each compiler type. 
-If you want to use the Cray defaults, then set them under *all:* in packages.yaml. 
-In the compiler field, set the compiler specs in your order of preference. 
+You can set the default compiler that Spack can use for each compiler type.
+If you want to use the Cray defaults, then set them under *all:* in packages.yaml.
+In the compiler field, set the compiler specs in your order of preference.
 Whenever you build with that compiler type, Spack will concretize to that version.
 
 Here is an example of a full packages.yaml used at NERSC
@@ -1917,11 +1922,11 @@ Here is an example of a full packages.yaml used at NERSC
 
 Here we tell spack that whenever we want to build with gcc use version 5.2.0 or
 if we want to build with intel compilers, use version 16.0.0.109. We add a spec
-for each compiler type for each cray modules. This ensures that for each 
+for each compiler type for each cray modules. This ensures that for each
 compiler on our system we can use that external module.
 
 
-For more on external packages check out the section :ref:`sec-external_packages`. 
+For more on external packages check out the section :ref:`sec-external_packages`.
 
 Getting Help
 -----------------------
diff --git a/lib/spack/docs/configuration.rst b/lib/spack/docs/configuration.rst
index f2ffa07264..d39c932021 100644
--- a/lib/spack/docs/configuration.rst
+++ b/lib/spack/docs/configuration.rst
@@ -142,8 +142,9 @@ Here's an example packages.yaml file that sets preferred packages:
 .. code-block:: sh
 
     packages:
-      dyninst:
+      opencv:
         compiler: [gcc@4.9]
+        variants: +debug
       gperftools:
         version: [2.2, 2.4, 2.3]
       all:
@@ -153,17 +154,17 @@ Here's an example packages.yaml file that sets preferred packages:
 
 
 At a high level, this example is specifying how packages should be
-concretized.  The dyninst package should prefer using gcc 4.9.
-The gperftools package should prefer version
+concretized.  The opencv package should prefer using gcc 4.9 and
+be built with debug options.  The gperftools package should prefer version
 2.2 over 2.4.  Every package on the system should prefer mvapich for
-its MPI and gcc 4.4.7 (except for Dyninst, which overrides this by preferring gcc 4.9).
+its MPI and gcc 4.4.7 (except for opencv, which overrides this by preferring gcc 4.9).
 These options are used to fill in implicit defaults.  Any of them can be overwritten
 on the command line if explicitly requested.
 
 Each packages.yaml file begins with the string ``packages:`` and
 package names are specified on the next level. The special string ``all``
 applies settings to each package. Underneath each package name is
-one or more components: ``compiler``, ``version``,
+one or more components: ``compiler``, ``variants``, ``version``,
 or ``providers``.  Each component has an ordered list of spec
 ``constraints``, with earlier entries in the list being preferred over
 later entries.
diff --git a/lib/spack/docs/packaging_guide.rst b/lib/spack/docs/packaging_guide.rst
index 6bafaecc7d..70def5c39a 100644
--- a/lib/spack/docs/packaging_guide.rst
+++ b/lib/spack/docs/packaging_guide.rst
@@ -1307,9 +1307,9 @@ The dependency types are:
 
 If not specified, ``type`` is assumed to be ``("build", "link")``. This is the
 common case for compiled language usage. Also available are the aliases
-``alldeps`` for all dependency types and ``nolink`` (``("build", "run")``) for
-use by dependencies which are not expressed via a linker (e.g., Python or Lua
-module loading).
+``"alldeps"`` for all dependency types and ``"nolink"`` (``("build", "run")``)
+for use by dependencies which are not expressed via a linker (e.g., Python or
+Lua module loading).
 
 .. _setup-dependent-environment:
 
diff --git a/lib/spack/env/cray/CC b/lib/spack/env/cray/CC
new file mode 120000
index 0000000000..82c2b8e90a
--- /dev/null
+++ b/lib/spack/env/cray/CC
@@ -0,0 +1 @@
+../cc
\ No newline at end of file
diff --git a/lib/spack/env/cray/cc b/lib/spack/env/cray/cc
new file mode 120000
index 0000000000..82c2b8e90a
--- /dev/null
+++ b/lib/spack/env/cray/cc
@@ -0,0 +1 @@
+../cc
\ No newline at end of file
diff --git a/lib/spack/env/cray/ftn b/lib/spack/env/cray/ftn
new file mode 120000
index 0000000000..82c2b8e90a
--- /dev/null
+++ b/lib/spack/env/cray/ftn
@@ -0,0 +1 @@
+../cc
\ No newline at end of file
diff --git a/lib/spack/llnl/util/filesystem.py b/lib/spack/llnl/util/filesystem.py
index 6e4cd338fe..22ca85abf9 100644
--- a/lib/spack/llnl/util/filesystem.py
+++ b/lib/spack/llnl/util/filesystem.py
@@ -29,8 +29,9 @@ import shutil
 import stat
 import errno
 import getpass
-from contextlib import contextmanager, closing
+from contextlib import contextmanager
 import subprocess
+import fileinput
 
 import llnl.util.tty as tty
 
@@ -85,13 +86,14 @@ def filter_file(regex, repl, *filenames, **kwargs):
         if ignore_absent and not os.path.exists(filename):
             continue
 
-        shutil.copy(filename, backup_filename)
+        # Create backup file. Don't overwrite an existing backup
+        # file in case this file is being filtered multiple times.
+        if not os.path.exists(backup_filename):
+            shutil.copy(filename, backup_filename)
+
         try:
-            with closing(open(backup_filename)) as infile:
-                with closing(open(filename, 'w')) as outfile:
-                    for line in infile:
-                        foo = re.sub(regex, repl, line)
-                        outfile.write(foo)
+            for line in fileinput.input(filename, inplace=True):
+                print(re.sub(regex, repl, line.rstrip('\n')))
         except:
             # clean up the original file on failure.
             shutil.move(backup_filename, filename)
@@ -104,6 +106,7 @@ def filter_file(regex, repl, *filenames, **kwargs):
 
 class FileFilter(object):
     """Convenience class for calling filter_file a lot."""
+
     def __init__(self, *filenames):
         self.filenames = filenames
 
@@ -189,7 +192,7 @@ def install(src, dest):
 
 
 def install_tree(src, dest, **kwargs):
-    """Manually install a file to a particular location."""
+    """Manually install a directory tree to a particular location."""
     tty.debug("Installing %s to %s" % (src, dest))
     shutil.copytree(src, dest, **kwargs)
 
@@ -353,7 +356,8 @@ def traverse_tree(source_root, dest_root, rel_path='', **kwargs):
             # When follow_nonexisting isn't set, don't descend into dirs
             # in source that do not exist in dest
             if follow_nonexisting or os.path.exists(dest_child):
-                tuples = traverse_tree(source_root, dest_root, rel_child, **kwargs)  # NOQA: ignore=E501
+                tuples = traverse_tree(
+                    source_root, dest_root, rel_child, **kwargs)
                 for t in tuples:
                     yield t
 
@@ -420,14 +424,20 @@ def fix_darwin_install_name(path):
     libs = glob.glob(join_path(path, "*.dylib"))
     for lib in libs:
         # fix install name first:
-        subprocess.Popen(["install_name_tool", "-id", lib, lib], stdout=subprocess.PIPE).communicate()[0]  # NOQA: ignore=E501
-        long_deps = subprocess.Popen(["otool", "-L", lib], stdout=subprocess.PIPE).communicate()[0].split('\n')  # NOQA: ignore=E501
+        subprocess.Popen(
+            ["install_name_tool", "-id", lib, lib],
+            stdout=subprocess.PIPE).communicate()[0]
+        long_deps = subprocess.Popen(
+            ["otool", "-L", lib],
+            stdout=subprocess.PIPE).communicate()[0].split('\n')
         deps = [dep.partition(' ')[0][1::] for dep in long_deps[2:-1]]
         # fix all dependencies:
         for dep in deps:
             for loc in libs:
                 if dep == os.path.basename(loc):
-                    subprocess.Popen(["install_name_tool", "-change", dep, loc, lib], stdout=subprocess.PIPE).communicate()[0]  # NOQA: ignore=E501
+                    subprocess.Popen(
+                        ["install_name_tool", "-change", dep, loc, lib],
+                        stdout=subprocess.PIPE).communicate()[0]
                     break
 
 
diff --git a/lib/spack/llnl/util/lang.py b/lib/spack/llnl/util/lang.py
index 63eb08d803..df32012e2d 100644
--- a/lib/spack/llnl/util/lang.py
+++ b/lib/spack/llnl/util/lang.py
@@ -24,7 +24,6 @@
 ##############################################################################
 import os
 import re
-import sys
 import functools
 import collections
 import inspect
@@ -39,14 +38,15 @@ def index_by(objects, *funcs):
        Values are used as keys.  For example, suppose you have four
        objects with attributes that look like this:
 
-           a = Spec(name="boost",    compiler="gcc",   arch="bgqos_0")
-           b = Spec(name="mrnet",    compiler="intel", arch="chaos_5_x86_64_ib")
-           c = Spec(name="libelf",   compiler="xlc",   arch="bgqos_0")
-           d = Spec(name="libdwarf", compiler="intel", arch="chaos_5_x86_64_ib")
+          a = Spec(name="boost",    compiler="gcc",   arch="bgqos_0")
+          b = Spec(name="mrnet",    compiler="intel", arch="chaos_5_x86_64_ib")
+          c = Spec(name="libelf",   compiler="xlc",   arch="bgqos_0")
+          d = Spec(name="libdwarf", compiler="intel", arch="chaos_5_x86_64_ib")
 
-           list_of_specs = [a,b,c,d]
-           index1 = index_by(list_of_specs, lambda s: s.arch, lambda s: s.compiler)
-           index2 = index_by(list_of_specs, lambda s: s.compiler)
+          list_of_specs = [a,b,c,d]
+          index1 = index_by(list_of_specs, lambda s: s.arch,
+                            lambda s: s.compiler)
+          index2 = index_by(list_of_specs, lambda s: s.compiler)
 
        ``index1'' now has two levels of dicts, with lists at the
        leaves, like this:
@@ -137,7 +137,7 @@ def get_calling_module_name():
     finally:
         del stack
 
-    if not '__module__' in caller_locals:
+    if '__module__' not in caller_locals:
         raise RuntimeError("Must invoke get_calling_module_name() "
                            "from inside a class definition!")
 
@@ -173,11 +173,11 @@ def has_method(cls, name):
 class memoized(object):
     """Decorator that caches the results of a function, storing them
        in an attribute of that function."""
+
     def __init__(self, func):
         self.func = func
         self.cache = {}
 
-
     def __call__(self, *args):
         if not isinstance(args, collections.Hashable):
             # Not hashable, so just call the function.
@@ -187,12 +187,10 @@ class memoized(object):
             self.cache[args] = self.func(*args)
         return self.cache[args]
 
-
     def __get__(self, obj, objtype):
         """Support instance methods."""
         return functools.partial(self.__call__, obj)
 
-
     def clear(self):
         """Expunge cache so that self.func will be called again."""
         self.cache.clear()
@@ -237,13 +235,21 @@ def key_ordering(cls):
     if not has_method(cls, '_cmp_key'):
         raise TypeError("'%s' doesn't define _cmp_key()." % cls.__name__)
 
-    setter('__eq__', lambda s,o: (s is o) or (o is not None and s._cmp_key() == o._cmp_key()))
-    setter('__lt__', lambda s,o: o is not None and s._cmp_key() <  o._cmp_key())
-    setter('__le__', lambda s,o: o is not None and s._cmp_key() <= o._cmp_key())
-
-    setter('__ne__', lambda s,o: (s is not o) and (o is None or s._cmp_key() != o._cmp_key()))
-    setter('__gt__', lambda s,o: o is None or s._cmp_key() >  o._cmp_key())
-    setter('__ge__', lambda s,o: o is None or s._cmp_key() >= o._cmp_key())
+    setter('__eq__',
+           lambda s, o:
+           (s is o) or (o is not None and s._cmp_key() == o._cmp_key()))
+    setter('__lt__',
+           lambda s, o: o is not None and s._cmp_key() < o._cmp_key())
+    setter('__le__',
+           lambda s, o: o is not None and s._cmp_key() <= o._cmp_key())
+
+    setter('__ne__',
+           lambda s, o:
+           (s is not o) and (o is None or s._cmp_key() != o._cmp_key()))
+    setter('__gt__',
+           lambda s, o: o is None or s._cmp_key() > o._cmp_key())
+    setter('__ge__',
+           lambda s, o: o is None or s._cmp_key() >= o._cmp_key())
 
     setter('__hash__', lambda self: hash(self._cmp_key()))
 
@@ -254,10 +260,10 @@ def key_ordering(cls):
 class HashableMap(dict):
     """This is a hashable, comparable dictionary.  Hash is performed on
        a tuple of the values in the dictionary."""
+
     def _cmp_key(self):
         return tuple(sorted(self.values()))
 
-
     def copy(self):
         """Type-agnostic clone method.  Preserves subclass type."""
         # Construct a new dict of my type
@@ -336,24 +342,39 @@ def match_predicate(*args):
     return match
 
 
-
 def DictWrapper(dictionary):
     """Returns a class that wraps a dictionary and enables it to be used
        like an object."""
     class wrapper(object):
-        def __getattr__(self, name):        return dictionary[name]
-        def __setattr__(self, name, value): dictionary[name] = value
-        def setdefault(self, *args):        return dictionary.setdefault(*args)
-        def get(self, *args):               return dictionary.get(*args)
-        def keys(self):                     return dictionary.keys()
-        def values(self):                   return dictionary.values()
-        def items(self):                    return dictionary.items()
-        def __iter__(self):                 return iter(dictionary)
 
+        def __getattr__(self, name):
+            return dictionary[name]
+
+        def __setattr__(self, name, value):
+            dictionary[name] = value
+
+        def setdefault(self, *args):
+            return dictionary.setdefault(*args)
+
+        def get(self, *args):
+            return dictionary.get(*args)
+
+        def keys(self):
+            return dictionary.keys()
+
+        def values(self):
+            return dictionary.values()
+
+        def items(self):
+            return dictionary.items()
+
+        def __iter__(self):
+            return iter(dictionary)
 
     return wrapper()
 
 
 class RequiredAttributeError(ValueError):
+
     def __init__(self, message):
         super(RequiredAttributeError, self).__init__(message)
diff --git a/lib/spack/llnl/util/link_tree.py b/lib/spack/llnl/util/link_tree.py
index b6d8796084..d6547e933a 100644
--- a/lib/spack/llnl/util/link_tree.py
+++ b/lib/spack/llnl/util/link_tree.py
@@ -23,12 +23,13 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 """LinkTree class for setting up trees of symbolic links."""
-__all__ = ['LinkTree']
 
 import os
 import shutil
 from llnl.util.filesystem import *
 
+__all__ = ['LinkTree']
+
 empty_file_name = '.spack-empty'
 
 
@@ -43,13 +44,13 @@ class LinkTree(object):
     modified.
 
     """
+
     def __init__(self, source_root):
         if not os.path.exists(source_root):
             raise IOError("No such file or directory: '%s'", source_root)
 
         self._root = source_root
 
-
     def find_conflict(self, dest_root, **kwargs):
         """Returns the first file in dest that conflicts with src"""
         kwargs['follow_nonexisting'] = False
@@ -61,9 +62,9 @@ class LinkTree(object):
                 return dest
         return None
 
-
     def merge(self, dest_root, **kwargs):
-        """Link all files in src into dest, creating directories if necessary."""
+        """Link all files in src into dest, creating directories
+           if necessary."""
         kwargs['order'] = 'pre'
         for src, dest in traverse_tree(self._root, dest_root, **kwargs):
             if os.path.isdir(src):
@@ -83,7 +84,6 @@ class LinkTree(object):
                 assert(not os.path.exists(dest))
                 os.symlink(src, dest)
 
-
     def unmerge(self, dest_root, **kwargs):
         """Unlink all files in dest that exist in src.
 
diff --git a/lib/spack/llnl/util/lock.py b/lib/spack/llnl/util/lock.py
index 479a1b0167..aa8272d5fe 100644
--- a/lib/spack/llnl/util/lock.py
+++ b/lib/spack/llnl/util/lock.py
@@ -28,6 +28,9 @@ import errno
 import time
 import socket
 
+__all__ = ['Lock', 'LockTransaction', 'WriteTransaction', 'ReadTransaction',
+           'LockError']
+
 # Default timeout in seconds, after which locks will raise exceptions.
 _default_timeout = 60
 
@@ -36,13 +39,21 @@ _sleep_time = 1e-5
 
 
 class Lock(object):
-    def __init__(self,file_path):
+    """This is an implementation of a filesystem lock using Python's lockf.
+
+    In Python, `lockf` actually calls `fcntl`, so this should work with any
+    filesystem implementation that supports locking through the fcntl calls.
+    This includes distributed filesystems like Lustre (when flock is enabled)
+    and recent NFS versions.
+
+    """
+
+    def __init__(self, file_path):
         self._file_path = file_path
         self._fd = None
         self._reads = 0
         self._writes = 0
 
-
     def _lock(self, op, timeout):
         """This takes a lock using POSIX locks (``fnctl.lockf``).
 
@@ -63,7 +74,9 @@ class Lock(object):
 
                 fcntl.lockf(self._fd, op | fcntl.LOCK_NB)
                 if op == fcntl.LOCK_EX:
-                    os.write(self._fd, "pid=%s,host=%s" % (os.getpid(), socket.getfqdn()))
+                    os.write(
+                        self._fd,
+                        "pid=%s,host=%s" % (os.getpid(), socket.getfqdn()))
                 return
 
             except IOError as error:
@@ -75,7 +88,6 @@ class Lock(object):
 
         raise LockError("Timed out waiting for lock.")
 
-
     def _unlock(self):
         """Releases a lock using POSIX locks (``fcntl.lockf``)
 
@@ -83,11 +95,10 @@ class Lock(object):
         be masquerading as write locks, but this removes either.
 
         """
-        fcntl.lockf(self._fd,fcntl.LOCK_UN)
+        fcntl.lockf(self._fd, fcntl.LOCK_UN)
         os.close(self._fd)
         self._fd = None
 
-
     def acquire_read(self, timeout=_default_timeout):
         """Acquires a recursive, shared lock for reading.
 
@@ -107,7 +118,6 @@ class Lock(object):
             self._reads += 1
             return False
 
-
     def acquire_write(self, timeout=_default_timeout):
         """Acquires a recursive, exclusive lock for writing.
 
@@ -127,7 +137,6 @@ class Lock(object):
             self._writes += 1
             return False
 
-
     def release_read(self):
         """Releases a read lock.
 
@@ -148,7 +157,6 @@ class Lock(object):
             self._reads -= 1
             return False
 
-
     def release_write(self):
         """Releases a write lock.
 
@@ -170,6 +178,70 @@ class Lock(object):
             return False
 
 
+class LockTransaction(object):
+    """Simple nested transaction context manager that uses a file lock.
+
+    This class can trigger actions when the lock is acquired for the
+    first time and released for the last.
+
+    If the acquire_fn returns a value, it is used as the return value for
+    __enter__, allowing it to be passed as the `as` argument of a `with`
+    statement.
+
+    If acquire_fn returns a context manager, *its* `__enter__` function will be
+    called in `__enter__` after acquire_fn, and its `__exit__` funciton will be
+    called before `release_fn` in `__exit__`, allowing you to nest a context
+    manager to be used along with the lock.
+
+    Timeout for lock is customizable.
+
+    """
+
+    def __init__(self, lock, acquire_fn=None, release_fn=None,
+                 timeout=_default_timeout):
+        self._lock = lock
+        self._timeout = timeout
+        self._acquire_fn = acquire_fn
+        self._release_fn = release_fn
+        self._as = None
+
+    def __enter__(self):
+        if self._enter() and self._acquire_fn:
+            self._as = self._acquire_fn()
+            if hasattr(self._as, '__enter__'):
+                return self._as.__enter__()
+            else:
+                return self._as
+
+    def __exit__(self, type, value, traceback):
+        suppress = False
+        if self._exit():
+            if self._as and hasattr(self._as, '__exit__'):
+                if self._as.__exit__(type, value, traceback):
+                    suppress = True
+            if self._release_fn:
+                if self._release_fn(type, value, traceback):
+                    suppress = True
+        return suppress
+
+
+class ReadTransaction(LockTransaction):
+
+    def _enter(self):
+        return self._lock.acquire_read(self._timeout)
+
+    def _exit(self):
+        return self._lock.release_read()
+
+
+class WriteTransaction(LockTransaction):
+
+    def _enter(self):
+        return self._lock.acquire_write(self._timeout)
+
+    def _exit(self):
+        return self._lock.release_write()
+
+
 class LockError(Exception):
     """Raised when an attempt to acquire a lock times out."""
-    pass
diff --git a/lib/spack/llnl/util/tty/__init__.py b/lib/spack/llnl/util/tty/__init__.py
index ee81e11a20..db74aaba6b 100644
--- a/lib/spack/llnl/util/tty/__init__.py
+++ b/lib/spack/llnl/util/tty/__init__.py
@@ -36,6 +36,7 @@ _debug   = False
 _verbose = False
 indent  = "  "
 
+
 def is_verbose():
     return _verbose
 
@@ -148,7 +149,8 @@ def get_yes_or_no(prompt, **kwargs):
     elif default_value is False:
         prompt += ' [y/N] '
     else:
-        raise ValueError("default for get_yes_no() must be True, False, or None.")
+        raise ValueError(
+            "default for get_yes_no() must be True, False, or None.")
 
     result = None
     while result is None:
@@ -174,8 +176,9 @@ def hline(label=None, **kwargs):
     char      = kwargs.pop('char', '-')
     max_width = kwargs.pop('max_width', 64)
     if kwargs:
-        raise TypeError("'%s' is an invalid keyword argument for this function."
-                        % next(kwargs.iterkeys()))
+        raise TypeError(
+            "'%s' is an invalid keyword argument for this function."
+            % next(kwargs.iterkeys()))
 
     rows, cols = terminal_size()
     if not cols:
@@ -200,7 +203,8 @@ def terminal_size():
     """Gets the dimensions of the console: (rows, cols)."""
     def ioctl_GWINSZ(fd):
         try:
-            rc = struct.unpack('hh', fcntl.ioctl(fd, termios.TIOCGWINSZ, '1234'))
+            rc = struct.unpack('hh', fcntl.ioctl(
+                fd, termios.TIOCGWINSZ, '1234'))
         except:
             return
         return rc
diff --git a/lib/spack/llnl/util/tty/colify.py b/lib/spack/llnl/util/tty/colify.py
index 81a83691d7..67acdfa517 100644
--- a/lib/spack/llnl/util/tty/colify.py
+++ b/lib/spack/llnl/util/tty/colify.py
@@ -27,15 +27,14 @@ Routines for printing columnar output.  See colify() for more information.
 """
 import os
 import sys
-import fcntl
-import termios
-import struct
 from StringIO import StringIO
 
 from llnl.util.tty import terminal_size
 from llnl.util.tty.color import clen, cextra
 
+
 class ColumnConfig:
+
     def __init__(self, cols):
         self.cols = cols
         self.line_length = 0
@@ -43,7 +42,8 @@ class ColumnConfig:
         self.widths = [0] * cols   # does not include ansi colors
 
     def __repr__(self):
-        attrs = [(a,getattr(self, a)) for a in dir(self) if not a.startswith("__")]
+        attrs = [(a, getattr(self, a))
+                 for a in dir(self) if not a.startswith("__")]
         return "<Config: %s>" % ", ".join("%s: %r" % a for a in attrs)
 
 
@@ -68,7 +68,7 @@ def config_variable_cols(elts, console_width, padding, cols=0):
     max_cols = min(len(elts), max_cols)
 
     # Range of column counts to try.  If forced, use the supplied value.
-    col_range = [cols] if cols else xrange(1, max_cols+1)
+    col_range = [cols] if cols else xrange(1, max_cols + 1)
 
     # Determine the most columns possible for the console width.
     configs = [ColumnConfig(c) for c in col_range]
@@ -106,7 +106,6 @@ def config_uniform_cols(elts, console_width, padding, cols=0):
 
     # 'clen' ignores length of ansi color sequences.
     max_len = max(clen(e) for e in elts) + padding
-    max_clen = max(len(e) for e in elts) + padding
     if cols == 0:
         cols = max(1, console_width / max_len)
         cols = min(len(elts), cols)
@@ -130,17 +129,19 @@ def colify(elts, **options):
     output=<stream>   A file object to write to.  Default is sys.stdout.
     indent=<int>      Optionally indent all columns by some number of spaces.
     padding=<int>     Spaces between columns.  Default is 2.
-    width=<int>       Width of the output.  Default is 80 if tty is not detected.
+    width=<int>       Width of the output.  Default is 80 if tty not detected.
 
     cols=<int>        Force number of columns. Default is to size to terminal,
                       or single-column if no tty
 
     tty=<bool>        Whether to attempt to write to a tty.  Default is to
-                      autodetect a tty. Set to False to force single-column output.
+                      autodetect a tty. Set to False to force
+                      single-column output.
 
-    method=<string>   Method to use to fit columns.  Options are variable or uniform.
-                      Variable-width columns are tighter, uniform columns are all the
-                      same width and fit less data on the screen.
+    method=<string>   Method to use to fit columns.  Options are variable or
+                      uniform. Variable-width columns are tighter, uniform
+                      columns are all the same width and fit less data on
+                      the screen.
     """
     # Get keyword arguments or set defaults
     cols         = options.pop("cols", 0)
@@ -152,8 +153,9 @@ def colify(elts, **options):
     console_cols = options.pop("width", None)
 
     if options:
-        raise TypeError("'%s' is an invalid keyword argument for this function."
-                        % next(options.iterkeys()))
+        raise TypeError(
+            "'%s' is an invalid keyword argument for this function."
+            % next(options.iterkeys()))
 
     # elts needs to be an array of strings so we can count the elements
     elts = [str(elt) for elt in elts]
@@ -167,7 +169,8 @@ def colify(elts, **options):
             r, c = env_size.split('x')
             console_rows, console_cols = int(r), int(c)
             tty = True
-        except: pass
+        except:
+            pass
 
     # Use only one column if not a tty.
     if not tty:
@@ -228,6 +231,7 @@ def colify_table(table, **options):
         raise ValueError("Table is empty in colify_table!")
 
     columns = len(table[0])
+
     def transpose():
         for i in xrange(columns):
             for row in table:
diff --git a/lib/spack/llnl/util/tty/color.py b/lib/spack/llnl/util/tty/color.py
index 0abcb09b97..b0c00f1502 100644
--- a/lib/spack/llnl/util/tty/color.py
+++ b/lib/spack/llnl/util/tty/color.py
@@ -75,25 +75,27 @@ To output an @, use '@@'.  To output a } inside braces, use '}}'.
 import re
 import sys
 
+
 class ColorParseError(Exception):
     """Raised when a color format fails to parse."""
+
     def __init__(self, message):
         super(ColorParseError, self).__init__(message)
 
 # Text styles for ansi codes
-styles = {'*'  : '1',       # bold
-          '_'  : '4',       # underline
-          None : '0' }      # plain
+styles = {'*': '1',       # bold
+          '_': '4',       # underline
+          None: '0'}      # plain
 
 # Dim and bright ansi colors
-colors = {'k' : 30, 'K' : 90,  # black
-          'r' : 31, 'R' : 91,  # red
-          'g' : 32, 'G' : 92,  # green
-          'y' : 33, 'Y' : 93,  # yellow
-          'b' : 34, 'B' : 94,  # blue
-          'm' : 35, 'M' : 95,  # magenta
-          'c' : 36, 'C' : 96,  # cyan
-          'w' : 37, 'W' : 97 } # white
+colors = {'k': 30, 'K': 90,  # black
+          'r': 31, 'R': 91,  # red
+          'g': 32, 'G': 92,  # green
+          'y': 33, 'Y': 93,  # yellow
+          'b': 34, 'B': 94,  # blue
+          'm': 35, 'M': 95,  # magenta
+          'c': 36, 'C': 96,  # cyan
+          'w': 37, 'W': 97}  # white
 
 # Regex to be used for color formatting
 color_re = r'@(?:@|\.|([*_])?([a-zA-Z])?(?:{((?:[^}]|}})*)})?)'
@@ -104,6 +106,7 @@ _force_color = False
 
 
 class match_to_ansi(object):
+
     def __init__(self, color=True):
         self.color = color
 
@@ -179,12 +182,14 @@ def cprint(string, stream=sys.stdout, color=None):
     """Same as cwrite, but writes a trailing newline to the stream."""
     cwrite(string + "\n", stream, color)
 
+
 def cescape(string):
     """Replace all @ with @@ in the string provided."""
     return str(string).replace('@', '@@')
 
 
 class ColorStream(object):
+
     def __init__(self, stream, color=None):
         self._stream = stream
         self._color = color
@@ -196,7 +201,7 @@ class ColorStream(object):
         color = self._color
         if self._color is None:
             if raw:
-                color=True
+                color = True
             else:
                 color = self._stream.isatty() or _force_color
         raw_write(colorize(string, color=color))
diff --git a/lib/spack/llnl/util/tty/log.py b/lib/spack/llnl/util/tty/log.py
index 747315f41c..25ed5254a5 100644
--- a/lib/spack/llnl/util/tty/log.py
+++ b/lib/spack/llnl/util/tty/log.py
@@ -37,6 +37,7 @@ import llnl.util.tty.color as color
 # Use this to strip escape sequences
 _escape = re.compile(r'\x1b[^m]*m|\x1b\[?1034h')
 
+
 def _strip(line):
     """Strip color and control characters from a line."""
     return _escape.sub('', line)
@@ -59,10 +60,10 @@ class keyboard_input(object):
     When the with block completes, this will restore settings before
     canonical and echo were disabled.
     """
+
     def __init__(self, stream):
         self.stream = stream
 
-
     def __enter__(self):
         self.old_cfg = None
 
@@ -87,10 +88,9 @@ class keyboard_input(object):
             # Apply new settings for terminal
             termios.tcsetattr(fd, termios.TCSADRAIN, self.new_cfg)
 
-        except Exception, e:
+        except Exception:
             pass  # Some OS's do not support termios, so ignore.
 
-
     def __exit__(self, exc_type, exception, traceback):
         # If termios was avaialble, restore old settings after the
         # with block
diff --git a/lib/spack/spack/__init__.py b/lib/spack/spack/__init__.py
index abbf3cc87b..c9c29a32cc 100644
--- a/lib/spack/spack/__init__.py
+++ b/lib/spack/spack/__init__.py
@@ -1,3 +1,4 @@
+# flake8: noqa
 ##############################################################################
 # Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
@@ -50,8 +51,15 @@ repos_path     = join_path(var_path, "repos")
 share_path     = join_path(spack_root, "share", "spack")
 cache_path     = join_path(var_path, "cache")
 
+# User configuration location
+user_config_path = os.path.expanduser('~/.spack')
+
 import spack.fetch_strategy
-cache = spack.fetch_strategy.FsCache(cache_path)
+fetch_cache = spack.fetch_strategy.FsCache(cache_path)
+
+from spack.file_cache import FileCache
+user_cache_path = join_path(user_config_path, 'cache')
+user_cache = FileCache(user_cache_path)
 
 prefix = spack_root
 opt_path       = join_path(prefix, "opt")
@@ -140,7 +148,7 @@ _tmp_user = getpass.getuser()
 _tmp_candidates = (_default_tmp, '/nfs/tmp2', '/tmp', '/var/tmp')
 for path in _tmp_candidates:
     # don't add a second username if it's already unique by user.
-    if not _tmp_user in path:
+    if _tmp_user not in path:
         tmp_dirs.append(join_path(path, '%u', 'spack-stage'))
     else:
         tmp_dirs.append(join_path(path, 'spack-stage'))
@@ -172,9 +180,10 @@ sys_type = None
 # Spack internal code should call 'import spack' and accesses other
 # variables (spack.repo, paths, etc.) directly.
 #
-# TODO: maybe this should be separated out and should go in build_environment.py?
-# TODO: it's not clear where all the stuff that needs to be included in packages
-#       should live.  This file is overloaded for spack core vs. for packages.
+# TODO: maybe this should be separated out to build_environment.py?
+# TODO: it's not clear where all the stuff that needs to be included in
+#       packages should live.  This file is overloaded for spack core vs.
+#       for packages.
 #
 __all__ = ['Package',
            'CMakePackage',
@@ -204,8 +213,8 @@ from spack.util.executable import *
 __all__ += spack.util.executable.__all__
 
 from spack.package import \
-    install_dependency_symlinks, flatten_dependencies, DependencyConflictError, \
-    InstallError, ExternalPackageError
+    install_dependency_symlinks, flatten_dependencies, \
+    DependencyConflictError, InstallError, ExternalPackageError
 __all__ += [
-    'install_dependency_symlinks', 'flatten_dependencies', 'DependencyConflictError',
-    'InstallError', 'ExternalPackageError']
+    'install_dependency_symlinks', 'flatten_dependencies',
+    'DependencyConflictError', 'InstallError', 'ExternalPackageError']
diff --git a/lib/spack/spack/abi.py b/lib/spack/spack/abi.py
index 38cff62af4..064abb9782 100644
--- a/lib/spack/spack/abi.py
+++ b/lib/spack/spack/abi.py
@@ -30,15 +30,15 @@ from spack.spec import CompilerSpec
 from spack.util.executable import Executable, ProcessError
 from llnl.util.lang import memoized
 
+
 class ABI(object):
     """This class provides methods to test ABI compatibility between specs.
        The current implementation is rather rough and could be improved."""
 
     def architecture_compatible(self, parent, child):
-        """Returns true iff the parent and child specs have ABI compatible targets."""
-        return not parent.architecture or not child.architecture \
-                        or parent.architecture == child.architecture
-
+        """Return true if parent and child have ABI compatible targets."""
+        return not parent.architecture or not child.architecture or \
+            parent.architecture == child.architecture
 
     @memoized
     def _gcc_get_libstdcxx_version(self, version):
@@ -61,8 +61,9 @@ class ABI(object):
         else:
             return None
         try:
-            output = rungcc("--print-file-name=%s" % libname, return_output=True)
-        except ProcessError, e:
+            output = rungcc("--print-file-name=%s" % libname,
+                            return_output=True)
+        except ProcessError:
             return None
         if not output:
             return None
@@ -71,7 +72,6 @@ class ABI(object):
             return None
         return os.path.basename(libpath)
 
-
     @memoized
     def _gcc_compiler_compare(self, pversion, cversion):
         """Returns true iff the gcc version pversion and cversion
@@ -82,7 +82,6 @@ class ABI(object):
             return False
         return plib == clib
 
-
     def _intel_compiler_compare(self, pversion, cversion):
         """Returns true iff the intel version pversion and cversion
            are ABI compatible"""
@@ -92,9 +91,8 @@ class ABI(object):
             return False
         return pversion.version[:2] == cversion.version[:2]
 
-
     def compiler_compatible(self, parent, child, **kwargs):
-        """Returns true iff the compilers for parent and child specs are ABI compatible"""
+        """Return true if compilers for parent and child are ABI compatible."""
         if not parent.compiler or not child.compiler:
             return True
 
@@ -109,8 +107,8 @@ class ABI(object):
         # TODO: into compiler classes?
         for pversion in parent.compiler.versions:
             for cversion in child.compiler.versions:
-                # For a few compilers use specialized comparisons.  Otherwise
-                # match on version match.
+                # For a few compilers use specialized comparisons.
+                # Otherwise match on version match.
                 if pversion.satisfies(cversion):
                     return True
                 elif (parent.compiler.name == "gcc" and
@@ -121,9 +119,8 @@ class ABI(object):
                     return True
         return False
 
-
     def compatible(self, parent, child, **kwargs):
         """Returns true iff a parent and child spec are ABI compatible"""
         loosematch = kwargs.get('loose', False)
         return self.architecture_compatible(parent, child) and \
-               self.compiler_compatible(parent, child, loose=loosematch)
+            self.compiler_compatible(parent, child, loose=loosematch)
diff --git a/lib/spack/spack/architecture.py b/lib/spack/spack/architecture.py
index a7cda2bf68..0d210f9741 100644
--- a/lib/spack/spack/architecture.py
+++ b/lib/spack/spack/architecture.py
@@ -76,7 +76,6 @@ attributes front_os and back_os. The operating system as described earlier,
 will be responsible for compiler detection.
 """
 import os
-import imp
 import inspect
 
 from llnl.util.lang import memoized, list_modules, key_ordering
@@ -92,6 +91,7 @@ import spack.error as serr
 
 
 class NoPlatformError(serr.SpackError):
+
     def __init__(self):
         super(NoPlatformError, self).__init__(
             "Could not determine a platform for this machine.")
@@ -190,6 +190,12 @@ class Platform(object):
 
         return self.operating_sys.get(name, None)
 
+    @classmethod
+    def setup_platform_environment(self, pkg, env):
+        """ Subclass can override this method if it requires any
+            platform-specific build environment modifications.
+        """
+        pass
 
     @classmethod
     def detect(self):
@@ -200,15 +206,12 @@ class Platform(object):
         """
         raise NotImplementedError()
 
-
     def __repr__(self):
         return self.__str__()
 
-
     def __str__(self):
         return self.name
 
-
     def _cmp_key(self):
         t_keys = ''.join(str(t._cmp_key()) for t in
                          sorted(self.targets.values()))
@@ -279,7 +282,7 @@ class OperatingSystem(object):
 
         # ensure all the version calls we made are cached in the parent
         # process, as well.  This speeds up Spack a lot.
-        clist = reduce(lambda x, y: x+y, compiler_lists)
+        clist = reduce(lambda x, y: x + y, compiler_lists)
         return clist
 
     def find_compiler(self, cmp_cls, *path):
@@ -320,7 +323,7 @@ class OperatingSystem(object):
 
                 # prefer the one with more compilers.
                 prev_paths = [prev.cc, prev.cxx, prev.f77, prev.fc]
-                newcount = len([p for p in paths       if p is not None])
+                newcount = len([p for p in paths if p is not None])
                 prevcount = len([p for p in prev_paths if p is not None])
 
                 # Don't add if it's not an improvement over prev compiler.
@@ -337,6 +340,7 @@ class OperatingSystem(object):
         d['version'] = self.version
         return d
 
+
 @key_ordering
 class Arch(object):
     """Architecture is now a class to help with setting attributes.
@@ -377,10 +381,15 @@ class Arch(object):
         else:
             return ''
 
-
     def __contains__(self, string):
         return string in str(self)
 
+    # TODO: make this unnecessary: don't include an empty arch on *every* spec.
+    def __nonzero__(self):
+        return (self.platform is not None or
+                self.platform_os is not None or
+                self.target is not None)
+    __bool__ = __nonzero__
 
     def _cmp_key(self):
         if isinstance(self.platform, Platform):
@@ -424,7 +433,7 @@ def _operating_system_from_dict(os_name, plat=None):
     if isinstance(os_name, dict):
         name = os_name['name']
         version = os_name['version']
-        return plat.operating_system(name+version)
+        return plat.operating_system(name + version)
     else:
         return plat.operating_system(os_name)
 
diff --git a/lib/spack/spack/build_environment.py b/lib/spack/spack/build_environment.py
index c4d900f53e..f9d795845e 100644
--- a/lib/spack/spack/build_environment.py
+++ b/lib/spack/spack/build_environment.py
@@ -436,6 +436,7 @@ def setup_package(pkg, dirty=False):
 
     set_compiler_environment_variables(pkg, spack_env)
     set_build_environment_variables(pkg, spack_env, dirty)
+    pkg.spec.architecture.platform.setup_platform_environment(pkg, spack_env)
     load_external_modules(pkg)
     # traverse in postorder so package can use vars from its dependencies
     spec = pkg.spec
diff --git a/lib/spack/spack/cmd/__init__.py b/lib/spack/spack/cmd/__init__.py
index 230115df50..f69f434afd 100644
--- a/lib/spack/spack/cmd/__init__.py
+++ b/lib/spack/spack/cmd/__init__.py
@@ -240,4 +240,4 @@ def display_specs(specs, **kwargs):
         else:
             raise ValueError(
                 "Invalid mode for display_specs: %s. Must be one of (paths,"
-                "deps, short)." % mode)  # NOQA: ignore=E501
+                "deps, short)." % mode)
diff --git a/lib/spack/spack/cmd/activate.py b/lib/spack/spack/cmd/activate.py
index 9867fa8835..797cdcb136 100644
--- a/lib/spack/spack/cmd/activate.py
+++ b/lib/spack/spack/cmd/activate.py
@@ -29,12 +29,14 @@ import spack.cmd
 
 description = "Activate a package extension."
 
+
 def setup_parser(subparser):
     subparser.add_argument(
         '-f', '--force', action='store_true',
         help="Activate without first activating dependencies.")
     subparser.add_argument(
-        'spec', nargs=argparse.REMAINDER, help="spec of package extension to activate.")
+        'spec', nargs=argparse.REMAINDER,
+        help="spec of package extension to activate.")
 
 
 def activate(parser, args):
diff --git a/lib/spack/spack/cmd/arch.py b/lib/spack/spack/cmd/arch.py
index cf2f96fd21..1badd40f7f 100644
--- a/lib/spack/spack/cmd/arch.py
+++ b/lib/spack/spack/cmd/arch.py
@@ -22,10 +22,10 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import spack
 import spack.architecture as architecture
 
 description = "Print the architecture for this machine"
 
+
 def arch(parser, args):
     print architecture.sys_type()
diff --git a/lib/spack/spack/cmd/cd.py b/lib/spack/spack/cmd/cd.py
index aa45f67ae1..cf7232258c 100644
--- a/lib/spack/spack/cmd/cd.py
+++ b/lib/spack/spack/cmd/cd.py
@@ -25,7 +25,8 @@
 import spack.cmd.location
 import spack.modules
 
-description="cd to spack directories in the shell."
+description = "cd to spack directories in the shell."
+
 
 def setup_parser(subparser):
     """This is for decoration -- spack cd is used through spack's
diff --git a/lib/spack/spack/cmd/clean.py b/lib/spack/spack/cmd/clean.py
index 514c5874ef..dc62fbcaf6 100644
--- a/lib/spack/spack/cmd/clean.py
+++ b/lib/spack/spack/cmd/clean.py
@@ -31,6 +31,7 @@ import spack.cmd
 
 description = "Remove build stage and source tarball for packages."
 
+
 def setup_parser(subparser):
     subparser.add_argument('packages', nargs=argparse.REMAINDER,
                            help="specs of packages to clean")
diff --git a/lib/spack/spack/cmd/common/arguments.py b/lib/spack/spack/cmd/common/arguments.py
index af04170824..afcba33714 100644
--- a/lib/spack/spack/cmd/common/arguments.py
+++ b/lib/spack/spack/cmd/common/arguments.py
@@ -35,7 +35,7 @@ _arguments = {}
 def add_common_arguments(parser, list_of_arguments):
     for argument in list_of_arguments:
         if argument not in _arguments:
-            message = 'Trying to add the non existing argument "{0}" to a command'  # NOQA: ignore=E501
+            message = 'Trying to add non existing argument "{0}" to a command'
             raise KeyError(message.format(argument))
         x = _arguments[argument]
         parser.add_argument(*x.flags, **x.kwargs)
@@ -82,7 +82,7 @@ parms = Bunch(
     kwargs={
         'action': 'store_true',
         'dest': 'yes_to_all',
-        'help': 'Assume "yes" is the answer to every confirmation asked to the user.'  # NOQA: ignore=E501
+        'help': 'Assume "yes" is the answer to every confirmation request.'
     })
 _arguments['yes_to_all'] = parms
 
diff --git a/lib/spack/spack/cmd/compiler.py b/lib/spack/spack/cmd/compiler.py
index c325628ebf..ea91c71479 100644
--- a/lib/spack/spack/cmd/compiler.py
+++ b/lib/spack/spack/cmd/compiler.py
@@ -37,6 +37,7 @@ from spack.util.environment import get_path
 
 description = "Manage compilers"
 
+
 def setup_parser(subparser):
     sp = subparser.add_subparsers(
         metavar='SUBCOMMAND', dest='compiler_command')
@@ -44,48 +45,58 @@ def setup_parser(subparser):
     scopes = spack.config.config_scopes
 
     # Find
-    find_parser = sp.add_parser('find', aliases=['add'], help='Search the system for compilers to add to the Spack configuration.')
+    find_parser = sp.add_parser(
+        'find', aliases=['add'],
+        help='Search the system for compilers to add to Spack configuration.')
     find_parser.add_argument('add_paths', nargs=argparse.REMAINDER)
-    find_parser.add_argument('--scope', choices=scopes, default=spack.cmd.default_modify_scope,
-                            help="Configuration scope to modify.")
+    find_parser.add_argument(
+        '--scope', choices=scopes, default=spack.cmd.default_modify_scope,
+        help="Configuration scope to modify.")
 
     # Remove
-    remove_parser = sp.add_parser('remove', aliases=['rm'], help='Remove compiler by spec.')
+    remove_parser = sp.add_parser(
+        'remove', aliases=['rm'], help='Remove compiler by spec.')
     remove_parser.add_argument(
-        '-a', '--all', action='store_true', help='Remove ALL compilers that match spec.')
+        '-a', '--all', action='store_true',
+        help='Remove ALL compilers that match spec.')
     remove_parser.add_argument('compiler_spec')
-    remove_parser.add_argument('--scope', choices=scopes, default=spack.cmd.default_modify_scope,
-                               help="Configuration scope to modify.")
+    remove_parser.add_argument(
+        '--scope', choices=scopes, default=spack.cmd.default_modify_scope,
+        help="Configuration scope to modify.")
 
     # List
     list_parser = sp.add_parser('list', help='list available compilers')
-    list_parser.add_argument('--scope', choices=scopes, default=spack.cmd.default_list_scope,
-                             help="Configuration scope to read from.")
+    list_parser.add_argument(
+        '--scope', choices=scopes, default=spack.cmd.default_list_scope,
+        help="Configuration scope to read from.")
 
     # Info
     info_parser = sp.add_parser('info', help='Show compiler paths.')
     info_parser.add_argument('compiler_spec')
-    info_parser.add_argument('--scope', choices=scopes, default=spack.cmd.default_list_scope,
-                             help="Configuration scope to read from.")
+    info_parser.add_argument(
+        '--scope', choices=scopes, default=spack.cmd.default_list_scope,
+        help="Configuration scope to read from.")
 
 
 def compiler_find(args):
-    """Search either $PATH or a list of paths OR MODULES for compilers and add them
-       to Spack's configuration."""
+    """Search either $PATH or a list of paths OR MODULES for compilers and
+       add them to Spack's configuration.
+
+    """
     paths = args.add_paths
     if not paths:
         paths = get_path('PATH')
 
-    # Don't initialize compilers config via compilers.get_compiler_config. 
-    # Just let compiler_find do the 
+    # Don't initialize compilers config via compilers.get_compiler_config.
+    # Just let compiler_find do the
     # entire process and return an empty config from all_compilers
     # Default for any other process is init_config=True
     compilers = [c for c in spack.compilers.find_compilers(*paths)
                  if c.spec not in spack.compilers.all_compilers(
-                     scope=args.scope, init_config=False)] 
+                     scope=args.scope, init_config=False)]
     if compilers:
         spack.compilers.add_compilers_to_config(compilers, scope=args.scope,
-                init_config=False)
+                                                init_config=False)
         n = len(compilers)
         s = 's' if n > 1 else ''
         filename = spack.config.get_config_filename(args.scope, 'compilers')
@@ -103,11 +114,12 @@ def compiler_remove(args):
     elif not args.all and len(compilers) > 1:
         tty.error("Multiple compilers match spec %s. Choose one:" % cspec)
         colify(reversed(sorted([c.spec for c in compilers])), indent=4)
-        tty.msg("Or, you can use `spack compiler remove -a` to remove all of them.")
+        tty.msg("Or, use `spack compiler remove -a` to remove all of them.")
         sys.exit(1)
 
     for compiler in compilers:
-        spack.compilers.remove_compiler_from_config(compiler.spec, scope=args.scope)
+        spack.compilers.remove_compiler_from_config(
+            compiler.spec, scope=args.scope)
         tty.msg("Removed compiler %s" % compiler.spec)
 
 
@@ -133,7 +145,8 @@ def compiler_list(args):
     tty.msg("Available compilers")
     index = index_by(spack.compilers.all_compilers(scope=args.scope), 'name')
     for i, (name, compilers) in enumerate(index.items()):
-        if i >= 1: print
+        if i >= 1:
+            print
 
         cname = "%s{%s}" % (spack.spec.compiler_color, name)
         tty.hline(colorize(cname), char='-')
@@ -141,10 +154,10 @@ def compiler_list(args):
 
 
 def compiler(parser, args):
-    action = {'add'    : compiler_find, 
-              'find'   : compiler_find,
-              'remove' : compiler_remove,
-              'rm'     : compiler_remove,
-              'info'   : compiler_info,
-              'list'   : compiler_list }
+    action = {'add': compiler_find,
+              'find': compiler_find,
+              'remove': compiler_remove,
+              'rm': compiler_remove,
+              'info': compiler_info,
+              'list': compiler_list}
     action[args.compiler_command](args)
diff --git a/lib/spack/spack/cmd/compilers.py b/lib/spack/spack/cmd/compilers.py
index 9fbc2bb952..b87f977e5a 100644
--- a/lib/spack/spack/cmd/compilers.py
+++ b/lib/spack/spack/cmd/compilers.py
@@ -22,18 +22,16 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import llnl.util.tty as tty
-from llnl.util.tty.colify import colify
-from llnl.util.lang import index_by
-
 import spack
 from spack.cmd.compiler import compiler_list
 
 description = "List available compilers. Same as 'spack compiler list'."
 
+
 def setup_parser(subparser):
     subparser.add_argument('--scope', choices=spack.config.config_scopes,
                            help="Configuration scope to read/modify.")
 
+
 def compilers(parser, args):
     compiler_list(args)
diff --git a/lib/spack/spack/cmd/config.py b/lib/spack/spack/cmd/config.py
index d6f56c270d..c189e37036 100644
--- a/lib/spack/spack/cmd/config.py
+++ b/lib/spack/spack/cmd/config.py
@@ -22,15 +22,11 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import sys
-import argparse
-
-import llnl.util.tty as tty
-
 import spack.config
 
 description = "Get and set configuration options."
 
+
 def setup_parser(subparser):
     # User can only choose one
     scope_group = subparser.add_mutually_exclusive_group()
@@ -64,6 +60,6 @@ def config_edit(args):
 
 
 def config(parser, args):
-    action = { 'get' : config_get,
-               'edit' : config_edit }
+    action = {'get': config_get,
+              'edit': config_edit}
     action[args.config_command](args)
diff --git a/lib/spack/spack/cmd/create.py b/lib/spack/spack/cmd/create.py
index 2c440096d1..52a82eb38f 100644
--- a/lib/spack/spack/cmd/create.py
+++ b/lib/spack/spack/cmd/create.py
@@ -96,8 +96,7 @@ class ${class_name}(Package):
 
 ${versions}
 
-    # FIXME: Add additional dependencies if required.
-    ${dependencies}
+${dependencies}
 
     def install(self, spec, prefix):
 ${install}
@@ -105,13 +104,39 @@ ${install}
 
 # Build dependencies and extensions
 dependencies_dict = {
-    'autotools': "# depends_on('foo')",
-    'cmake':     "depends_on('cmake')",
-    'scons':     "depends_on('scons')",
-    'python':    "extends('python')",
-    'R':         "extends('R')",
-    'octave':    "extends('octave')",
-    'unknown':   "# depends_on('foo')"
+    'autotools': """\
+    # FIXME: Add dependencies if required.
+    # depends_on('foo')""",
+
+    'cmake': """\
+    # FIXME: Add additional dependencies if required.
+    depends_on('cmake', type='build')""",
+
+    'scons': """\
+    # FIXME: Add additional dependencies if required.
+    depends_on('scons', type='build')""",
+
+    'python': """\
+    extends('python')
+
+    # FIXME: Add additional dependencies if required.
+    # depends_on('py-foo', type=nolink)""",
+
+    'R': """\
+    extends('R')
+
+    # FIXME: Add additional dependencies if required.
+    # depends_on('r-foo', type=nolink)""",
+
+    'octave': """\
+    extends('octave')
+
+    # FIXME: Add additional dependencies if required.
+    # depends_on('octave-foo', type=nolink)""",
+
+    'unknown': """\
+    # FIXME: Add dependencies if required.
+    # depends_on('foo')"""
 }
 
 # Default installation instructions
@@ -140,7 +165,7 @@ install_dict = {
 
     'python': """\
         # FIXME: Add logic to build and install here.
-        python('setup.py', 'install', '--prefix={0}'.format(prefix))""",
+        setup_py('install', '--prefix={0}'.format(prefix))""",
 
     'R': """\
         # FIXME: Add logic to build and install here.
@@ -192,6 +217,7 @@ def setup_parser(subparser):
 
 
 class BuildSystemGuesser(object):
+
     def __call__(self, stage, url):
         """Try to guess the type of build system used by a project based on
         the contents of its archive or the URL it was downloaded from."""
diff --git a/lib/spack/spack/cmd/deactivate.py b/lib/spack/spack/cmd/deactivate.py
index 990309ee48..2b15a0331e 100644
--- a/lib/spack/spack/cmd/deactivate.py
+++ b/lib/spack/spack/cmd/deactivate.py
@@ -31,6 +31,7 @@ from spack.graph import topological_sort
 
 description = "Deactivate a package extension."
 
+
 def setup_parser(subparser):
     subparser.add_argument(
         '-f', '--force', action='store_true',
@@ -40,7 +41,8 @@ def setup_parser(subparser):
         help="Deactivate all extensions of an extendable package, or "
         "deactivate an extension AND its dependencies.")
     subparser.add_argument(
-        'spec', nargs=argparse.REMAINDER, help="spec of package extension to deactivate.")
+        'spec', nargs=argparse.REMAINDER,
+        help="spec of package extension to deactivate.")
 
 
 def deactivate(parser, args):
@@ -65,7 +67,8 @@ def deactivate(parser, args):
             if not args.force and not spec.package.activated:
                 tty.die("%s is not activated." % pkg.spec.short_spec)
 
-            tty.msg("Deactivating %s and all dependencies." % pkg.spec.short_spec)
+            tty.msg("Deactivating %s and all dependencies." %
+                    pkg.spec.short_spec)
 
             topo_order = topological_sort(spec)
             index = spec.index()
@@ -79,7 +82,9 @@ def deactivate(parser, args):
                         epkg.do_deactivate(force=args.force)
 
         else:
-            tty.die("spack deactivate --all requires an extendable package or an extension.")
+            tty.die(
+                "spack deactivate --all requires an extendable package "
+                "or an extension.")
 
     else:
         if not pkg.is_extension:
diff --git a/lib/spack/spack/cmd/dependents.py b/lib/spack/spack/cmd/dependents.py
index 78eb6847b8..7729105e62 100644
--- a/lib/spack/spack/cmd/dependents.py
+++ b/lib/spack/spack/cmd/dependents.py
@@ -31,9 +31,11 @@ import spack.cmd
 
 description = "Show installed packages that depend on another."
 
+
 def setup_parser(subparser):
     subparser.add_argument(
-        'spec', nargs=argparse.REMAINDER, help="specs to list dependencies of.")
+        'spec', nargs=argparse.REMAINDER,
+        help="specs to list dependencies of.")
 
 
 def dependents(parser, args):
@@ -42,5 +44,6 @@ def dependents(parser, args):
         tty.die("spack dependents takes only one spec.")
 
     fmt = '$_$@$%@$+$=$#'
-    deps = [d.format(fmt, color=True) for d in specs[0].package.installed_dependents]
+    deps = [d.format(fmt, color=True)
+            for d in specs[0].package.installed_dependents]
     tty.msg("Dependents of %s" % specs[0].format(fmt, color=True), *deps)
diff --git a/lib/spack/spack/cmd/diy.py b/lib/spack/spack/cmd/diy.py
index 643e6374b2..487654d261 100644
--- a/lib/spack/spack/cmd/diy.py
+++ b/lib/spack/spack/cmd/diy.py
@@ -35,6 +35,7 @@ from spack.stage import DIYStage
 
 description = "Do-It-Yourself: build from an existing source directory."
 
+
 def setup_parser(subparser):
     subparser.add_argument(
         '-i', '--ignore-dependencies', action='store_true', dest='ignore_deps',
@@ -76,14 +77,17 @@ def diy(self, args):
                 return
 
         if not spec.versions.concrete:
-            tty.die("spack diy spec must have a single, concrete version.  Did you forget a package version number?")
+            tty.die(
+                "spack diy spec must have a single, concrete version. "
+                "Did you forget a package version number?")
 
         spec.concretize()
         package = spack.repo.get(spec)
 
         if package.installed:
             tty.error("Already installed in %s" % package.prefix)
-            tty.msg("Uninstall or try adding a version suffix for this DIY build.")
+            tty.msg("Uninstall or try adding a version suffix for this "
+                    "DIY build.")
             sys.exit(1)
 
         # Forces the build to run out of the current directory.
diff --git a/lib/spack/spack/cmd/doc.py b/lib/spack/spack/cmd/doc.py
index b3d0737d13..291b17216f 100644
--- a/lib/spack/spack/cmd/doc.py
+++ b/lib/spack/spack/cmd/doc.py
@@ -25,6 +25,7 @@
 
 description = "Run pydoc from within spack."
 
+
 def setup_parser(subparser):
     subparser.add_argument('entity', help="Run pydoc help on entity")
 
diff --git a/lib/spack/spack/cmd/edit.py b/lib/spack/spack/cmd/edit.py
index 49ab83867a..286136dd67 100644
--- a/lib/spack/spack/cmd/edit.py
+++ b/lib/spack/spack/cmd/edit.py
@@ -68,7 +68,7 @@ def edit_package(name, repo_path, namespace, force=False):
     if os.path.exists(path):
         if not os.path.isfile(path):
             tty.die("Something's wrong.  '%s' is not a file!" % path)
-        if not os.access(path, os.R_OK|os.W_OK):
+        if not os.access(path, os.R_OK | os.W_OK):
             tty.die("Insufficient permissions on '%s'!" % path)
     elif not force:
         tty.die("No package '%s'.  Use spack create, or supply -f/--force "
@@ -93,19 +93,23 @@ def setup_parser(subparser):
     # Various filetypes you can edit directly from the cmd line.
     excl_args.add_argument(
         '-c', '--command', dest='path', action='store_const',
-        const=spack.cmd.command_path, help="Edit the command with the supplied name.")
+        const=spack.cmd.command_path,
+        help="Edit the command with the supplied name.")
     excl_args.add_argument(
         '-t', '--test', dest='path', action='store_const',
         const=spack.test_path, help="Edit the test with the supplied name.")
     excl_args.add_argument(
         '-m', '--module', dest='path', action='store_const',
-        const=spack.module_path, help="Edit the main spack module with the supplied name.")
+        const=spack.module_path,
+        help="Edit the main spack module with the supplied name.")
 
     # Options for editing packages
     excl_args.add_argument(
-        '-r', '--repo', default=None, help="Path to repo to edit package in.")
+        '-r', '--repo', default=None,
+        help="Path to repo to edit package in.")
     excl_args.add_argument(
-        '-N', '--namespace', default=None, help="Namespace of package to edit.")
+        '-N', '--namespace', default=None,
+        help="Namespace of package to edit.")
 
     subparser.add_argument(
         'name', nargs='?', default=None, help="name of package to edit")
diff --git a/lib/spack/spack/cmd/env.py b/lib/spack/spack/cmd/env.py
index 85d111e91e..f3bad039d4 100644
--- a/lib/spack/spack/cmd/env.py
+++ b/lib/spack/spack/cmd/env.py
@@ -28,11 +28,13 @@ import llnl.util.tty as tty
 import spack.cmd
 import spack.build_environment as build_env
 
-description = "Run a command with the environment for a particular spec's install."
+description = "Run a command with the install environment for a spec."
+
 
 def setup_parser(subparser):
     subparser.add_argument(
-        'spec', nargs=argparse.REMAINDER, help="specs of package environment to emulate.")
+        'spec', nargs=argparse.REMAINDER,
+        help="specs of package environment to emulate.")
 
 
 def env(parser, args):
@@ -47,7 +49,7 @@ def env(parser, args):
     if sep in args.spec:
         s = args.spec.index(sep)
         spec = args.spec[:s]
-        cmd  = args.spec[s+1:]
+        cmd  = args.spec[s + 1:]
     else:
         spec = args.spec[0]
         cmd  = args.spec[1:]
diff --git a/lib/spack/spack/cmd/extensions.py b/lib/spack/spack/cmd/extensions.py
index 11659e0c96..b5c484305f 100644
--- a/lib/spack/spack/cmd/extensions.py
+++ b/lib/spack/spack/cmd/extensions.py
@@ -22,7 +22,6 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import sys
 import argparse
 
 import llnl.util.tty as tty
@@ -34,6 +33,7 @@ import spack.cmd.find
 
 description = "List extensions for package."
 
+
 def setup_parser(subparser):
     format_group = subparser.add_mutually_exclusive_group()
     format_group.add_argument(
@@ -47,7 +47,8 @@ def setup_parser(subparser):
         help='Show full dependency DAG of extensions')
 
     subparser.add_argument(
-        'spec', nargs=argparse.REMAINDER, help='Spec of package to list extensions for')
+        'spec', nargs=argparse.REMAINDER,
+        help='Spec of package to list extensions for')
 
 
 def extensions(parser, args):
@@ -85,7 +86,8 @@ def extensions(parser, args):
     #
     # List specs of installed extensions.
     #
-    installed = [s.spec for s in spack.installed_db.installed_extensions_for(spec)]
+    installed = [
+        s.spec for s in spack.installed_db.installed_extensions_for(spec)]
     print
     if not installed:
         tty.msg("None installed.")
@@ -102,4 +104,5 @@ def extensions(parser, args):
         tty.msg("None activated.")
         return
     tty.msg("%d currently activated:" % len(activated))
-    spack.cmd.find.display_specs(activated.values(), mode=args.mode, long=args.long)
+    spack.cmd.find.display_specs(
+        activated.values(), mode=args.mode, long=args.long)
diff --git a/lib/spack/spack/cmd/fetch.py b/lib/spack/spack/cmd/fetch.py
index 1afc51d9fa..c1ac2ed48d 100644
--- a/lib/spack/spack/cmd/fetch.py
+++ b/lib/spack/spack/cmd/fetch.py
@@ -29,16 +29,21 @@ import spack.cmd
 
 description = "Fetch archives for packages"
 
+
 def setup_parser(subparser):
     subparser.add_argument(
         '-n', '--no-checksum', action='store_true', dest='no_checksum',
         help="Do not check packages against checksum")
     subparser.add_argument(
-        '-m', '--missing', action='store_true', help="Also fetch all missing dependencies")
+        '-m', '--missing', action='store_true',
+        help="Also fetch all missing dependencies")
     subparser.add_argument(
-        '-D', '--dependencies', action='store_true', help="Also fetch all dependencies")
+        '-D', '--dependencies', action='store_true',
+        help="Also fetch all dependencies")
     subparser.add_argument(
-        'packages', nargs=argparse.REMAINDER, help="specs of packages to fetch")
+        'packages', nargs=argparse.REMAINDER,
+        help="specs of packages to fetch")
+
 
 def fetch(parser, args):
     if not args.packages:
@@ -50,7 +55,6 @@ def fetch(parser, args):
     specs = spack.cmd.parse_specs(args.packages, concretize=True)
     for spec in specs:
         if args.missing or args.dependencies:
-            to_fetch = set()
             for s in spec.traverse(deptype_query=spack.alldeps):
                 package = spack.repo.get(s)
                 if args.missing and package.installed:
diff --git a/lib/spack/spack/cmd/graph.py b/lib/spack/spack/cmd/graph.py
index da65121836..8faabfbb7b 100644
--- a/lib/spack/spack/cmd/graph.py
+++ b/lib/spack/spack/cmd/graph.py
@@ -30,6 +30,7 @@ from spack.graph import *
 
 description = "Generate graphs of package dependency relationships."
 
+
 def setup_parser(subparser):
     setup_parser.parser = subparser
 
@@ -42,10 +43,12 @@ def setup_parser(subparser):
         help="Generate graph in dot format and print to stdout.")
 
     subparser.add_argument(
-        '--concretize', action='store_true', help="Concretize specs before graphing.")
+        '--concretize', action='store_true',
+        help="Concretize specs before graphing.")
 
     subparser.add_argument(
-        'specs', nargs=argparse.REMAINDER, help="specs of packages to graph.")
+        'specs', nargs=argparse.REMAINDER,
+        help="specs of packages to graph.")
 
 
 def graph(parser, args):
@@ -56,11 +59,11 @@ def graph(parser, args):
         setup_parser.parser.print_help()
         return 1
 
-    if args.dot:    # Dot graph only if asked for.
+    if args.dot:  # Dot graph only if asked for.
         graph_dot(*specs)
 
-    elif specs:     # ascii is default: user doesn't need to provide it explicitly
+    elif specs:  # ascii is default: user doesn't need to provide it explicitly
         graph_ascii(specs[0], debug=spack.debug)
         for spec in specs[1:]:
-            print # extra line bt/w independent graphs
+            print  # extra line bt/w independent graphs
             graph_ascii(spec, debug=spack.debug)
diff --git a/lib/spack/spack/cmd/help.py b/lib/spack/spack/cmd/help.py
index 1d23161839..5bc8fc3e74 100644
--- a/lib/spack/spack/cmd/help.py
+++ b/lib/spack/spack/cmd/help.py
@@ -22,14 +22,14 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import sys
-
 description = "Get help on spack and its commands"
 
+
 def setup_parser(subparser):
     subparser.add_argument('help_command', nargs='?', default=None,
                            help='command to get help on')
 
+
 def help(parser, args):
     if args.help_command:
         parser.parse_args([args.help_command, '-h'])
diff --git a/lib/spack/spack/cmd/install.py b/lib/spack/spack/cmd/install.py
index ae34e06c22..634a603ddc 100644
--- a/lib/spack/spack/cmd/install.py
+++ b/lib/spack/spack/cmd/install.py
@@ -31,6 +31,7 @@ import spack.cmd
 
 description = "Build and install packages"
 
+
 def setup_parser(subparser):
     subparser.add_argument(
         '-i', '--ignore-dependencies', action='store_true', dest='ignore_deps',
@@ -52,7 +53,7 @@ def setup_parser(subparser):
         help="Display verbose build output while installing.")
     subparser.add_argument(
         '--fake', action='store_true', dest='fake',
-        help="Fake install.  Just remove the prefix and touch a fake file in it.")
+        help="Fake install. Just remove prefix and create a fake file.")
     subparser.add_argument(
         '--dirty', action='store_true', dest='dirty',
         help="Install a package *without* cleaning the environment.")
@@ -60,13 +61,13 @@ def setup_parser(subparser):
         '--stop-at', help="Stop at a particular phase of installation"
     )
     subparser.add_argument(
-        'packages', nargs=argparse.REMAINDER, help="specs of packages to install")
+        'packages', nargs=argparse.REMAINDER,
+        help="specs of packages to install")
     subparser.add_argument(
         '--run-tests', action='store_true', dest='run_tests',
         help="Run tests during installation of a package.")
 
 
-
 def install(parser, args):
     if not args.packages:
         tty.die("install requires at least one package argument")
diff --git a/lib/spack/spack/cmd/load.py b/lib/spack/spack/cmd/load.py
index 205abbb6b3..85190a5d0b 100644
--- a/lib/spack/spack/cmd/load.py
+++ b/lib/spack/spack/cmd/load.py
@@ -25,13 +25,16 @@
 import argparse
 import spack.modules
 
-description ="Add package to environment using modules."
+description = "Add package to environment using modules."
+
 
 def setup_parser(subparser):
     """Parser is only constructed so that this prints a nice help
        message with -h. """
     subparser.add_argument(
-        'spec', nargs=argparse.REMAINDER, help="Spec of package to load with modules.  (If -, read specs from STDIN)")
+        'spec', nargs=argparse.REMAINDER,
+        help="Spec of package to load with modules. "
+             "(If -, read specs from STDIN)")
 
 
 def load(parser, args):
diff --git a/lib/spack/spack/cmd/location.py b/lib/spack/spack/cmd/location.py
index b0dbb1a550..b9c8b5c330 100644
--- a/lib/spack/spack/cmd/location.py
+++ b/lib/spack/spack/cmd/location.py
@@ -22,8 +22,6 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import os
-import sys
 import argparse
 
 import llnl.util.tty as tty
@@ -32,16 +30,19 @@ from llnl.util.filesystem import join_path
 import spack
 import spack.cmd
 
-description="Print out locations of various directories used by Spack"
+description = "Print out locations of various directories used by Spack"
+
 
 def setup_parser(subparser):
     global directories
     directories = subparser.add_mutually_exclusive_group()
 
     directories.add_argument(
-        '-m', '--module-dir', action='store_true', help="Spack python module directory.")
+        '-m', '--module-dir', action='store_true',
+        help="Spack python module directory.")
     directories.add_argument(
-        '-r', '--spack-root', action='store_true', help="Spack installation root.")
+        '-r', '--spack-root', action='store_true',
+        help="Spack installation root.")
 
     directories.add_argument(
         '-i', '--install-dir', action='store_true',
@@ -53,15 +54,19 @@ def setup_parser(subparser):
         '-P', '--packages', action='store_true',
         help="Top-level packages directory for Spack.")
     directories.add_argument(
-        '-s', '--stage-dir', action='store_true', help="Stage directory for a spec.")
+        '-s', '--stage-dir', action='store_true',
+        help="Stage directory for a spec.")
     directories.add_argument(
-        '-S', '--stages', action='store_true', help="Top level Stage directory.")
+        '-S', '--stages', action='store_true',
+        help="Top level Stage directory.")
     directories.add_argument(
         '-b', '--build-dir', action='store_true',
-        help="Checked out or expanded source directory for a spec (requires it to be staged first).")
+        help="Checked out or expanded source directory for a spec "
+             "(requires it to be staged first).")
 
     subparser.add_argument(
-        'spec', nargs=argparse.REMAINDER, help="spec of package to fetch directory for.")
+        'spec', nargs=argparse.REMAINDER,
+        help="spec of package to fetch directory for.")
 
 
 def location(parser, args):
@@ -104,9 +109,9 @@ def location(parser, args):
                 if args.stage_dir:
                     print pkg.stage.path
 
-                else:  #  args.build_dir is the default.
+                else:  # args.build_dir is the default.
                     if not pkg.stage.source_path:
-                        tty.die("Build directory does not exist yet. Run this to create it:",
+                        tty.die("Build directory does not exist yet. "
+                                "Run this to create it:",
                                 "spack stage " + " ".join(args.spec))
                     print pkg.stage.source_path
-
diff --git a/lib/spack/spack/cmd/mirror.py b/lib/spack/spack/cmd/mirror.py
index 0cf682fc4f..585faaf524 100644
--- a/lib/spack/spack/cmd/mirror.py
+++ b/lib/spack/spack/cmd/mirror.py
@@ -23,7 +23,6 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
-import sys
 from datetime import datetime
 
 import argparse
@@ -40,6 +39,7 @@ from spack.util.spack_yaml import syaml_dict
 
 description = "Manage mirrors."
 
+
 def setup_parser(subparser):
     subparser.add_argument(
         '-n', '--no-checksum', action='store_true', dest='no_checksum',
@@ -61,8 +61,9 @@ def setup_parser(subparser):
         '-D', '--dependencies', action='store_true',
         help="Also fetch all dependencies")
     create_parser.add_argument(
-        '-o', '--one-version-per-spec', action='store_const', const=1, default=0,
-        help="Only fetch one 'preferred' version per spec, not all known versions.")
+        '-o', '--one-version-per-spec', action='store_const',
+        const=1, default=0,
+        help="Only fetch one 'preferred' version per spec, not all known.")
 
     scopes = spack.config.config_scopes
 
@@ -70,7 +71,7 @@ def setup_parser(subparser):
     add_parser = sp.add_parser('add', help=mirror_add.__doc__)
     add_parser.add_argument('name', help="Mnemonic name for mirror.")
     add_parser.add_argument(
-        'url', help="URL of mirror directory created by 'spack mirror create'.")
+        'url', help="URL of mirror directory from 'spack mirror create'.")
     add_parser.add_argument(
         '--scope', choices=scopes, default=spack.cmd.default_modify_scope,
         help="Configuration scope to modify.")
@@ -107,7 +108,7 @@ def mirror_add(args):
             tty.die("Mirror with url %s already exists." % url)
         # should only be one item per mirror dict.
 
-    items = [(n,u) for n,u in mirrors.items()]
+    items = [(n, u) for n, u in mirrors.items()]
     items.insert(0, (args.name, url))
     mirrors = syaml_dict(items)
     spack.config.update_config('mirrors', mirrors, scope=args.scope)
@@ -121,7 +122,7 @@ def mirror_remove(args):
     if not mirrors:
         mirrors = syaml_dict()
 
-    if not name in mirrors:
+    if name not in mirrors:
         tty.die("No mirror with name %s" % name)
 
     old_value = mirrors.pop(name)
@@ -152,7 +153,7 @@ def _read_specs_from_file(filename):
                 s.package
                 specs.append(s)
             except SpackError, e:
-                tty.die("Parse error in %s, line %d:" % (args.file, i+1),
+                tty.die("Parse error in %s, line %d:" % (args.file, i + 1),
                         ">>> " + string, str(e))
     return specs
 
@@ -214,10 +215,10 @@ def mirror_create(args):
 
 
 def mirror(parser, args):
-    action = { 'create' : mirror_create,
-               'add'    : mirror_add,
-               'remove' : mirror_remove,
-               'rm'     : mirror_remove,
-               'list'   : mirror_list }
+    action = {'create': mirror_create,
+              'add': mirror_add,
+              'remove': mirror_remove,
+              'rm': mirror_remove,
+              'list': mirror_list}
 
     action[args.mirror_command](args)
diff --git a/lib/spack/spack/cmd/module.py b/lib/spack/spack/cmd/module.py
index a10e36e077..2d0b83fe00 100644
--- a/lib/spack/spack/cmd/module.py
+++ b/lib/spack/spack/cmd/module.py
@@ -118,7 +118,8 @@ def loads(mtype, specs, args):
         seen_add = seen.add
         for spec in specs_from_user_constraint:
             specs.extend(
-                [item for item in spec.traverse(order='post', cover='nodes') if not (item in seen or seen_add(item))]  # NOQA: ignore=E501
+                [item for item in spec.traverse(order='post', cover='nodes')
+                 if not (item in seen or seen_add(item))]
             )
 
     module_cls = module_types[mtype]
@@ -178,7 +179,9 @@ def rm(mtype, specs, args):
 
     # Ask for confirmation
     if not args.yes_to_all:
-        tty.msg('You are about to remove {0} module files the following specs:\n'.format(mtype))  # NOQA: ignore=E501
+        tty.msg(
+            'You are about to remove {0} module files the following specs:\n'
+            .format(mtype))
         spack.cmd.display_specs(specs_with_modules, long=True)
         print('')
         spack.cmd.ask_for_confirmation('Do you want to proceed ? ')
@@ -197,7 +200,9 @@ def refresh(mtype, specs, args):
         return
 
     if not args.yes_to_all:
-        tty.msg('You are about to regenerate {name} module files for the following specs:\n'.format(name=mtype))  # NOQA: ignore=E501
+        tty.msg(
+            'You are about to regenerate {name} module files for:\n'
+            .format(name=mtype))
         spack.cmd.display_specs(specs, long=True)
         print('')
         spack.cmd.ask_for_confirmation('Do you want to proceed ? ')
@@ -245,11 +250,13 @@ def module(parser, args):
     try:
         callbacks[args.subparser_name](module_type, args.specs, args)
     except MultipleMatches:
-        message = 'the constraint \'{query}\' matches multiple packages, and this is not allowed in this context'  # NOQA: ignore=E501
+        message = ('the constraint \'{query}\' matches multiple packages, '
+                   'and this is not allowed in this context')
         tty.error(message.format(query=constraint))
         for s in args.specs:
             sys.stderr.write(s.format(color=True) + '\n')
         raise SystemExit(1)
     except NoMatch:
-        message = 'the constraint \'{query}\' match no package, and this is not allowed in this context'  # NOQA: ignore=E501
+        message = ('the constraint \'{query}\' match no package, '
+                   'and this is not allowed in this context')
         tty.die(message.format(query=constraint))
diff --git a/lib/spack/spack/cmd/package-list.py b/lib/spack/spack/cmd/package-list.py
index a27502d30e..9ed42de823 100644
--- a/lib/spack/spack/cmd/package-list.py
+++ b/lib/spack/spack/cmd/package-list.py
@@ -32,7 +32,7 @@ description = "Print a list of all packages in reStructuredText."
 
 def github_url(pkg):
     """Link to a package file on github."""
-    url = "https://github.com/llnl/spack/blob/master/var/spack/packages/%s/package.py"  # NOQA: ignore=E501
+    url = "https://github.com/llnl/spack/blob/master/var/spack/packages/%s/package.py"
     return (url % pkg.name)
 
 
diff --git a/lib/spack/spack/cmd/patch.py b/lib/spack/spack/cmd/patch.py
index a5507e42cf..9c72da40b5 100644
--- a/lib/spack/spack/cmd/patch.py
+++ b/lib/spack/spack/cmd/patch.py
@@ -29,14 +29,16 @@ import spack.cmd
 import spack
 
 
-description="Patch expanded archive sources in preparation for install"
+description = "Patch expanded archive sources in preparation for install"
+
 
 def setup_parser(subparser):
     subparser.add_argument(
         '-n', '--no-checksum', action='store_true', dest='no_checksum',
         help="Do not check downloaded packages against checksum")
     subparser.add_argument(
-        'packages', nargs=argparse.REMAINDER, help="specs of packages to stage")
+        'packages', nargs=argparse.REMAINDER,
+        help="specs of packages to stage")
 
 
 def patch(parser, args):
diff --git a/lib/spack/spack/cmd/pkg.py b/lib/spack/spack/cmd/pkg.py
index a24c2759fe..7791b93cf5 100644
--- a/lib/spack/spack/cmd/pkg.py
+++ b/lib/spack/spack/cmd/pkg.py
@@ -33,6 +33,7 @@ from spack.util.executable import *
 
 description = "Query packages associated with particular git revisions."
 
+
 def setup_parser(subparser):
     sp = subparser.add_subparsers(
         metavar='SUBCOMMAND', dest='pkg_command')
@@ -46,22 +47,28 @@ def setup_parser(subparser):
                              help="Revision to list packages for.")
 
     diff_parser = sp.add_parser('diff', help=pkg_diff.__doc__)
-    diff_parser.add_argument('rev1', nargs='?', default='HEAD^',
-                             help="Revision to compare against.")
-    diff_parser.add_argument('rev2', nargs='?', default='HEAD',
-                             help="Revision to compare to rev1 (default is HEAD).")
+    diff_parser.add_argument(
+        'rev1', nargs='?', default='HEAD^',
+        help="Revision to compare against.")
+    diff_parser.add_argument(
+        'rev2', nargs='?', default='HEAD',
+        help="Revision to compare to rev1 (default is HEAD).")
 
     add_parser = sp.add_parser('added', help=pkg_added.__doc__)
-    add_parser.add_argument('rev1', nargs='?', default='HEAD^',
-                             help="Revision to compare against.")
-    add_parser.add_argument('rev2', nargs='?', default='HEAD',
-                            help="Revision to compare to rev1 (default is HEAD).")
+    add_parser.add_argument(
+        'rev1', nargs='?', default='HEAD^',
+        help="Revision to compare against.")
+    add_parser.add_argument(
+        'rev2', nargs='?', default='HEAD',
+        help="Revision to compare to rev1 (default is HEAD).")
 
     rm_parser = sp.add_parser('removed', help=pkg_removed.__doc__)
-    rm_parser.add_argument('rev1', nargs='?', default='HEAD^',
-                           help="Revision to compare against.")
-    rm_parser.add_argument('rev2', nargs='?', default='HEAD',
-                           help="Revision to compare to rev1 (default is HEAD).")
+    rm_parser.add_argument(
+        'rev1', nargs='?', default='HEAD^',
+        help="Revision to compare against.")
+    rm_parser.add_argument(
+        'rev2', nargs='?', default='HEAD',
+        help="Revision to compare to rev1 (default is HEAD).")
 
 
 def get_git():
@@ -88,7 +95,8 @@ def pkg_add(args):
     for pkg_name in args.packages:
         filename = spack.repo.filename_for_package_name(pkg_name)
         if not os.path.isfile(filename):
-            tty.die("No such package: %s.  Path does not exist:" % pkg_name, filename)
+            tty.die("No such package: %s.  Path does not exist:" %
+                    pkg_name, filename)
 
         git = get_git()
         git('-C', spack.packages_path, 'add', filename)
@@ -112,7 +120,8 @@ def pkg_diff(args):
     if u1:
         print "%s:" % args.rev1
         colify(sorted(u1), indent=4)
-        if u1: print
+        if u1:
+            print
 
     if u2:
         print "%s:" % args.rev2
@@ -122,19 +131,21 @@ def pkg_diff(args):
 def pkg_removed(args):
     """Show packages removed since a commit."""
     u1, u2 = diff_packages(args.rev1, args.rev2)
-    if u1: colify(sorted(u1))
+    if u1:
+        colify(sorted(u1))
 
 
 def pkg_added(args):
     """Show packages added since a commit."""
     u1, u2 = diff_packages(args.rev1, args.rev2)
-    if u2: colify(sorted(u2))
+    if u2:
+        colify(sorted(u2))
 
 
 def pkg(parser, args):
-    action = { 'add'    : pkg_add,
-               'diff'    : pkg_diff,
-               'list'    : pkg_list,
-               'removed' : pkg_removed,
-               'added'   : pkg_added }
+    action = {'add': pkg_add,
+              'diff': pkg_diff,
+              'list': pkg_list,
+              'removed': pkg_removed,
+              'added': pkg_added}
     action[args.pkg_command](args)
diff --git a/lib/spack/spack/cmd/providers.py b/lib/spack/spack/cmd/providers.py
index e9007486d2..0f4a97cc4a 100644
--- a/lib/spack/spack/cmd/providers.py
+++ b/lib/spack/spack/cmd/providers.py
@@ -22,7 +22,6 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import os
 import argparse
 
 from llnl.util.tty.colify import colify
@@ -30,11 +29,13 @@ from llnl.util.tty.colify import colify
 import spack
 import spack.cmd
 
-description ="List packages that provide a particular virtual package"
+description = "List packages that provide a particular virtual package"
+
 
 def setup_parser(subparser):
-    subparser.add_argument('vpkg_spec', metavar='VPACKAGE_SPEC', nargs=argparse.REMAINDER,
-                           help='Find packages that provide this virtual package')
+    subparser.add_argument(
+        'vpkg_spec', metavar='VPACKAGE_SPEC', nargs=argparse.REMAINDER,
+        help='Find packages that provide this virtual package')
 
 
 def providers(parser, args):
diff --git a/lib/spack/spack/cmd/purge.py b/lib/spack/spack/cmd/purge.py
index f4e27a3969..26d160635c 100644
--- a/lib/spack/spack/cmd/purge.py
+++ b/lib/spack/spack/cmd/purge.py
@@ -33,7 +33,11 @@ def setup_parser(subparser):
         '-s', '--stage', action='store_true', default=True,
         help="Remove all temporary build stages (default).")
     subparser.add_argument(
-        '-c', '--cache', action='store_true', help="Remove cached downloads.")
+        '-d', '--downloads', action='store_true',
+        help="Remove cached downloads.")
+    subparser.add_argument(
+        '-u', '--user-cache', action='store_true',
+        help="Remove caches in user home directory. Includes virtual indices.")
     subparser.add_argument(
         '-a', '--all', action='store_true',
         help="Remove all of the above.")
@@ -41,12 +45,14 @@ def setup_parser(subparser):
 
 def purge(parser, args):
     # Special case: no flags.
-    if not any((args.stage, args.cache, args.all)):
+    if not any((args.stage, args.downloads, args.user_cache, args.all)):
         stage.purge()
         return
 
     # handle other flags with fall through.
     if args.stage or args.all:
         stage.purge()
-    if args.cache or args.all:
-        spack.cache.destroy()
+    if args.downloads or args.all:
+        spack.fetch_cache.destroy()
+    if args.user_cache or args.all:
+        spack.user_cache.destroy()
diff --git a/lib/spack/spack/cmd/python.py b/lib/spack/spack/cmd/python.py
index 59423271b9..12727cb599 100644
--- a/lib/spack/spack/cmd/python.py
+++ b/lib/spack/spack/cmd/python.py
@@ -30,18 +30,22 @@ import platform
 
 import spack
 
+
 def setup_parser(subparser):
     subparser.add_argument(
         '-c', dest='python_command', help='Command to execute.')
     subparser.add_argument(
-        'python_args', nargs=argparse.REMAINDER, help="File to run plus arguments.")
+        'python_args', nargs=argparse.REMAINDER,
+        help="File to run plus arguments.")
+
 
 description = "Launch an interpreter as spack would launch a command"
 
+
 def python(parser, args):
     # Fake a main python shell by setting __name__ to __main__.
-    console = code.InteractiveConsole({'__name__' : '__main__',
-                                       'spack'    : spack})
+    console = code.InteractiveConsole({'__name__': '__main__',
+                                       'spack': spack})
 
     if "PYTHONSTARTUP" in os.environ:
         startup_file = os.environ["PYTHONSTARTUP"]
diff --git a/lib/spack/spack/cmd/reindex.py b/lib/spack/spack/cmd/reindex.py
index 93eba7a0f1..e37eebbd92 100644
--- a/lib/spack/spack/cmd/reindex.py
+++ b/lib/spack/spack/cmd/reindex.py
@@ -22,10 +22,10 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import argparse
 import spack
 
 description = "Rebuild Spack's package database."
 
+
 def reindex(parser, args):
     spack.installed_db.reindex(spack.install_layout)
diff --git a/lib/spack/spack/cmd/repo.py b/lib/spack/spack/cmd/repo.py
index cbd8f4784e..5ab2ac0833 100644
--- a/lib/spack/spack/cmd/repo.py
+++ b/lib/spack/spack/cmd/repo.py
@@ -23,20 +23,16 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
-import re
-import shutil
 
-import argparse
 import llnl.util.tty as tty
-from llnl.util.filesystem import join_path, mkdirp
 
 import spack.spec
 import spack.config
-from spack.util.environment import get_path
 from spack.repository import *
 
 description = "Manage package source repositories."
 
+
 def setup_parser(subparser):
     sp = subparser.add_subparsers(metavar='SUBCOMMAND', dest='repo_command')
     scopes = spack.config.config_scopes
@@ -57,13 +53,15 @@ def setup_parser(subparser):
 
     # Add
     add_parser = sp.add_parser('add', help=repo_add.__doc__)
-    add_parser.add_argument('path', help="Path to a Spack package repository directory.")
+    add_parser.add_argument(
+        'path', help="Path to a Spack package repository directory.")
     add_parser.add_argument(
         '--scope', choices=scopes, default=spack.cmd.default_modify_scope,
         help="Configuration scope to modify.")
 
     # Remove
-    remove_parser = sp.add_parser('remove', help=repo_remove.__doc__, aliases=['rm'])
+    remove_parser = sp.add_parser(
+        'remove', help=repo_remove.__doc__, aliases=['rm'])
     remove_parser.add_argument(
         'path_or_namespace',
         help="Path or namespace of a Spack package repository.")
@@ -100,7 +98,8 @@ def repo_add(args):
 
     # If that succeeds, finally add it to the configuration.
     repos = spack.config.get_config('repos', args.scope)
-    if not repos: repos = []
+    if not repos:
+        repos = []
 
     if repo.root in repos or path in repos:
         tty.die("Repository is already registered with Spack: %s" % path)
@@ -135,7 +134,7 @@ def repo_remove(args):
                 tty.msg("Removed repository %s with namespace '%s'."
                         % (repo.root, repo.namespace))
                 return
-        except RepoError as e:
+        except RepoError:
             continue
 
     tty.die("No repository with path or namespace: %s"
@@ -149,7 +148,7 @@ def repo_list(args):
     for r in roots:
         try:
             repos.append(Repo(r))
-        except RepoError as e:
+        except RepoError:
             continue
 
     msg = "%d package repositor" % len(repos)
@@ -166,9 +165,9 @@ def repo_list(args):
 
 
 def repo(parser, args):
-    action = { 'create' : repo_create,
-               'list'   : repo_list,
-               'add'    : repo_add,
-               'remove' : repo_remove,
-               'rm'     : repo_remove}
+    action = {'create': repo_create,
+              'list': repo_list,
+              'add': repo_add,
+              'remove': repo_remove,
+              'rm': repo_remove}
     action[args.repo_command](args)
diff --git a/lib/spack/spack/cmd/restage.py b/lib/spack/spack/cmd/restage.py
index 325d30662f..969afe09bd 100644
--- a/lib/spack/spack/cmd/restage.py
+++ b/lib/spack/spack/cmd/restage.py
@@ -31,6 +31,7 @@ import spack.cmd
 
 description = "Revert checked out package source code."
 
+
 def setup_parser(subparser):
     subparser.add_argument('packages', nargs=argparse.REMAINDER,
                            help="specs of packages to restage")
diff --git a/lib/spack/spack/cmd/setup.py b/lib/spack/spack/cmd/setup.py
index 8cf05b5c8b..9553942017 100644
--- a/lib/spack/spack/cmd/setup.py
+++ b/lib/spack/spack/cmd/setup.py
@@ -143,7 +143,8 @@ def setup(self, args):
 
         if not spec.versions.concrete:
             tty.die(
-                "spack setup spec must have a single, concrete version.  Did you forget a package version number?")
+                "spack setup spec must have a single, concrete version. "
+                "Did you forget a package version number?")
 
         spec.concretize()
         package = spack.repo.get(spec)
diff --git a/lib/spack/spack/cmd/spec.py b/lib/spack/spack/cmd/spec.py
index 321e3e429b..6e6d1c1277 100644
--- a/lib/spack/spack/cmd/spec.py
+++ b/lib/spack/spack/cmd/spec.py
@@ -25,23 +25,22 @@
 import argparse
 import spack.cmd
 
-import llnl.util.tty as tty
-
 import spack
-import spack.url as url
 
 description = "print out abstract and concrete versions of a spec."
 
+
 def setup_parser(subparser):
     subparser.add_argument('-i', '--ids', action='store_true',
                            help="show numerical ids for dependencies.")
-    subparser.add_argument('specs', nargs=argparse.REMAINDER, help="specs of packages")
+    subparser.add_argument(
+        'specs', nargs=argparse.REMAINDER, help="specs of packages")
 
 
 def spec(parser, args):
-    kwargs = { 'ids'    : args.ids,
-               'indent' : 2,
-               'color'  : True }
+    kwargs = {'ids': args.ids,
+              'indent': 2,
+              'color': True}
 
     for spec in spack.cmd.parse_specs(args.specs):
         print "Input spec"
diff --git a/lib/spack/spack/cmd/stage.py b/lib/spack/spack/cmd/stage.py
index 61e9c6d9ff..bfc2e5f456 100644
--- a/lib/spack/spack/cmd/stage.py
+++ b/lib/spack/spack/cmd/stage.py
@@ -22,14 +22,14 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import os
 import argparse
 
 import llnl.util.tty as tty
 import spack
 import spack.cmd
 
-description="Expand downloaded archive in preparation for install"
+description = "Expand downloaded archive in preparation for install"
+
 
 def setup_parser(subparser):
     subparser.add_argument(
diff --git a/lib/spack/spack/cmd/test-install.py b/lib/spack/spack/cmd/test-install.py
index 14c06d136d..8e7173e9a2 100644
--- a/lib/spack/spack/cmd/test-install.py
+++ b/lib/spack/spack/cmd/test-install.py
@@ -36,25 +36,25 @@ from llnl.util.filesystem import *
 from spack.build_environment import InstallError
 from spack.fetch_strategy import FetchError
 
-description = "Run package installation as a unit test, output formatted results."
+description = "Run package install as a unit test, output formatted results."
 
 
 def setup_parser(subparser):
-    subparser.add_argument('-j',
-                           '--jobs',
-                           action='store',
-                           type=int,
-                           help="Explicitly set number of make jobs.  Default is #cpus.")
+    subparser.add_argument(
+        '-j', '--jobs', action='store', type=int,
+        help="Explicitly set number of make jobs.  Default is #cpus.")
 
-    subparser.add_argument('-n',
-                           '--no-checksum',
-                           action='store_true',
-                           dest='no_checksum',
-                           help="Do not check packages against checksum")
+    subparser.add_argument(
+        '-n', '--no-checksum', action='store_true', dest='no_checksum',
+        help="Do not check packages against checksum")
 
-    subparser.add_argument('-o', '--output', action='store', help="test output goes in this file")
+    subparser.add_argument(
+        '-o', '--output', action='store',
+        help="test output goes in this file")
 
-    subparser.add_argument('package', nargs=argparse.REMAINDER, help="spec of package to install")
+    subparser.add_argument(
+        'package', nargs=argparse.REMAINDER,
+        help="spec of package to install")
 
 
 class TestResult(object):
@@ -65,6 +65,7 @@ class TestResult(object):
 
 
 class TestSuite(object):
+
     def __init__(self, filename):
         self.filename = filename
         self.root = ET.Element('testsuite')
@@ -75,14 +76,17 @@ class TestSuite(object):
 
     def append(self, item):
         if not isinstance(item, TestCase):
-            raise TypeError('only TestCase instances may be appended to a TestSuite instance')
+            raise TypeError(
+                'only TestCase instances may be appended to TestSuite')
         self.tests.append(item)  # Append the item to the list of tests
 
     def __exit__(self, exc_type, exc_val, exc_tb):
         # Prepare the header for the entire test suite
-        number_of_errors = sum(x.result_type == TestResult.ERRORED for x in self.tests)
+        number_of_errors = sum(
+            x.result_type == TestResult.ERRORED for x in self.tests)
         self.root.set('errors', str(number_of_errors))
-        number_of_failures = sum(x.result_type == TestResult.FAILED for x in self.tests)
+        number_of_failures = sum(
+            x.result_type == TestResult.FAILED for x in self.tests)
         self.root.set('failures', str(number_of_failures))
         self.root.set('tests', str(len(self.tests)))
 
@@ -112,7 +116,8 @@ class TestCase(object):
             self.element.set('time', str(time))
         self.result_type = None
 
-    def set_result(self, result_type, message=None, error_type=None, text=None):
+    def set_result(self, result_type,
+                   message=None, error_type=None, text=None):
         self.result_type = result_type
         result = TestCase.results[self.result_type]
         if result is not None and result is not TestResult.PASSED:
@@ -155,13 +160,19 @@ def install_single_spec(spec, number_of_jobs):
     # If it is already installed, skip the test
     if spack.repo.get(spec).installed:
         testcase = TestCase(package.name, package.spec.short_spec, time=0.0)
-        testcase.set_result(TestResult.SKIPPED, message='Skipped [already installed]', error_type='already_installed')
+        testcase.set_result(
+            TestResult.SKIPPED,
+            message='Skipped [already installed]',
+            error_type='already_installed')
         return testcase
 
     # If it relies on dependencies that did not install, skip
     if failed_dependencies(spec):
         testcase = TestCase(package.name, package.spec.short_spec, time=0.0)
-        testcase.set_result(TestResult.SKIPPED, message='Skipped [failed dependencies]', error_type='dep_failed')
+        testcase.set_result(
+            TestResult.SKIPPED,
+            message='Skipped [failed dependencies]',
+            error_type='dep_failed')
         return testcase
 
     # Otherwise try to install the spec
@@ -177,26 +188,30 @@ def install_single_spec(spec, number_of_jobs):
         testcase = TestCase(package.name, package.spec.short_spec, duration)
         testcase.set_result(TestResult.PASSED)
     except InstallError:
-        # An InstallError is considered a failure (the recipe didn't work correctly)
+        # An InstallError is considered a failure (the recipe didn't work
+        # correctly)
         duration = time.time() - start_time
         # Try to get the log
         lines = fetch_log(package.build_log_path)
         text = '\n'.join(lines)
         testcase = TestCase(package.name, package.spec.short_spec, duration)
-        testcase.set_result(TestResult.FAILED, message='Installation failure', text=text)
+        testcase.set_result(TestResult.FAILED,
+                            message='Installation failure', text=text)
 
     except FetchError:
         # A FetchError is considered an error (we didn't even start building)
         duration = time.time() - start_time
         testcase = TestCase(package.name, package.spec.short_spec, duration)
-        testcase.set_result(TestResult.ERRORED, message='Unable to fetch package')
+        testcase.set_result(TestResult.ERRORED,
+                            message='Unable to fetch package')
 
     return testcase
 
 
 def get_filename(args, top_spec):
     if not args.output:
-        fname = 'test-{x.name}-{x.version}-{hash}.xml'.format(x=top_spec, hash=top_spec.dag_hash())
+        fname = 'test-{x.name}-{x.version}-{hash}.xml'.format(
+            x=top_spec, hash=top_spec.dag_hash())
         output_directory = join_path(os.getcwd(), 'test-output')
         if not os.path.exists(output_directory):
             os.mkdir(output_directory)
diff --git a/lib/spack/spack/cmd/test.py b/lib/spack/spack/cmd/test.py
index 36810321ef..bf7342f606 100644
--- a/lib/spack/spack/cmd/test.py
+++ b/lib/spack/spack/cmd/test.py
@@ -23,28 +23,28 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
-from pprint import pprint
 
 from llnl.util.filesystem import join_path, mkdirp
 from llnl.util.tty.colify import colify
-from llnl.util.lang import list_modules
 
 import spack
 import spack.test
 from spack.fetch_strategy import FetchError
 
-description ="Run unit tests"
+description = "Run unit tests"
+
 
 def setup_parser(subparser):
     subparser.add_argument(
         'names', nargs='*', help="Names of tests to run.")
     subparser.add_argument(
-        '-l', '--list', action='store_true', dest='list', help="Show available tests")
+        '-l', '--list', action='store_true', dest='list',
+        help="Show available tests")
     subparser.add_argument(
-        '--createXmlOutput', action='store_true', dest='createXmlOutput', 
+        '--createXmlOutput', action='store_true', dest='createXmlOutput',
         help="Create JUnit XML from test results")
     subparser.add_argument(
-        '--xmlOutputDir', dest='xmlOutputDir', 
+        '--xmlOutputDir', dest='xmlOutputDir',
         help="Nose creates XML files in this directory")
     subparser.add_argument(
         '-v', '--verbose', action='store_true', dest='verbose',
@@ -52,6 +52,7 @@ def setup_parser(subparser):
 
 
 class MockCache(object):
+
     def store(self, copyCmd, relativeDst):
         pass
 
@@ -60,15 +61,17 @@ class MockCache(object):
 
 
 class MockCacheFetcher(object):
+
     def set_stage(self, stage):
         pass
-    
+
     def fetch(self):
         raise FetchError("Mock cache always fails for tests")
 
     def __str__(self):
         return "[mock fetcher]"
 
+
 def test(parser, args):
     if args.list:
         print "Available tests:"
@@ -82,8 +85,8 @@ def test(parser, args):
                 outputDir = join_path(os.getcwd(), "test-output")
             else:
                 outputDir = os.path.abspath(args.xmlOutputDir)
-            
+
             if not os.path.exists(outputDir):
                 mkdirp(outputDir)
-        spack.cache = MockCache()
+        spack.fetch_cache = MockCache()
         spack.test.run(args.names, outputDir, args.verbose)
diff --git a/lib/spack/spack/cmd/uninstall.py b/lib/spack/spack/cmd/uninstall.py
index a17b7c685c..8957d1c908 100644
--- a/lib/spack/spack/cmd/uninstall.py
+++ b/lib/spack/spack/cmd/uninstall.py
@@ -50,25 +50,27 @@ def setup_parser(subparser):
     subparser.add_argument(
         '-f', '--force', action='store_true', dest='force',
         help="Remove regardless of whether other packages depend on this one.")
+
     subparser.add_argument(
         '-a', '--all', action='store_true', dest='all',
-        help="USE CAREFULLY. Remove ALL installed packages that match each " +
-             "supplied spec. i.e., if you say uninstall libelf, ALL versions of " +  # NOQA: ignore=E501
-             "libelf are uninstalled. This is both useful and dangerous, like rm -r.")  # NOQA: ignore=E501
+        help="USE CAREFULLY. Remove ALL installed packages that match each "
+             "supplied spec. i.e., if you say uninstall libelf, ALL versions "
+             "of libelf are uninstalled. This is both useful and dangerous, "
+             "like rm -r.")
+
     subparser.add_argument(
         '-d', '--dependents', action='store_true', dest='dependents',
-        help='Also uninstall any packages that depend on the ones given via command line.'  # NOQA: ignore=E501
-    )
+        help='Also uninstall any packages that depend on the ones given '
+             'via command line.')
+
     subparser.add_argument(
         '-y', '--yes-to-all', action='store_true', dest='yes_to_all',
-        help='Assume "yes" is the answer to every confirmation asked to the user.'  # NOQA: ignore=E501
+        help='Assume "yes" is the answer to every confirmation requested')
 
-    )
     subparser.add_argument(
         'packages',
         nargs=argparse.REMAINDER,
-        help="specs of packages to uninstall"
-    )
+        help="specs of packages to uninstall")
 
 
 def concretize_specs(specs, allow_multiple_matches=False, force=False):
@@ -184,7 +186,8 @@ def uninstall(parser, args):
             uninstall_list = list(set(uninstall_list))
 
         if has_error:
-            tty.die('You can use spack uninstall --dependents to uninstall these dependencies as well')  # NOQA: ignore=E501
+            tty.die('You can use spack uninstall --dependents '
+                    'to uninstall these dependencies as well')
 
         if not args.yes_to_all:
             tty.msg("The following packages will be uninstalled : ")
diff --git a/lib/spack/spack/cmd/unload.py b/lib/spack/spack/cmd/unload.py
index 7bd15750ed..b52bedb7b4 100644
--- a/lib/spack/spack/cmd/unload.py
+++ b/lib/spack/spack/cmd/unload.py
@@ -25,13 +25,15 @@
 import argparse
 import spack.modules
 
-description ="Remove package from environment using module."
+description = "Remove package from environment using module."
+
 
 def setup_parser(subparser):
     """Parser is only constructed so that this prints a nice help
        message with -h. """
     subparser.add_argument(
-        'spec', nargs=argparse.REMAINDER, help='Spec of package to unload with modules.')
+        'spec', nargs=argparse.REMAINDER,
+        help='Spec of package to unload with modules.')
 
 
 def unload(parser, args):
diff --git a/lib/spack/spack/cmd/unuse.py b/lib/spack/spack/cmd/unuse.py
index 789a690e9c..6403cf6162 100644
--- a/lib/spack/spack/cmd/unuse.py
+++ b/lib/spack/spack/cmd/unuse.py
@@ -25,13 +25,15 @@
 import argparse
 import spack.modules
 
-description ="Remove package from environment using dotkit."
+description = "Remove package from environment using dotkit."
+
 
 def setup_parser(subparser):
     """Parser is only constructed so that this prints a nice help
        message with -h. """
     subparser.add_argument(
-        'spec', nargs=argparse.REMAINDER, help='Spec of package to unuse with dotkit.')
+        'spec', nargs=argparse.REMAINDER,
+        help='Spec of package to unuse with dotkit.')
 
 
 def unuse(parser, args):
diff --git a/lib/spack/spack/cmd/url-parse.py b/lib/spack/spack/cmd/url-parse.py
index ce12a17d13..b8c7c95040 100644
--- a/lib/spack/spack/cmd/url-parse.py
+++ b/lib/spack/spack/cmd/url-parse.py
@@ -22,28 +22,28 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import sys
-
 import llnl.util.tty as tty
 
 import spack
 import spack.url
 from spack.util.web import find_versions_of_archive
 
-description = "Show parsing of a URL, optionally spider web for other versions."
+description = "Show parsing of a URL, optionally spider web for versions."
+
 
 def setup_parser(subparser):
     subparser.add_argument('url', help="url of a package archive")
     subparser.add_argument(
-        '-s', '--spider', action='store_true', help="Spider the source page for versions.")
+        '-s', '--spider', action='store_true',
+        help="Spider the source page for versions.")
 
 
 def print_name_and_version(url):
     name, ns, nl, ntup, ver, vs, vl, vtup = spack.url.substitution_offsets(url)
-    underlines = [" "] * max(ns+nl, vs+vl)
-    for i in range(ns, ns+nl):
+    underlines = [" "] * max(ns + nl, vs + vl)
+    for i in range(ns, ns + nl):
         underlines[i] = '-'
-    for i in range(vs, vs+vl):
+    for i in range(vs, vs + vl):
         underlines[i] = '~'
 
     print "    %s" % url
diff --git a/lib/spack/spack/cmd/urls.py b/lib/spack/spack/cmd/urls.py
index 2fe2019a22..f151581d7d 100644
--- a/lib/spack/spack/cmd/urls.py
+++ b/lib/spack/spack/cmd/urls.py
@@ -22,12 +22,12 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import sys
 import spack
 import spack.url
 
 description = "Inspect urls used by packages in spack."
 
+
 def setup_parser(subparser):
     subparser.add_argument(
         '-c', '--color', action='store_true',
@@ -53,6 +53,7 @@ def urls(parser, args):
 
     for url in sorted(urls):
         if args.color or args.extrapolation:
-            print spack.url.color_url(url, subs=args.extrapolation, errors=True)
+            print spack.url.color_url(
+                url, subs=args.extrapolation, errors=True)
         else:
             print url
diff --git a/lib/spack/spack/cmd/use.py b/lib/spack/spack/cmd/use.py
index bbb90fde1b..e3612ace48 100644
--- a/lib/spack/spack/cmd/use.py
+++ b/lib/spack/spack/cmd/use.py
@@ -25,13 +25,15 @@
 import argparse
 import spack.modules
 
-description ="Add package to environment using dotkit."
+description = "Add package to environment using dotkit."
+
 
 def setup_parser(subparser):
     """Parser is only constructed so that this prints a nice help
        message with -h. """
     subparser.add_argument(
-        'spec', nargs=argparse.REMAINDER, help='Spec of package to use with dotkit.')
+        'spec', nargs=argparse.REMAINDER,
+        help='Spec of package to use with dotkit.')
 
 
 def use(parser, args):
diff --git a/lib/spack/spack/cmd/versions.py b/lib/spack/spack/cmd/versions.py
index ec3a4b2e34..1e95225ab8 100644
--- a/lib/spack/spack/cmd/versions.py
+++ b/lib/spack/spack/cmd/versions.py
@@ -22,15 +22,16 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import os
 from llnl.util.tty.colify import colify
 import llnl.util.tty as tty
 import spack
 
-description ="List available versions of a package"
+description = "List available versions of a package"
+
 
 def setup_parser(subparser):
-    subparser.add_argument('package', metavar='PACKAGE', help='Package to list versions for')
+    subparser.add_argument('package', metavar='PACKAGE',
+                           help='Package to list versions for')
 
 
 def versions(parser, args):
diff --git a/lib/spack/spack/compiler.py b/lib/spack/spack/compiler.py
index ce4555bc56..a77991e4dc 100644
--- a/lib/spack/spack/compiler.py
+++ b/lib/spack/spack/compiler.py
@@ -25,10 +25,8 @@
 import os
 import re
 import itertools
-from datetime import datetime
 
 import llnl.util.tty as tty
-from llnl.util.lang import memoized
 from llnl.util.filesystem import join_path
 
 import spack.error
@@ -37,10 +35,10 @@ import spack.architecture
 from spack.util.multiproc import parmap
 from spack.util.executable import *
 from spack.util.environment import get_path
-from spack.version import Version
 
 __all__ = ['Compiler', 'get_compiler_version']
 
+
 def _verify_executables(*paths):
     for path in paths:
         if not os.path.isfile(path) and os.access(path, os.X_OK):
@@ -49,8 +47,9 @@ def _verify_executables(*paths):
 
 _version_cache = {}
 
+
 def get_compiler_version(compiler_path, version_arg, regex='(.*)'):
-    if not compiler_path in _version_cache:
+    if compiler_path not in _version_cache:
         compiler = Executable(compiler_path)
         output = compiler(version_arg, output=str, error=str)
 
@@ -113,7 +112,7 @@ class Compiler(object):
     # Name of module used to switch versions of this compiler
     PrgEnv_compiler = None
 
-    def __init__(self, cspec, operating_system, 
+    def __init__(self, cspec, operating_system,
                  paths, modules=[], alias=None, **kwargs):
         def check(exe):
             if exe is None:
@@ -130,11 +129,6 @@ class Compiler(object):
             else:
                 self.fc  = check(paths[3])
 
-        #self.cc  = check(cc)
-        #self.cxx = check(cxx)
-        #self.f77 = check(f77)
-        #self.fc  = check(fc)
-
         # Unfortunately have to make sure these params are accepted
         # in the same order they are returned by sorted(flags)
         # in compilers/__init__.py
@@ -158,31 +152,30 @@ class Compiler(object):
     @property
     def openmp_flag(self):
         # If it is not overridden, assume it is not supported and warn the user
-        tty.die("The compiler you have chosen does not currently support OpenMP.",
-                "If you think it should, please edit the compiler subclass and",
-                "submit a pull request or issue.")
-
+        tty.die(
+            "The compiler you have chosen does not currently support OpenMP.",
+            "If you think it should, please edit the compiler subclass and",
+            "submit a pull request or issue.")
 
     # This property should be overridden in the compiler subclass if
     # C++11 is supported by that compiler
     @property
     def cxx11_flag(self):
         # If it is not overridden, assume it is not supported and warn the user
-        tty.die("The compiler you have chosen does not currently support C++11.",
-                "If you think it should, please edit the compiler subclass and",
-                "submit a pull request or issue.")
-
+        tty.die(
+            "The compiler you have chosen does not currently support C++11.",
+            "If you think it should, please edit the compiler subclass and",
+            "submit a pull request or issue.")
 
     # This property should be overridden in the compiler subclass if
     # C++14 is supported by that compiler
     @property
     def cxx14_flag(self):
         # If it is not overridden, assume it is not supported and warn the user
-        tty.die("The compiler you have chosen does not currently support C++14.",
-                "If you think it should, please edit the compiler subclass and",
-                "submit a pull request or issue.")
-
-
+        tty.die(
+            "The compiler you have chosen does not currently support C++14.",
+            "If you think it should, please edit the compiler subclass and",
+            "submit a pull request or issue.")
 
     #
     # Compiler classes have methods for querying the version of
@@ -191,7 +184,6 @@ class Compiler(object):
     # Compiler *instances* are just data objects, and can only be
     # constructed from an actual set of executables.
     #
-
     @classmethod
     def default_version(cls, cc):
         """Override just this to override all compiler version functions."""
@@ -258,16 +250,19 @@ class Compiler(object):
                 version = detect_version(full_path)
                 return (version, prefix, suffix, full_path)
             except ProcessError, e:
-                tty.debug("Couldn't get version for compiler %s" % full_path, e)
+                tty.debug(
+                    "Couldn't get version for compiler %s" % full_path, e)
                 return None
             except Exception, e:
                 # Catching "Exception" here is fine because it just
                 # means something went wrong running a candidate executable.
-                tty.debug("Error while executing candidate compiler %s" % full_path,
-                          "%s: %s" %(e.__class__.__name__, e))
+                tty.debug("Error while executing candidate compiler %s"
+                          % full_path,
+                          "%s: %s" % (e.__class__.__name__, e))
                 return None
 
-        successful = [key for key in parmap(check, checks) if key is not None]
+        successful = [k for k in parmap(check, checks) if k is not None]
+
         # The 'successful' list is ordered like the input paths.
         # Reverse it here so that the dict creation (last insert wins)
         # does not spoil the intented precedence.
@@ -278,20 +273,23 @@ class Compiler(object):
         """Return a string representation of the compiler toolchain."""
         return self.__str__()
 
-
     def __str__(self):
         """Return a string representation of the compiler toolchain."""
         return "%s(%s)" % (
-            self.name, '\n     '.join((str(s) for s in (self.cc, self.cxx, self.f77, self.fc, self.modules, str(self.operating_system)))))
+            self.name, '\n     '.join((str(s) for s in (
+                self.cc, self.cxx, self.f77, self.fc, self.modules,
+                str(self.operating_system)))))
 
 
 class CompilerAccessError(spack.error.SpackError):
+
     def __init__(self, path):
         super(CompilerAccessError, self).__init__(
             "'%s' is not a valid compiler." % path)
 
 
 class InvalidCompilerError(spack.error.SpackError):
+
     def __init__(self):
         super(InvalidCompilerError, self).__init__(
             "Compiler has no executables.")
diff --git a/lib/spack/spack/compilers/__init__.py b/lib/spack/spack/compilers/__init__.py
index 0ba94741da..eb866c8bbb 100644
--- a/lib/spack/spack/compilers/__init__.py
+++ b/lib/spack/spack/compilers/__init__.py
@@ -26,15 +26,9 @@
 system and configuring Spack to use multiple compilers.
 """
 import imp
-import os
 import platform
-import copy
-import hashlib
-import base64
-import yaml
-import sys
 
-from llnl.util.lang import memoized, list_modules
+from llnl.util.lang import list_modules
 from llnl.util.filesystem import join_path
 
 import spack
@@ -43,11 +37,7 @@ import spack.spec
 import spack.config
 import spack.architecture
 
-from spack.util.multiproc import parmap
-from spack.compiler import Compiler
-from spack.util.executable import which
 from spack.util.naming import mod_to_class
-from spack.util.environment import get_path
 
 _imported_compilers_module = 'spack.compilers'
 _path_instance_vars = ['cc', 'cxx', 'f77', 'fc']
@@ -73,7 +63,8 @@ def _to_dict(compiler):
     """Return a dict version of compiler suitable to insert in YAML."""
     d = {}
     d['spec'] = str(compiler.spec)
-    d['paths'] = dict( (attr, getattr(compiler, attr, None)) for attr in _path_instance_vars )
+    d['paths'] = dict((attr, getattr(compiler, attr, None))
+                      for attr in _path_instance_vars)
     d['operating_system'] = str(compiler.operating_system)
     d['modules'] = compiler.modules if compiler.modules else []
 
@@ -140,15 +131,19 @@ def remove_compiler_from_config(compiler_spec, scope=None):
       - compiler_specs: a list of CompilerSpec objects.
       - scope:          configuration scope to modify.
     """
+    # Need a better way for this
+    global _cache_config_file
+
     compiler_config = get_compiler_config(scope)
     config_length = len(compiler_config)
 
-    filtered_compiler_config = [comp for comp in compiler_config
-               if spack.spec.CompilerSpec(comp['compiler']['spec']) != compiler_spec]
-    # Need a better way for this
-    global _cache_config_file
-    _cache_config_file = filtered_compiler_config # Update the cache for changes
-    if len(filtered_compiler_config) == config_length: # No items removed
+    filtered_compiler_config = [
+        comp for comp in compiler_config
+        if spack.spec.CompilerSpec(comp['compiler']['spec']) != compiler_spec]
+
+    # Update the cache for changes
+    _cache_config_file = filtered_compiler_config
+    if len(filtered_compiler_config) == config_length:  # No items removed
         CompilerSpecInsufficientlySpecificError(compiler_spec)
     spack.config.update_config('compilers', filtered_compiler_config, scope)
 
@@ -158,7 +153,8 @@ def all_compilers_config(scope=None, init_config=True):
        available to build with.  These are instances of CompilerSpec.
     """
     # Get compilers for this architecture.
-    global _cache_config_file #Create a cache of the config file so we don't load all the time.
+    # Create a cache of the config file so we don't load all the time.
+    global _cache_config_file
     if not _cache_config_file:
         _cache_config_file = get_compiler_config(scope, init_config)
         return _cache_config_file
@@ -236,7 +232,8 @@ def compilers_for_spec(compiler_spec, scope=None, **kwargs):
                 continue
             items = items['compiler']
 
-            if not ('paths' in items and all(n in items['paths'] for n in _path_instance_vars)):
+            if not ('paths' in items and
+                    all(n in items['paths'] for n in _path_instance_vars)):
                 raise InvalidCompilerConfigurationError(cspec)
 
             cls  = class_for_compiler_name(cspec.name)
@@ -254,10 +251,10 @@ def compilers_for_spec(compiler_spec, scope=None, **kwargs):
                 mods = []
 
             if 'operating_system' in items:
-                operating_system = spack.architecture._operating_system_from_dict(items['operating_system'], platform)
+                os = spack.architecture._operating_system_from_dict(
+                    items['operating_system'], platform)
             else:
-                operating_system = None
-
+                os = None
 
             alias = items['alias'] if 'alias' in items else None
 
@@ -266,7 +263,8 @@ def compilers_for_spec(compiler_spec, scope=None, **kwargs):
                 if f in items:
                     flags[f] = items[f]
 
-            compilers.append(cls(cspec, operating_system, compiler_paths, mods, alias, **flags))
+            compilers.append(
+                cls(cspec, os, compiler_paths, mods, alias, **flags))
 
         return compilers
 
@@ -275,7 +273,6 @@ def compilers_for_spec(compiler_spec, scope=None, **kwargs):
     for cspec in matches:
         compilers.extend(get_compilers(cspec))
     return compilers
-#    return [get_compilers(cspec) for cspec in matches]
 
 
 @_auto_compiler_spec
@@ -285,8 +282,9 @@ def compiler_for_spec(compiler_spec, arch):
     operating_system = arch.platform_os
     assert(compiler_spec.concrete)
 
-    compilers = [c for c in compilers_for_spec(compiler_spec, platform=arch.platform)
-                if c.operating_system == operating_system]
+    compilers = [
+        c for c in compilers_for_spec(compiler_spec, platform=arch.platform)
+        if c.operating_system == operating_system]
     if len(compilers) < 1:
         raise NoCompilerForSpecError(compiler_spec, operating_system)
     if len(compilers) > 1:
@@ -321,11 +319,13 @@ def all_os_classes():
 
     return classes
 
+
 def all_compiler_types():
     return [class_for_compiler_name(c) for c in supported_compilers()]
 
 
 class InvalidCompilerConfigurationError(spack.error.SpackError):
+
     def __init__(self, compiler_spec):
         super(InvalidCompilerConfigurationError, self).__init__(
             "Invalid configuration for [compiler \"%s\"]: " % compiler_spec,
@@ -335,14 +335,18 @@ class InvalidCompilerConfigurationError(spack.error.SpackError):
 
 class NoCompilersError(spack.error.SpackError):
     def __init__(self):
-        super(NoCompilersError, self).__init__("Spack could not find any compilers!")
+        super(NoCompilersError, self).__init__(
+            "Spack could not find any compilers!")
+
 
 class NoCompilerForSpecError(spack.error.SpackError):
     def __init__(self, compiler_spec, target):
-        super(NoCompilerForSpecError, self).__init__("No compilers for operating system %s satisfy spec %s" % (
-                                                     target, compiler_spec))
+        super(NoCompilerForSpecError, self).__init__(
+            "No compilers for operating system %s satisfy spec %s"
+            % (target, compiler_spec))
+
 
 class CompilerSpecInsufficientlySpecificError(spack.error.SpackError):
     def __init__(self, compiler_spec):
-        super(CompilerSpecInsufficientlySpecificError, self).__init__("Multiple compilers satisfy spec %s",
-                                                                      compiler_spec)
+        super(CompilerSpecInsufficientlySpecificError, self).__init__(
+            "Multiple compilers satisfy spec %s" % compiler_spec)
diff --git a/lib/spack/spack/compilers/clang.py b/lib/spack/spack/compilers/clang.py
index 00b406d820..4cf65222ae 100644
--- a/lib/spack/spack/compilers/clang.py
+++ b/lib/spack/spack/compilers/clang.py
@@ -29,6 +29,7 @@ from spack.util.executable import *
 import llnl.util.tty as tty
 from spack.version import ver
 
+
 class Clang(Compiler):
     # Subclasses use possible names of C compiler
     cc_names = ['clang']
@@ -43,11 +44,12 @@ class Clang(Compiler):
     fc_names = []
 
     # Named wrapper links within spack.build_env_path
-    link_paths = { 'cc'  : 'clang/clang',
-                   'cxx' : 'clang/clang++',
-                   # Use default wrappers for fortran, in case provided in compilers.yaml
-                   'f77' : 'f77',
-                   'fc'  : 'f90' }
+    link_paths = {'cc': 'clang/clang',
+                  'cxx': 'clang/clang++',
+                  # Use default wrappers for fortran, in case provided in
+                  # compilers.yaml
+                  'f77': 'f77',
+                  'fc': 'f90'}
 
     @property
     def is_apple(self):
diff --git a/lib/spack/spack/compilers/craype.py b/lib/spack/spack/compilers/craype.py
index 4ba8b110ec..c92e5c131a 100644
--- a/lib/spack/spack/compilers/craype.py
+++ b/lib/spack/spack/compilers/craype.py
@@ -1,34 +1,33 @@
-##############################################################################}
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
-# For details, see https://scalability-llnl.github.io/spack
+# For details, see https://github.com/llnl/spack
 # Please also see the LICENSE file for our notice and the LGPL.
 #
 # This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
 #
 # This program is distributed in the hope that it will be useful, but
 # WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
+# conditions of the GNU Lesser General Public License for more details.
 #
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import llnl.util.tty as tty
-
-#from spack.build_environment import load_module
 from spack.compiler import *
-#from spack.version import ver
+
 
 class Craype(Compiler):
+    """Cray programming environment compiler."""
+
     # Subclasses use possible names of C compiler
     cc_names = ['cc']
 
@@ -47,12 +46,11 @@ class Craype(Compiler):
     PrgEnv = 'PrgEnv-cray'
     PrgEnv_compiler = 'craype'
 
-    link_paths = { 'cc'  : 'cc',
-                   'cxx' : 'c++',
-                   'f77' : 'f77',
-                   'fc'  : 'fc'}
- 
+    link_paths = {'cc': 'cc',
+                  'cxx': 'c++',
+                  'f77': 'f77',
+                  'fc': 'fc'}
+
     @classmethod
     def default_version(cls, comp):
         return get_compiler_version(comp, r'([Vv]ersion).*(\d+(\.\d+)+)')
-
diff --git a/lib/spack/spack/compilers/gcc.py b/lib/spack/spack/compilers/gcc.py
index 2fae6688db..a556f346d7 100644
--- a/lib/spack/spack/compilers/gcc.py
+++ b/lib/spack/spack/compilers/gcc.py
@@ -26,6 +26,7 @@ import llnl.util.tty as tty
 from spack.compiler import *
 from spack.version import ver
 
+
 class Gcc(Compiler):
     # Subclasses use possible names of C compiler
     cc_names = ['gcc']
@@ -44,10 +45,10 @@ class Gcc(Compiler):
     suffixes = [r'-mp-\d\.\d', r'-\d\.\d', r'-\d']
 
     # Named wrapper links within spack.build_env_path
-    link_paths = {'cc'  : 'gcc/gcc',
-                  'cxx' : 'gcc/g++',
-                  'f77' : 'gcc/gfortran',
-                  'fc'  : 'gcc/gfortran' }
+    link_paths = {'cc': 'gcc/gcc',
+                  'cxx': 'gcc/g++',
+                  'f77': 'gcc/gfortran',
+                  'fc': 'gcc/gfortran'}
 
     PrgEnv = 'PrgEnv-gnu'
     PrgEnv_compiler = 'gcc'
@@ -79,7 +80,6 @@ class Gcc(Compiler):
             # older gfortran versions don't have simple dumpversion output.
             r'(?:GNU Fortran \(GCC\))?(\d+\.\d+(?:\.\d+)?)')
 
-
     @classmethod
     def f77_version(cls, f77):
         return cls.fc_version(f77)
diff --git a/lib/spack/spack/compilers/intel.py b/lib/spack/spack/compilers/intel.py
index 6cad03ff47..8531ecd19a 100644
--- a/lib/spack/spack/compilers/intel.py
+++ b/lib/spack/spack/compilers/intel.py
@@ -26,6 +26,7 @@ from spack.compiler import *
 import llnl.util.tty as tty
 from spack.version import ver
 
+
 class Intel(Compiler):
     # Subclasses use possible names of C compiler
     cc_names = ['icc']
@@ -40,10 +41,10 @@ class Intel(Compiler):
     fc_names = ['ifort']
 
     # Named wrapper links within spack.build_env_path
-    link_paths = { 'cc'  : 'intel/icc',
-                   'cxx' : 'intel/icpc',
-                   'f77' : 'intel/ifort',
-                   'fc'  : 'intel/ifort' }
+    link_paths = {'cc': 'intel/icc',
+                  'cxx': 'intel/icpc',
+                  'f77': 'intel/ifort',
+                  'fc': 'intel/ifort'}
 
     PrgEnv = 'PrgEnv-intel'
     PrgEnv_compiler = 'intel'
@@ -64,7 +65,6 @@ class Intel(Compiler):
         else:
             return "-std=c++11"
 
-
     @classmethod
     def default_version(cls, comp):
         """The '--version' option seems to be the most consistent one
diff --git a/lib/spack/spack/compilers/nag.py b/lib/spack/spack/compilers/nag.py
index cee11bc97a..fdfc078b5e 100644
--- a/lib/spack/spack/compilers/nag.py
+++ b/lib/spack/spack/compilers/nag.py
@@ -23,7 +23,7 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack.compiler import *
-import llnl.util.tty as tty
+
 
 class Nag(Compiler):
     # Subclasses use possible names of C compiler
@@ -39,11 +39,12 @@ class Nag(Compiler):
     fc_names = ['nagfor']
 
     # Named wrapper links within spack.build_env_path
-    link_paths = { # Use default wrappers for C and C++, in case provided in compilers.yaml
-                   'cc'  : 'cc',
-                   'cxx' : 'c++',
-                   'f77' : 'nag/nagfor',
-                   'fc'  : 'nag/nagfor' }
+    # Use default wrappers for C and C++, in case provided in compilers.yaml
+    link_paths = {
+        'cc': 'cc',
+        'cxx': 'c++',
+        'f77': 'nag/nagfor',
+        'fc': 'nag/nagfor'}
 
     @property
     def openmp_flag(self):
@@ -71,9 +72,8 @@ class Nag(Compiler):
         """The '-V' option works for nag compilers.
            Output looks like this::
 
-               NAG Fortran Compiler Release 6.0(Hibiya) Build 1037
-               Product NPL6A60NA for x86-64 Linux
-               Copyright 1990-2015 The Numerical Algorithms Group Ltd., Oxford, U.K.
+           NAG Fortran Compiler Release 6.0(Hibiya) Build 1037
+           Product NPL6A60NA for x86-64 Linux
         """
         return get_compiler_version(
             comp, '-V', r'NAG Fortran Compiler Release ([0-9.]+)')
diff --git a/lib/spack/spack/compilers/pgi.py b/lib/spack/spack/compilers/pgi.py
index 6d36d8bfa6..0e4be6e9ba 100644
--- a/lib/spack/spack/compilers/pgi.py
+++ b/lib/spack/spack/compilers/pgi.py
@@ -23,7 +23,7 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack.compiler import *
-import llnl.util.tty as tty
+
 
 class Pgi(Compiler):
     # Subclasses use possible names of C compiler
@@ -39,17 +39,14 @@ class Pgi(Compiler):
     fc_names = ['pgfortran', 'pgf95', 'pgf90']
 
     # Named wrapper links within spack.build_env_path
-    link_paths = { 'cc'  : 'pgi/pgcc',
-                   'cxx' : 'pgi/pgc++',
-                   'f77' : 'pgi/pgfortran',
-                   'fc'  : 'pgi/pgfortran' }
-
-
+    link_paths = {'cc': 'pgi/pgcc',
+                  'cxx': 'pgi/pgc++',
+                  'f77': 'pgi/pgfortran',
+                  'fc': 'pgi/pgfortran'}
 
     PrgEnv = 'PrgEnv-pgi'
     PrgEnv_compiler = 'pgi'
 
-
     @property
     def openmp_flag(self):
         return "-mp"
diff --git a/lib/spack/spack/compilers/xl.py b/lib/spack/spack/compilers/xl.py
index b1431436ad..5c83209781 100644
--- a/lib/spack/spack/compilers/xl.py
+++ b/lib/spack/spack/compilers/xl.py
@@ -26,24 +26,26 @@ from spack.compiler import *
 import llnl.util.tty as tty
 from spack.version import ver
 
+
 class Xl(Compiler):
     # Subclasses use possible names of C compiler
-    cc_names = ['xlc','xlc_r']
+    cc_names = ['xlc', 'xlc_r']
 
     # Subclasses use possible names of C++ compiler
-    cxx_names = ['xlC','xlC_r','xlc++','xlc++_r']
+    cxx_names = ['xlC', 'xlC_r', 'xlc++', 'xlc++_r']
 
     # Subclasses use possible names of Fortran 77 compiler
-    f77_names = ['xlf','xlf_r']
+    f77_names = ['xlf', 'xlf_r']
 
     # Subclasses use possible names of Fortran 90 compiler
-    fc_names = ['xlf90','xlf90_r','xlf95','xlf95_r','xlf2003','xlf2003_r','xlf2008','xlf2008_r']
+    fc_names = ['xlf90', 'xlf90_r', 'xlf95', 'xlf95_r',
+                'xlf2003', 'xlf2003_r', 'xlf2008', 'xlf2008_r']
 
     # Named wrapper links within spack.build_env_path
-    link_paths = { 'cc'  : 'xl/xlc',
-                   'cxx' : 'xl/xlc++',
-                   'f77' : 'xl/xlf',
-                   'fc'  : 'xl/xlf90' }
+    link_paths = {'cc': 'xl/xlc',
+                  'cxx': 'xl/xlc++',
+                  'f77': 'xl/xlf',
+                  'fc': 'xl/xlf90'}
 
     @property
     def openmp_flag(self):
@@ -56,7 +58,6 @@ class Xl(Compiler):
         else:
             return "-qlanglvl=extended0x"
 
-
     @classmethod
     def default_version(cls, comp):
         """The '-qversion' is the standard option fo XL compilers.
@@ -82,29 +83,28 @@ class Xl(Compiler):
         """
 
         return get_compiler_version(
-            comp, '-qversion',r'([0-9]?[0-9]\.[0-9])')
-
+            comp, '-qversion', r'([0-9]?[0-9]\.[0-9])')
 
     @classmethod
     def fc_version(cls, fc):
-        """The fortran and C/C++ versions of the XL compiler are always two units apart.
-           By this we mean that the fortran release that goes with XL C/C++ 11.1 is 13.1.
-           Having such a difference in version number is confusing spack quite a lot.
-           Most notably if you keep the versions as is the default xl compiler will only
-           have fortran and no C/C++.
-           So we associate the Fortran compiler with the version associated to the C/C++
-           compiler.
-           One last stumble. Version numbers over 10 have at least a .1 those under 10
-           a .0. There is no xlf 9.x or under currently available. BG/P and BG/L can
-           such a compiler mix and possibly older version of AIX and linux on power.
+        """The fortran and C/C++ versions of the XL compiler are always
+           two units apart.  By this we mean that the fortran release that
+           goes with XL C/C++ 11.1 is 13.1.  Having such a difference in
+           version number is confusing spack quite a lot.  Most notably
+           if you keep the versions as is the default xl compiler will
+           only have fortran and no C/C++.  So we associate the Fortran
+           compiler with the version associated to the C/C++ compiler.
+           One last stumble. Version numbers over 10 have at least a .1
+           those under 10 a .0. There is no xlf 9.x or under currently
+           available. BG/P and BG/L can such a compiler mix and possibly
+           older version of AIX and linux on power.
         """
-        fver = get_compiler_version(fc, '-qversion',r'([0-9]?[0-9]\.[0-9])')
+        fver = get_compiler_version(fc, '-qversion', r'([0-9]?[0-9]\.[0-9])')
         cver = float(fver) - 2
-        if cver < 10 :
-          cver = cver - 0.1
+        if cver < 10:
+            cver = cver - 0.1
         return str(cver)
 
-
     @classmethod
     def f77_version(cls, f77):
         return cls.fc_version(f77)
diff --git a/lib/spack/spack/concretize.py b/lib/spack/spack/concretize.py
index 386df08b2e..726dee62e3 100644
--- a/lib/spack/spack/concretize.py
+++ b/lib/spack/spack/concretize.py
@@ -40,12 +40,12 @@ import spack.architecture
 import spack.error
 from spack.version import *
 from functools import partial
-from spec import DependencyMap
 from itertools import chain
 from spack.config import *
 
 
 class DefaultConcretizer(object):
+
     """This class doesn't have any state, it just provides some methods for
        concretization.  You can subclass it to override just some of the
        default concretization strategies, or you can override all of them.
@@ -61,14 +61,19 @@ class DefaultConcretizer(object):
             if not providers:
                 raise UnsatisfiableProviderSpecError(providers[0], spec)
             spec_w_preferred_providers = find_spec(
-                spec, lambda(x): spack.pkgsort.spec_has_preferred_provider(x.name, spec.name))
+                spec,
+                lambda x: spack.pkgsort.spec_has_preferred_provider(
+                    x.name, spec.name))
             if not spec_w_preferred_providers:
                 spec_w_preferred_providers = spec
-            provider_cmp = partial(spack.pkgsort.provider_compare, spec_w_preferred_providers.name, spec.name)
+            provider_cmp = partial(spack.pkgsort.provider_compare,
+                                   spec_w_preferred_providers.name,
+                                   spec.name)
             candidates = sorted(providers, cmp=provider_cmp)
 
-        # For each candidate package, if it has externals, add those to the usable list.
-        # if it's not buildable, then *only* add the externals.
+        # For each candidate package, if it has externals, add those
+        # to the usable list.  if it's not buildable, then *only* add
+        # the externals.
         usable = []
         for cspec in candidates:
             if is_spec_buildable(cspec):
@@ -85,7 +90,7 @@ class DefaultConcretizer(object):
 
         def cmp_externals(a, b):
             if a.name != b.name and (not a.external or a.external_module and
-                    not b.external and b.external_module):
+                                     not b.external and b.external_module):
                 # We're choosing between different providers, so
                 # maintain order from provider sort
                 return candidates.index(a) - candidates.index(b)
@@ -114,26 +119,26 @@ class DefaultConcretizer(object):
 
         # Find the nearest spec in the dag that has a compiler.  We'll
         # use that spec to calibrate compiler compatibility.
-        abi_exemplar = find_spec(spec, lambda(x): x.compiler)
+        abi_exemplar = find_spec(spec, lambda x: x.compiler)
         if not abi_exemplar:
             abi_exemplar = spec.root
 
         # Make a list including ABI compatibility of specs with the exemplar.
         strict = [spack.abi.compatible(c, abi_exemplar) for c in candidates]
-        loose  = [spack.abi.compatible(c, abi_exemplar, loose=True) for c in candidates]
+        loose = [spack.abi.compatible(c, abi_exemplar, loose=True)
+                 for c in candidates]
         keys = zip(strict, loose, candidates)
 
         # Sort candidates from most to least compatibility.
         # Note:
         #   1. We reverse because True > False.
         #   2. Sort is stable, so c's keep their order.
-        keys.sort(key=lambda k:k[:2], reverse=True)
+        keys.sort(key=lambda k: k[:2], reverse=True)
 
         # Pull the candidates back out and return them in order
-        candidates = [c for s,l,c in keys]
+        candidates = [c for s, l, c in keys]
         return candidates
 
-
     def concretize_version(self, spec):
         """If the spec is already concrete, return.  Otherwise take
            the preferred version from spackconfig, and default to the package's
@@ -167,7 +172,8 @@ class DefaultConcretizer(object):
 
         if valid_versions:
             # Disregard @develop and take the next valid version
-            if ver(valid_versions[0]) == ver('develop') and len(valid_versions) > 1:
+            if ver(valid_versions[0]) == ver('develop') and \
+                    len(valid_versions) > 1:
                 spec.versions = ver([valid_versions[1]])
             else:
                 spec.versions = ver([valid_versions[0]])
@@ -193,40 +199,45 @@ class DefaultConcretizer(object):
         return True   # Things changed
 
     def _concretize_operating_system(self, spec):
-        platform = spec.architecture.platform
         if spec.architecture.platform_os is not None and isinstance(
-            spec.architecture.platform_os,spack.architecture.OperatingSystem):
+                spec.architecture.platform_os,
+                spack.architecture.OperatingSystem):
             return False
 
         if spec.root.architecture and spec.root.architecture.platform_os:
-            if isinstance(spec.root.architecture.platform_os,spack.architecture.OperatingSystem):
-                spec.architecture.platform_os = spec.root.architecture.platform_os
+            if isinstance(spec.root.architecture.platform_os,
+                          spack.architecture.OperatingSystem):
+                spec.architecture.platform_os = \
+                    spec.root.architecture.platform_os
         else:
-            spec.architecture.platform_os = spec.architecture.platform.operating_system('default_os')
-        return True #changed
+            spec.architecture.platform_os = \
+                spec.architecture.platform.operating_system('default_os')
+        return True  # changed
 
     def _concretize_target(self, spec):
-        platform = spec.architecture.platform
         if spec.architecture.target is not None and isinstance(
                 spec.architecture.target, spack.architecture.Target):
             return False
         if spec.root.architecture and spec.root.architecture.target:
-            if isinstance(spec.root.architecture.target,spack.architecture.Target):
+            if isinstance(spec.root.architecture.target,
+                          spack.architecture.Target):
                 spec.architecture.target = spec.root.architecture.target
         else:
-            spec.architecture.target = spec.architecture.platform.target('default_target')
-        return True #changed
+            spec.architecture.target = spec.architecture.platform.target(
+                'default_target')
+        return True  # changed
 
     def _concretize_platform(self, spec):
         if spec.architecture.platform is not None and isinstance(
                 spec.architecture.platform, spack.architecture.Platform):
             return False
         if spec.root.architecture and spec.root.architecture.platform:
-            if isinstance(spec.root.architecture.platform,spack.architecture.Platform):
+            if isinstance(spec.root.architecture.platform,
+                          spack.architecture.Platform):
                 spec.architecture.platform = spec.root.architecture.platform
         else:
             spec.architecture.platform = spack.architecture.platform()
-        return True #changed?
+        return True  # changed?
 
     def concretize_architecture(self, spec):
         """If the spec is empty provide the defaults of the platform. If the
@@ -245,25 +256,29 @@ class DefaultConcretizer(object):
             return True
 
             # Concretize the operating_system and target based of the spec
-        ret =  any((self._concretize_platform(spec),
-                    self._concretize_operating_system(spec),
-                    self._concretize_target(spec)))
+        ret = any((self._concretize_platform(spec),
+                   self._concretize_operating_system(spec),
+                   self._concretize_target(spec)))
         return ret
 
-
-
     def concretize_variants(self, spec):
         """If the spec already has variants filled in, return.  Otherwise, add
-           the default variants from the package specification.
+           the user preferences from packages.yaml or the default variants from
+           the package specification.
         """
         changed = False
+        preferred_variants = spack.pkgsort.spec_preferred_variants(
+            spec.package_class.name)
         for name, variant in spec.package_class.variants.items():
             if name not in spec.variants:
-                spec.variants[name] = spack.spec.VariantSpec(name, variant.default)
                 changed = True
+                if name in preferred_variants:
+                    spec.variants[name] = preferred_variants.get(name)
+                else:
+                    spec.variants[name] = \
+                        spack.spec.VariantSpec(name, variant.default)
         return changed
 
-
     def concretize_compiler(self, spec):
         """If the spec already has a compiler, we're done.  If not, then take
            the compiler used for the nearest ancestor with a compiler
@@ -278,30 +293,32 @@ class DefaultConcretizer(object):
         """
         # Pass on concretizing the compiler if the target is not yet determined
         if not spec.architecture.platform_os:
-            #Although this usually means changed, this means awaiting other changes
+            # Although this usually means changed, this means awaiting other
+            # changes
             return True
 
         # Only use a matching compiler if it is of the proper style
-        # Takes advantage of the proper logic already existing in compiler_for_spec
-        # Should think whether this can be more efficient
+        # Takes advantage of the proper logic already existing in
+        # compiler_for_spec Should think whether this can be more
+        # efficient
         def _proper_compiler_style(cspec, arch):
             platform = arch.platform
             compilers = spack.compilers.compilers_for_spec(cspec,
                                                            platform=platform)
             return filter(lambda c: c.operating_system ==
-                                    arch.platform_os, compilers)
-            #return compilers
-
+                          arch.platform_os, compilers)
+            # return compilers
 
         all_compilers = spack.compilers.all_compilers()
 
         if (spec.compiler and
             spec.compiler.concrete and
-            spec.compiler in all_compilers):
+                spec.compiler in all_compilers):
             return False
 
-        #Find the another spec that has a compiler, or the root if none do
-        other_spec = spec if spec.compiler else find_spec(spec, lambda(x) : x.compiler)
+        # Find the another spec that has a compiler, or the root if none do
+        other_spec = spec if spec.compiler else find_spec(
+            spec, lambda x: x.compiler)
 
         if not other_spec:
             other_spec = spec.root
@@ -313,24 +330,30 @@ class DefaultConcretizer(object):
             spec.compiler = other_compiler.copy()
             return True
 
-        # Filter the compilers into a sorted list based on the compiler_order from spackconfig
-        compiler_list = all_compilers if not other_compiler else spack.compilers.find(other_compiler)
-        cmp_compilers = partial(spack.pkgsort.compiler_compare, other_spec.name)
+        # Filter the compilers into a sorted list based on the compiler_order
+        # from spackconfig
+        compiler_list = all_compilers if not other_compiler else \
+            spack.compilers.find(other_compiler)
+        cmp_compilers = partial(
+            spack.pkgsort.compiler_compare, other_spec.name)
         matches = sorted(compiler_list, cmp=cmp_compilers)
         if not matches:
-            raise UnavailableCompilerVersionError(other_compiler)
+            arch = spec.architecture
+            raise UnavailableCompilerVersionError(other_compiler,
+                                                  arch.platform_os)
 
         # copy concrete version into other_compiler
         index = 0
         while not _proper_compiler_style(matches[index], spec.architecture):
             index += 1
             if index == len(matches) - 1:
-                raise NoValidVersionError(spec)
+                arch = spec.architecture
+                raise UnavailableCompilerVersionError(spec.compiler,
+                                                      arch.platform_os)
         spec.compiler = matches[index].copy()
         assert(spec.compiler.concrete)
         return True  # things changed.
 
-
     def concretize_compiler_flags(self, spec):
         """
         The compiler flags are updated to match those of the spec whose
@@ -338,54 +361,66 @@ class DefaultConcretizer(object):
         Default specs set at the compiler level will still be added later.
         """
 
-
         if not spec.architecture.platform_os:
-            #Although this usually means changed, this means awaiting other changes
+            # Although this usually means changed, this means awaiting other
+            # changes
             return True
 
         ret = False
         for flag in spack.spec.FlagMap.valid_compiler_flags():
             try:
                 nearest = next(p for p in spec.traverse(direction='parents')
-                               if ((p.compiler == spec.compiler and p is not spec)
-                               and flag in p.compiler_flags))
-                if not flag in spec.compiler_flags or \
-                    not (sorted(spec.compiler_flags[flag]) >= sorted(nearest.compiler_flags[flag])):
+                               if ((p.compiler == spec.compiler and
+                                    p is not spec) and
+                                   flag in p.compiler_flags))
+                if flag not in spec.compiler_flags or \
+                        not (sorted(spec.compiler_flags[flag]) >=
+                             sorted(nearest.compiler_flags[flag])):
                     if flag in spec.compiler_flags:
-                        spec.compiler_flags[flag] = list(set(spec.compiler_flags[flag]) |
-                                                         set(nearest.compiler_flags[flag]))
+                        spec.compiler_flags[flag] = list(
+                            set(spec.compiler_flags[flag]) |
+                            set(nearest.compiler_flags[flag]))
                     else:
-                        spec.compiler_flags[flag] = nearest.compiler_flags[flag]
+                        spec.compiler_flags[
+                            flag] = nearest.compiler_flags[flag]
                     ret = True
 
             except StopIteration:
-                if (flag in spec.root.compiler_flags and ((not flag in spec.compiler_flags) or
-                    sorted(spec.compiler_flags[flag]) != sorted(spec.root.compiler_flags[flag]))):
+                if (flag in spec.root.compiler_flags and
+                    ((flag not in spec.compiler_flags) or
+                     sorted(spec.compiler_flags[flag]) !=
+                     sorted(spec.root.compiler_flags[flag]))):
                     if flag in spec.compiler_flags:
-                        spec.compiler_flags[flag] = list(set(spec.compiler_flags[flag]) |
-                                                         set(spec.root.compiler_flags[flag]))
+                        spec.compiler_flags[flag] = list(
+                            set(spec.compiler_flags[flag]) |
+                            set(spec.root.compiler_flags[flag]))
                     else:
-                        spec.compiler_flags[flag] = spec.root.compiler_flags[flag]
+                        spec.compiler_flags[
+                            flag] = spec.root.compiler_flags[flag]
                     ret = True
                 else:
-                    if not flag in spec.compiler_flags:
+                    if flag not in spec.compiler_flags:
                         spec.compiler_flags[flag] = []
 
         # Include the compiler flag defaults from the config files
         # This ensures that spack will detect conflicts that stem from a change
         # in default compiler flags.
-        compiler = spack.compilers.compiler_for_spec(spec.compiler, spec.architecture)
+        compiler = spack.compilers.compiler_for_spec(
+            spec.compiler, spec.architecture)
         for flag in compiler.flags:
             if flag not in spec.compiler_flags:
                 spec.compiler_flags[flag] = compiler.flags[flag]
                 if compiler.flags[flag] != []:
                     ret = True
             else:
-                if ((sorted(spec.compiler_flags[flag]) != sorted(compiler.flags[flag])) and
-                    (not set(spec.compiler_flags[flag]) >= set(compiler.flags[flag]))):
+                if ((sorted(spec.compiler_flags[flag]) !=
+                     sorted(compiler.flags[flag])) and
+                    (not set(spec.compiler_flags[flag]) >=
+                     set(compiler.flags[flag]))):
                     ret = True
-                    spec.compiler_flags[flag] = list(set(spec.compiler_flags[flag]) |
-                                                     set(compiler.flags[flag]))
+                    spec.compiler_flags[flag] = list(
+                        set(spec.compiler_flags[flag]) |
+                        set(compiler.flags[flag]))
 
         return ret
 
@@ -396,8 +431,8 @@ def find_spec(spec, condition):
     # First search parents, then search children
     deptype = ('build', 'link')
     dagiter = chain(
-            spec.traverse(direction='parents',  deptype=deptype, root=False),
-            spec.traverse(direction='children', deptype=deptype, root=False))
+        spec.traverse(direction='parents',  deptype=deptype, root=False),
+        spec.traverse(direction='children', deptype=deptype, root=False))
     visited = set()
     for relative in dagiter:
         if condition(relative):
@@ -406,8 +441,10 @@ def find_spec(spec, condition):
 
     # Then search all other relatives in the DAG *except* spec
     for relative in spec.root.traverse(deptypes=spack.alldeps):
-        if relative is spec: continue
-        if id(relative) in visited: continue
+        if relative is spec:
+            continue
+        if id(relative) in visited:
+            continue
         if condition(relative):
             return relative
 
@@ -454,25 +491,33 @@ def cmp_specs(lhs, rhs):
 
 
 class UnavailableCompilerVersionError(spack.error.SpackError):
+
     """Raised when there is no available compiler that satisfies a
        compiler spec."""
-    def __init__(self, compiler_spec):
+
+    def __init__(self, compiler_spec, operating_system):
         super(UnavailableCompilerVersionError, self).__init__(
-            "No available compiler version matches '%s'" % compiler_spec,
+            "No available compiler version matches '%s' on operating_system %s"
+            % (compiler_spec, operating_system),
             "Run 'spack compilers' to see available compiler Options.")
 
 
 class NoValidVersionError(spack.error.SpackError):
+
     """Raised when there is no way to have a concrete version for a
        particular spec."""
+
     def __init__(self, spec):
         super(NoValidVersionError, self).__init__(
-            "There are no valid versions for %s that match '%s'" % (spec.name, spec.versions))
+            "There are no valid versions for %s that match '%s'"
+            % (spec.name, spec.versions))
 
 
 class NoBuildError(spack.error.SpackError):
     """Raised when a package is configured with the buildable option False, but
        no satisfactory external versions can be found"""
+
     def __init__(self, spec):
-        super(NoBuildError, self).__init__(
-            "The spec '%s' is configured as not buildable, and no matching external installs were found" % spec.name)
+        msg = ("The spec '%s' is configured as not buildable, "
+               "and no matching external installs were found")
+        super(NoBuildError, self).__init__(msg % spec.name)
diff --git a/lib/spack/spack/config.py b/lib/spack/spack/config.py
index 8b5e96f97d..c90eff4229 100644
--- a/lib/spack/spack/config.py
+++ b/lib/spack/spack/config.py
@@ -1,4 +1,3 @@
-# flake8: noqa
 ##############################################################################
 # Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
@@ -123,15 +122,18 @@ import os
 import re
 import sys
 
-import jsonschema
-import llnl.util.tty as tty
-import spack
 import yaml
+import jsonschema
+from yaml.error import MarkedYAMLError
 from jsonschema import Draft4Validator, validators
-from llnl.util.filesystem import mkdirp
 from ordereddict_backport import OrderedDict
+
+import llnl.util.tty as tty
+from llnl.util.filesystem import mkdirp
+
+import spack
 from spack.error import SpackError
-from yaml.error import MarkedYAMLError
+import spack.schema
 
 # Hacked yaml for configuration files preserves line numbers.
 import spack.util.spack_yaml as syaml
@@ -139,251 +141,12 @@ from spack.build_environment import get_path_from_module
 
 """Dict from section names -> schema for that section."""
 section_schemas = {
-    'compilers': {
-        '$schema': 'http://json-schema.org/schema#',
-        'title': 'Spack compiler configuration file schema',
-        'type': 'object',
-        'additionalProperties': False,
-        'patternProperties': {
-            'compilers:?': {  # optional colon for overriding site config.
-                'type': 'array',
-                'items': {
-                    'compiler': {
-                        'type': 'object',
-                        'additionalProperties': False,
-                        'required': ['paths', 'spec', 'modules', 'operating_system'],
-                        'properties': {
-                            'paths': {
-                                'type': 'object',
-                                'required': ['cc', 'cxx', 'f77', 'fc'],
-                                'additionalProperties': False,
-                                'properties': {
-                                    'cc':  { 'anyOf': [ {'type' : 'string' },
-                                                        {'type' : 'null' }]},
-                                    'cxx': { 'anyOf': [ {'type' : 'string' },
-                                                        {'type' : 'null' }]},
-                                    'f77': { 'anyOf': [ {'type' : 'string' },
-                                                        {'type' : 'null' }]},
-                                    'fc':  { 'anyOf': [ {'type' : 'string' },
-                                                        {'type' : 'null' }]},
-                                    'cflags': { 'anyOf': [ {'type' : 'string' },
-                                                        {'type' : 'null' }]},
-                                    'cxxflags': { 'anyOf': [ {'type' : 'string' },
-                                                        {'type' : 'null' }]},
-                                    'fflags': { 'anyOf': [ {'type' : 'string' },
-                                                        {'type' : 'null' }]},
-                                    'cppflags': { 'anyOf': [ {'type' : 'string' },
-                                                        {'type' : 'null' }]},
-                                    'ldflags': { 'anyOf': [ {'type' : 'string' },
-                                                        {'type' : 'null' }]},
-                                    'ldlibs': { 'anyOf': [ {'type' : 'string' },
-                                                        {'type' : 'null' }]}}},
-                            'spec': { 'type': 'string'},
-                            'operating_system': { 'type': 'string'},
-                            'alias': { 'anyOf': [ {'type' : 'string'},
-                                                    {'type' : 'null' }]},
-                            'modules': { 'anyOf': [ {'type' : 'string'},
-                                                    {'type' : 'null' },
-                                                    {'type': 'array'},
-                                                    ]}
-                            },},},},},},
-    'mirrors': {
-        '$schema': 'http://json-schema.org/schema#',
-        'title': 'Spack mirror configuration file schema',
-        'type': 'object',
-        'additionalProperties': False,
-        'patternProperties': {
-            r'mirrors:?': {
-                'type': 'object',
-                'default': {},
-                'additionalProperties': False,
-                'patternProperties': {
-                    r'\w[\w-]*': {
-                        'type': 'string'},},},},},
-
-    'repos': {
-        '$schema': 'http://json-schema.org/schema#',
-        'title': 'Spack repository configuration file schema',
-        'type': 'object',
-        'additionalProperties': False,
-        'patternProperties': {
-            r'repos:?': {
-                'type': 'array',
-                'default': [],
-                'items': {
-                    'type': 'string'},},},},
-    'packages': {
-        '$schema': 'http://json-schema.org/schema#',
-        'title': 'Spack package configuration file schema',
-        'type': 'object',
-        'additionalProperties': False,
-        'patternProperties': {
-            r'packages:?': {
-                'type': 'object',
-                'default': {},
-                'additionalProperties': False,
-                'patternProperties': {
-                    r'\w[\w-]*': { # package name
-                        'type': 'object',
-                        'default': {},
-                        'additionalProperties': False,
-                        'properties': {
-                            'version': {
-                                'type' : 'array',
-                                'default' : [],
-                                'items' : { 'anyOf' : [ { 'type' : 'string' },
-                                                        { 'type' : 'number'}]}}, #version strings
-                            'compiler': {
-                                'type' : 'array',
-                                'default' : [],
-                                'items' : { 'type' : 'string' } }, #compiler specs
-                            'buildable': {
-                                'type':  'boolean',
-                                'default': True,
-                             },
-                            'modules': {
-                                'type' : 'object',
-                                'default' : {},
-                             },
-                            'providers': {
-                                'type':  'object',
-                                'default': {},
-                                'additionalProperties': False,
-                                'patternProperties': {
-                                    r'\w[\w-]*': {
-                                        'type' : 'array',
-                                        'default' : [],
-                                        'items' : { 'type' : 'string' },},},},
-                            'paths': {
-                                'type' : 'object',
-                                'default' : {},
-                            }
-                        },},},},},},
-
-    'modules': {
-        '$schema': 'http://json-schema.org/schema#',
-        'title': 'Spack module file configuration file schema',
-        'type': 'object',
-        'additionalProperties': False,
-        'definitions': {
-            'array_of_strings': {
-                'type': 'array',
-                'default': [],
-                'items': {
-                    'type': 'string'
-                }
-            },
-            'dictionary_of_strings': {
-                'type': 'object',
-                'patternProperties': {
-                    r'\w[\w-]*': {  # key
-                        'type': 'string'
-                    }
-                }
-            },
-            'dependency_selection': {
-                'type': 'string',
-                'enum': ['none', 'direct', 'all']
-            },
-            'module_file_configuration': {
-                'type': 'object',
-                'default': {},
-                'additionalProperties': False,
-                'properties': {
-                    'filter': {
-                        'type': 'object',
-                        'default': {},
-                        'additionalProperties': False,
-                        'properties': {
-                            'environment_blacklist': {
-                                'type': 'array',
-                                'default': [],
-                                'items': {
-                                    'type': 'string'
-                                }
-                            }
-                        }
-                    },
-                    'autoload': {'$ref': '#/definitions/dependency_selection'},
-                    'prerequisites': {'$ref': '#/definitions/dependency_selection'},
-                    'conflict': {'$ref': '#/definitions/array_of_strings'},
-                    'load': {'$ref': '#/definitions/array_of_strings'},
-                    'suffixes': {'$ref': '#/definitions/dictionary_of_strings'},
-                    'environment': {
-                        'type': 'object',
-                        'default': {},
-                        'additionalProperties': False,
-                        'properties': {
-                            'set': {'$ref': '#/definitions/dictionary_of_strings'},
-                            'unset': {'$ref': '#/definitions/array_of_strings'},
-                            'prepend_path': {'$ref': '#/definitions/dictionary_of_strings'},
-                            'append_path': {'$ref': '#/definitions/dictionary_of_strings'}
-                        }
-                    }
-                }
-            },
-            'module_type_configuration': {
-                'type': 'object',
-                'default': {},
-                'anyOf': [
-                    {
-                        'properties': {
-                            'hash_length': {
-                                'type': 'integer',
-                                'minimum': 0,
-                                'default': 7
-                            },
-                            'whitelist': {'$ref': '#/definitions/array_of_strings'},
-                            'blacklist': {'$ref': '#/definitions/array_of_strings'},
-                            'naming_scheme': {
-                                'type': 'string'  # Can we be more specific here?
-                            }
-                        }
-                    },
-                    {
-                        'patternProperties': {r'\w[\w-]*': {'$ref': '#/definitions/module_file_configuration'}}
-                    }
-                ]
-            }
-        },
-        'patternProperties': {
-            r'modules:?': {
-                'type': 'object',
-                'default': {},
-                'additionalProperties': False,
-                'properties': {
-                    'prefix_inspections': {
-                        'type': 'object',
-                        'patternProperties': {
-                            r'\w[\w-]*': {  # path to be inspected for existence (relative to prefix)
-                                '$ref': '#/definitions/array_of_strings'
-                            }
-                        }
-                    },
-                    'enable': {
-                        'type': 'array',
-                        'default': [],
-                        'items': {
-                            'type': 'string',
-                            'enum': ['tcl', 'dotkit']
-                        }
-                    },
-                    'tcl': {
-                        'allOf': [
-                            {'$ref': '#/definitions/module_type_configuration'},  # Base configuration
-                            {}  # Specific tcl extensions
-                        ]
-                    },
-                    'dotkit': {
-                        'allOf': [
-                            {'$ref': '#/definitions/module_type_configuration'},  # Base configuration
-                            {}  # Specific dotkit extensions
-                        ]
-                    },
-                }
-            },
-        },
-    },
+    'compilers': spack.schema.compilers.schema,
+    'mirrors': spack.schema.mirrors.schema,
+    'repos': spack.schema.repos.schema,
+    'packages': spack.schema.packages.schema,
+    'targets': spack.schema.targets.schema,
+    'modules': spack.schema.modules.schema,
 }
 
 """OrderedDict of config scopes keyed by name.
@@ -400,7 +163,7 @@ def validate_section_name(section):
 
 
 def extend_with_default(validator_class):
-    """Add support for the 'default' attribute for properties and patternProperties.
+    """Add support for the 'default' attr for properties and patternProperties.
 
        jsonschema does not handle this out of the box -- it only
        validates.  This allows us to set default values for configs
@@ -409,13 +172,15 @@ def extend_with_default(validator_class):
 
     """
     validate_properties = validator_class.VALIDATORS["properties"]
-    validate_pattern_properties = validator_class.VALIDATORS["patternProperties"]
+    validate_pattern_properties = validator_class.VALIDATORS[
+        "patternProperties"]
 
     def set_defaults(validator, properties, instance, schema):
         for property, subschema in properties.iteritems():
             if "default" in subschema:
                 instance.setdefault(property, subschema["default"])
-        for err in validate_properties(validator, properties, instance, schema):
+        for err in validate_properties(
+                validator, properties, instance, schema):
             yield err
 
     def set_pp_defaults(validator, properties, instance, schema):
@@ -426,7 +191,8 @@ def extend_with_default(validator_class):
                         if re.match(property, key) and val is None:
                             instance[key] = subschema["default"]
 
-        for err in validate_pattern_properties(validator, properties, instance, schema):
+        for err in validate_pattern_properties(
+                validator, properties, instance, schema):
             yield err
 
     return validators.extend(validator_class, {
@@ -491,7 +257,8 @@ class ConfigScope(object):
         except jsonschema.ValidationError as e:
             raise ConfigSanityError(e, data)
         except (yaml.YAMLError, IOError) as e:
-            raise ConfigFileError("Error writing to config file: '%s'" % str(e))
+            raise ConfigFileError(
+                "Error writing to config file: '%s'" % str(e))
 
     def clear(self):
         """Empty cached config information."""
@@ -506,7 +273,7 @@ ConfigScope('defaults', os.path.join(spack.etc_path, 'spack', 'defaults'))
 ConfigScope('site', os.path.join(spack.etc_path, 'spack'))
 
 """User configuration can override both spack defaults and site config."""
-ConfigScope('user', os.path.expanduser('~/.spack'))
+ConfigScope('user', spack.user_config_path)
 
 
 def highest_precedence_scope():
@@ -689,7 +456,7 @@ def print_section(section):
         data = syaml.syaml_dict()
         data[section] = get_config(section)
         syaml.dump(data, stream=sys.stdout, default_flow_style=False)
-    except (yaml.YAMLError, IOError) as e:
+    except (yaml.YAMLError, IOError):
         raise ConfigError("Error reading configuration: %s" % section)
 
 
@@ -720,7 +487,8 @@ def spec_externals(spec):
 
         path = get_path_from_module(module)
 
-        external_spec = spack.spec.Spec(external_spec, external=path, external_module=module)
+        external_spec = spack.spec.Spec(
+            external_spec, external=path, external_module=module)
         if external_spec.satisfies(spec):
             external_specs.append(external_spec)
 
@@ -754,6 +522,7 @@ def get_path(path, data):
 
 class ConfigFormatError(ConfigError):
     """Raised when a configuration format does not match its schema."""
+
     def __init__(self, validation_error, data):
         # Try to get line number from erroneous instance and its parent
         instance_mark = getattr(validation_error.instance, '_start_mark', None)
diff --git a/lib/spack/spack/database.py b/lib/spack/spack/database.py
index 317b0d5784..f3dcdef0a9 100644
--- a/lib/spack/spack/database.py
+++ b/lib/spack/spack/database.py
@@ -119,6 +119,7 @@ class InstallRecord(object):
 
 
 class Database(object):
+
     def __init__(self, root, db_dir=None):
         """Create a Database for Spack installations under ``root``.
 
@@ -165,11 +166,11 @@ class Database(object):
 
     def write_transaction(self, timeout=_db_lock_timeout):
         """Get a write lock context manager for use in a `with` block."""
-        return WriteTransaction(self, self._read, self._write, timeout)
+        return WriteTransaction(self.lock, self._read, self._write, timeout)
 
     def read_transaction(self, timeout=_db_lock_timeout):
         """Get a read lock context manager for use in a `with` block."""
-        return ReadTransaction(self, self._read, None, timeout)
+        return ReadTransaction(self.lock, self._read, timeout=timeout)
 
     def _write_to_yaml(self, stream):
         """Write out the databsae to a YAML file.
@@ -352,12 +353,22 @@ class Database(object):
                     "Invalid ref_count: %s: %d (expected %d), in DB %s" %
                     (key, found, expected, self._index_path))
 
-    def _write(self):
+    def _write(self, type, value, traceback):
         """Write the in-memory database index to its file path.
 
-        Does no locking.
+        This is a helper function called by the WriteTransaction context
+        manager. If there is an exception while the write lock is active,
+        nothing will be written to the database file, but the in-memory
+        database *may* be left in an inconsistent state.  It will be consistent
+        after the start of the next transaction, when it read from disk again.
+
+        This routine does no locking.
 
         """
+        # Do not write if exceptions were raised
+        if type is not None:
+            return
+
         temp_file = self._index_path + (
             '.%s.%s.temp' % (socket.getfqdn(), os.getpid()))
 
@@ -589,50 +600,8 @@ class Database(object):
             return key in self._data and not self._data[key].installed
 
 
-class _Transaction(object):
-    """Simple nested transaction context manager that uses a file lock.
-
-    This class can trigger actions when the lock is acquired for the
-    first time and released for the last.
-
-    Timeout for lock is customizable.
-    """
-
-    def __init__(self, db,
-                 acquire_fn=None,
-                 release_fn=None,
-                 timeout=_db_lock_timeout):
-        self._db = db
-        self._timeout = timeout
-        self._acquire_fn = acquire_fn
-        self._release_fn = release_fn
-
-    def __enter__(self):
-        if self._enter() and self._acquire_fn:
-            self._acquire_fn()
-
-    def __exit__(self, type, value, traceback):
-        if self._exit() and self._release_fn:
-            self._release_fn()
-
-
-class ReadTransaction(_Transaction):
-    def _enter(self):
-        return self._db.lock.acquire_read(self._timeout)
-
-    def _exit(self):
-        return self._db.lock.release_read()
-
-
-class WriteTransaction(_Transaction):
-    def _enter(self):
-        return self._db.lock.acquire_write(self._timeout)
-
-    def _exit(self):
-        return self._db.lock.release_write()
-
-
 class CorruptDatabaseError(SpackError):
+
     def __init__(self, path, msg=''):
         super(CorruptDatabaseError, self).__init__(
             "Spack database is corrupt: %s.  %s." % (path, msg),
@@ -640,6 +609,7 @@ class CorruptDatabaseError(SpackError):
 
 
 class InvalidDatabaseVersionError(SpackError):
+
     def __init__(self, expected, found):
         super(InvalidDatabaseVersionError, self).__init__(
             "Expected database version %s but found version %s."
diff --git a/lib/spack/spack/directives.py b/lib/spack/spack/directives.py
index 88d2aaf472..313bf48f0d 100644
--- a/lib/spack/spack/directives.py
+++ b/lib/spack/spack/directives.py
@@ -189,7 +189,7 @@ def _depends_on(pkg, spec, when=None, type=None):
         type = ('build', 'link')
 
     if isinstance(type, str):
-        type = (type,)
+        type = spack.spec.special_types.get(type, (type,))
 
     for deptype in type:
         if deptype not in spack.spec.alldeps:
@@ -349,9 +349,10 @@ class CircularReferenceError(DirectiveError):
 
 class UnknownDependencyTypeError(DirectiveError):
     """This is raised when a dependency is of an unknown type."""
+
     def __init__(self, directive, package, deptype):
         super(UnknownDependencyTypeError, self).__init__(
             directive,
-            "Package '%s' cannot depend on a package via %s." %
-                (package, deptype))
+            "Package '%s' cannot depend on a package via %s."
+            % (package, deptype))
         self.package = package
diff --git a/lib/spack/spack/directory_layout.py b/lib/spack/spack/directory_layout.py
index 8150a6da2b..0ae6f765f4 100644
--- a/lib/spack/spack/directory_layout.py
+++ b/lib/spack/spack/directory_layout.py
@@ -22,16 +22,13 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import re
 import os
 import exceptions
-import hashlib
 import shutil
 import glob
 import tempfile
 import yaml
 
-import llnl.util.tty as tty
 from llnl.util.filesystem import join_path, mkdirp
 
 import spack
@@ -51,10 +48,10 @@ class DirectoryLayout(object):
        install, and they can use this to customize the nesting structure of
        spack installs.
     """
+
     def __init__(self, root):
         self.root = root
 
-
     @property
     def hidden_file_paths(self):
         """Return a list of hidden files used by the directory layout.
@@ -67,25 +64,21 @@ class DirectoryLayout(object):
         """
         raise NotImplementedError()
 
-
     def all_specs(self):
         """To be implemented by subclasses to traverse all specs for which there is
            a directory within the root.
         """
         raise NotImplementedError()
 
-
     def relative_path_for_spec(self, spec):
         """Implemented by subclasses to return a relative path from the install
            root to a unique location for the provided spec."""
         raise NotImplementedError()
 
-
     def create_install_directory(self, spec):
         """Creates the installation directory for a spec."""
         raise NotImplementedError()
 
-
     def check_installed(self, spec):
         """Checks whether a spec is installed.
 
@@ -95,7 +88,6 @@ class DirectoryLayout(object):
         """
         raise NotImplementedError()
 
-
     def extension_map(self, spec):
         """Get a dict of currently installed extension packages for a spec.
 
@@ -104,7 +96,6 @@ class DirectoryLayout(object):
         """
         raise NotImplementedError()
 
-
     def check_extension_conflict(self, spec, ext_spec):
         """Ensure that ext_spec can be activated in spec.
 
@@ -113,7 +104,6 @@ class DirectoryLayout(object):
         """
         raise NotImplementedError()
 
-
     def check_activated(self, spec, ext_spec):
         """Ensure that ext_spec can be removed from spec.
 
@@ -121,26 +111,22 @@ class DirectoryLayout(object):
         """
         raise NotImplementedError()
 
-
     def add_extension(self, spec, ext_spec):
         """Add to the list of currently installed extensions."""
         raise NotImplementedError()
 
-
     def remove_extension(self, spec, ext_spec):
         """Remove from the list of currently installed extensions."""
         raise NotImplementedError()
 
-
     def path_for_spec(self, spec):
-        """Return an absolute path from the root to a directory for the spec."""
+        """Return absolute path from the root to a directory for the spec."""
         _check_concrete(spec)
 
         path = self.relative_path_for_spec(spec)
         assert(not path.startswith(self.root))
         return os.path.join(self.root, path)
 
-
     def remove_install_directory(self, spec):
         """Removes a prefix and any empty parent directories from the root.
            Raised RemoveFailedError if something goes wrong.
@@ -177,6 +163,7 @@ class YamlDirectoryLayout(DirectoryLayout):
        only enabled variants are included in the install path.
        Disabled variants are omitted.
     """
+
     def __init__(self, root, **kwargs):
         super(YamlDirectoryLayout, self).__init__(root)
         self.metadata_dir   = kwargs.get('metadata_dir', '.spack')
@@ -191,12 +178,10 @@ class YamlDirectoryLayout(DirectoryLayout):
         # Cache of already written/read extension maps.
         self._extension_maps = {}
 
-
     @property
     def hidden_file_paths(self):
         return (self.metadata_dir,)
 
-
     def relative_path_for_spec(self, spec):
         _check_concrete(spec)
 
@@ -208,20 +193,19 @@ class YamlDirectoryLayout(DirectoryLayout):
             spec.version,
             spec.dag_hash(self.hash_len))
 
-        path = join_path(spec.architecture,
+        path = join_path(
+            spec.architecture,
             "%s-%s" % (spec.compiler.name, spec.compiler.version),
             dir_name)
 
         return path
 
-
     def write_spec(self, spec, path):
         """Write a spec out to a file."""
         _check_concrete(spec)
         with open(path, 'w') as f:
             spec.to_yaml(f)
 
-
     def read_spec(self, path):
         """Read the contents of a file and parse them as a spec"""
         try:
@@ -237,32 +221,26 @@ class YamlDirectoryLayout(DirectoryLayout):
         spec._mark_concrete()
         return spec
 
-
     def spec_file_path(self, spec):
         """Gets full path to spec file"""
         _check_concrete(spec)
         return join_path(self.metadata_path(spec), self.spec_file_name)
 
-
     def metadata_path(self, spec):
         return join_path(self.path_for_spec(spec), self.metadata_dir)
 
-
     def build_log_path(self, spec):
         return join_path(self.path_for_spec(spec), self.metadata_dir,
                          self.build_log_name)
 
-
     def build_env_path(self, spec):
         return join_path(self.path_for_spec(spec), self.metadata_dir,
                          self.build_env_name)
 
-
     def build_packages_path(self, spec):
         return join_path(self.path_for_spec(spec), self.metadata_dir,
                          self.packages_dir)
 
-
     def create_install_directory(self, spec):
         _check_concrete(spec)
 
@@ -273,7 +251,6 @@ class YamlDirectoryLayout(DirectoryLayout):
         mkdirp(self.metadata_path(spec))
         self.write_spec(spec, self.spec_file_path(spec))
 
-
     def check_installed(self, spec):
         _check_concrete(spec)
         path = self.path_for_spec(spec)
@@ -284,7 +261,7 @@ class YamlDirectoryLayout(DirectoryLayout):
 
         if not os.path.isfile(spec_file_path):
             raise InconsistentInstallDirectoryError(
-                'Inconsistent state: install prefix exists but contains no spec.yaml:',
+                'Install prefix exists but contains no spec.yaml:',
                 "  " + path)
 
         installed_spec = self.read_spec(spec_file_path)
@@ -297,7 +274,6 @@ class YamlDirectoryLayout(DirectoryLayout):
             raise InconsistentInstallDirectoryError(
                 'Spec file in %s does not match hash!' % spec_file_path)
 
-
     def all_specs(self):
         if not os.path.isdir(self.root):
             return []
@@ -307,20 +283,17 @@ class YamlDirectoryLayout(DirectoryLayout):
         spec_files = glob.glob(pattern)
         return [self.read_spec(s) for s in spec_files]
 
-
     def specs_by_hash(self):
         by_hash = {}
         for spec in self.all_specs():
             by_hash[spec.dag_hash()] = spec
         return by_hash
 
-
     def extension_file_path(self, spec):
         """Gets full path to an installed package's extension file"""
         _check_concrete(spec)
         return join_path(self.metadata_path(spec), self.extension_file_name)
 
-
     def _write_extensions(self, spec, extensions):
         path = self.extension_file_path(spec)
 
@@ -332,23 +305,22 @@ class YamlDirectoryLayout(DirectoryLayout):
         # write tmp file
         with tmp:
             yaml.dump({
-                'extensions' : [
-                    { ext.name : {
-                        'hash' : ext.dag_hash(),
-                        'path' : str(ext.prefix)
+                'extensions': [
+                    {ext.name: {
+                        'hash': ext.dag_hash(),
+                        'path': str(ext.prefix)
                     }} for ext in sorted(extensions.values())]
             }, tmp, default_flow_style=False)
 
         # Atomic update by moving tmpfile on top of old one.
         os.rename(tmp.name, path)
 
-
     def _extension_map(self, spec):
         """Get a dict<name -> spec> for all extensions currently
            installed for this package."""
         _check_concrete(spec)
 
-        if not spec in self._extension_maps:
+        if spec not in self._extension_maps:
             path = self.extension_file_path(spec)
             if not os.path.exists(path):
                 self._extension_maps[spec] = {}
@@ -363,14 +335,14 @@ class YamlDirectoryLayout(DirectoryLayout):
                         dag_hash = entry[name]['hash']
                         prefix   = entry[name]['path']
 
-                        if not dag_hash in by_hash:
+                        if dag_hash not in by_hash:
                             raise InvalidExtensionSpecError(
                                 "Spec %s not found in %s" % (dag_hash, prefix))
 
                         ext_spec = by_hash[dag_hash]
-                        if not prefix == ext_spec.prefix:
+                        if prefix != ext_spec.prefix:
                             raise InvalidExtensionSpecError(
-                                "Prefix %s does not match spec with hash %s: %s"
+                                "Prefix %s does not match spec hash %s: %s"
                                 % (prefix, dag_hash, ext_spec))
 
                         exts[ext_spec.name] = ext_spec
@@ -378,13 +350,11 @@ class YamlDirectoryLayout(DirectoryLayout):
 
         return self._extension_maps[spec]
 
-
     def extension_map(self, spec):
         """Defensive copying version of _extension_map() for external API."""
         _check_concrete(spec)
         return self._extension_map(spec).copy()
 
-
     def check_extension_conflict(self, spec, ext_spec):
         exts = self._extension_map(spec)
         if ext_spec.name in exts:
@@ -394,13 +364,11 @@ class YamlDirectoryLayout(DirectoryLayout):
             else:
                 raise ExtensionConflictError(spec, ext_spec, installed_spec)
 
-
     def check_activated(self, spec, ext_spec):
         exts = self._extension_map(spec)
-        if (not ext_spec.name in exts) or (ext_spec != exts[ext_spec.name]):
+        if (ext_spec.name not in exts) or (ext_spec != exts[ext_spec.name]):
             raise NoSuchExtensionError(spec, ext_spec)
 
-
     def add_extension(self, spec, ext_spec):
         _check_concrete(spec)
         _check_concrete(ext_spec)
@@ -413,7 +381,6 @@ class YamlDirectoryLayout(DirectoryLayout):
         exts[ext_spec.name] = ext_spec
         self._write_extensions(spec, exts)
 
-
     def remove_extension(self, spec, ext_spec):
         _check_concrete(spec)
         _check_concrete(ext_spec)
@@ -429,12 +396,14 @@ class YamlDirectoryLayout(DirectoryLayout):
 
 class DirectoryLayoutError(SpackError):
     """Superclass for directory layout errors."""
+
     def __init__(self, message, long_msg=None):
         super(DirectoryLayoutError, self).__init__(message, long_msg)
 
 
 class SpecHashCollisionError(DirectoryLayoutError):
     """Raised when there is a hash collision in an install layout."""
+
     def __init__(self, installed_spec, new_spec):
         super(SpecHashCollisionError, self).__init__(
             'Specs %s and %s have the same SHA-1 prefix!'
@@ -443,6 +412,7 @@ class SpecHashCollisionError(DirectoryLayoutError):
 
 class RemoveFailedError(DirectoryLayoutError):
     """Raised when a DirectoryLayout cannot remove an install prefix."""
+
     def __init__(self, installed_spec, prefix, error):
         super(RemoveFailedError, self).__init__(
             'Could not remove prefix %s for %s : %s'
@@ -452,12 +422,15 @@ class RemoveFailedError(DirectoryLayoutError):
 
 class InconsistentInstallDirectoryError(DirectoryLayoutError):
     """Raised when a package seems to be installed to the wrong place."""
+
     def __init__(self, message, long_msg=None):
-        super(InconsistentInstallDirectoryError, self).__init__(message, long_msg)
+        super(InconsistentInstallDirectoryError, self).__init__(
+            message, long_msg)
 
 
 class InstallDirectoryAlreadyExistsError(DirectoryLayoutError):
     """Raised when create_install_directory is called unnecessarily."""
+
     def __init__(self, path):
         super(InstallDirectoryAlreadyExistsError, self).__init__(
             "Install path %s already exists!")
@@ -473,22 +446,26 @@ class InvalidExtensionSpecError(DirectoryLayoutError):
 
 class ExtensionAlreadyInstalledError(DirectoryLayoutError):
     """Raised when an extension is added to a package that already has it."""
+
     def __init__(self, spec, ext_spec):
         super(ExtensionAlreadyInstalledError, self).__init__(
-            "%s is already installed in %s" % (ext_spec.short_spec, spec.short_spec))
+            "%s is already installed in %s"
+            % (ext_spec.short_spec, spec.short_spec))
 
 
 class ExtensionConflictError(DirectoryLayoutError):
     """Raised when an extension is added to a package that already has it."""
+
     def __init__(self, spec, ext_spec, conflict):
         super(ExtensionConflictError, self).__init__(
-            "%s cannot be installed in %s because it conflicts with %s"% (
-                ext_spec.short_spec, spec.short_spec, conflict.short_spec))
+            "%s cannot be installed in %s because it conflicts with %s"
+            % (ext_spec.short_spec, spec.short_spec, conflict.short_spec))
 
 
 class NoSuchExtensionError(DirectoryLayoutError):
     """Raised when an extension isn't there on deactivate."""
+
     def __init__(self, spec, ext_spec):
         super(NoSuchExtensionError, self).__init__(
-            "%s cannot be removed from %s because it's not activated."% (
-                ext_spec.short_spec, spec.short_spec))
+            "%s cannot be removed from %s because it's not activated."
+            % (ext_spec.short_spec, spec.short_spec))
diff --git a/lib/spack/spack/environment.py b/lib/spack/spack/environment.py
index 30c6228ca4..613ece2f45 100644
--- a/lib/spack/spack/environment.py
+++ b/lib/spack/spack/environment.py
@@ -1,4 +1,4 @@
-#
+##############################################################################
 # Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
@@ -21,7 +21,7 @@
 # You should have received a copy of the GNU Lesser General Public
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-#
+##############################################################################
 import collections
 import inspect
 import json
@@ -37,6 +37,10 @@ class NameModifier(object):
         self.args = {'name': name}
         self.args.update(kwargs)
 
+    def update_args(self, **kwargs):
+        self.__dict__.update(kwargs)
+        self.args.update(kwargs)
+
 
 class NameValueModifier(object):
 
@@ -44,7 +48,11 @@ class NameValueModifier(object):
         self.name = name
         self.value = value
         self.separator = kwargs.get('separator', ':')
-        self.args = {'name': name, 'value': value, 'delim': self.separator}
+        self.args = {'name': name, 'value': value, 'separator': self.separator}
+        self.args.update(kwargs)
+
+    def update_args(self, **kwargs):
+        self.__dict__.update(kwargs)
         self.args.update(kwargs)
 
 
@@ -279,7 +287,10 @@ class EnvironmentModifications(object):
         shell = '{shell}'.format(**info)
         shell_options = '{shell_options}'.format(**info)
         source_file = '{source_command} {file} {concatenate_on_success}'
-        dump_environment = 'python -c "import os, json; print json.dumps(dict(os.environ))"'  # NOQA: ignore=E501
+
+        dump_cmd = "import os, json; print json.dumps(dict(os.environ))"
+        dump_environment = 'python -c "%s"' % dump_cmd
+
         # Construct the command that will be executed
         command = [source_file.format(file=file, **info) for file in args]
         command.append(dump_environment)
@@ -318,8 +329,10 @@ class EnvironmentModifications(object):
         for x in unset_variables:
             env.unset(x)
         # Variables that have been modified
-        common_variables = set(this_environment).intersection(set(after_source_env))  # NOQA: ignore=E501
-        modified_variables = [x for x in common_variables if this_environment[x] != after_source_env[x]]  # NOQA: ignore=E501
+        common_variables = set(
+            this_environment).intersection(set(after_source_env))
+        modified_variables = [x for x in common_variables
+                              if this_environment[x] != after_source_env[x]]
 
         def return_separator_if_any(first_value, second_value):
             separators = ':', ';'
@@ -397,7 +410,7 @@ def set_or_unset_not_first(variable, changes, errstream):
     if indexes:
         good = '\t    \t{context} at {filename}:{lineno}'
         nogood = '\t--->\t{context} at {filename}:{lineno}'
-        message = 'Suspicious requests to set or unset the variable \'{var}\' found'  # NOQA: ignore=E501
+        message = "Suspicious requests to set or unset '{var}' found"
         errstream(message.format(var=variable))
         for ii, item in enumerate(changes):
             print_format = nogood if ii in indexes else good
diff --git a/lib/spack/spack/error.py b/lib/spack/spack/error.py
index 85ad2fe249..c94875e91a 100644
--- a/lib/spack/spack/error.py
+++ b/lib/spack/spack/error.py
@@ -27,21 +27,21 @@ import sys
 import llnl.util.tty as tty
 import spack
 
+
 class SpackError(Exception):
     """This is the superclass for all Spack errors.
        Subclasses can be found in the modules they have to do with.
     """
+
     def __init__(self, message, long_message=None):
         super(SpackError, self).__init__()
         self.message = message
         self._long_message = long_message
 
-
     @property
     def long_message(self):
         return self._long_message
 
-
     def die(self):
         if spack.debug:
             sys.excepthook(*sys.exc_info())
@@ -52,21 +52,23 @@ class SpackError(Exception):
                 print self.long_message
             os._exit(1)
 
-
     def __str__(self):
         msg = self.message
         if self._long_message:
             msg += "\n    %s" % self._long_message
         return msg
 
+
 class UnsupportedPlatformError(SpackError):
     """Raised by packages when a platform is not supported"""
+
     def __init__(self, message):
         super(UnsupportedPlatformError, self).__init__(message)
 
 
 class NoNetworkConnectionError(SpackError):
     """Raised when an operation needs an internet connection."""
+
     def __init__(self, message, url):
         super(NoNetworkConnectionError, self).__init__(
             "No network connection: " + str(message),
diff --git a/lib/spack/spack/fetch_strategy.py b/lib/spack/spack/fetch_strategy.py
index bcb33bd0e6..c69a23033c 100644
--- a/lib/spack/spack/fetch_strategy.py
+++ b/lib/spack/spack/fetch_strategy.py
@@ -356,6 +356,7 @@ class URLFetchStrategy(FetchStrategy):
 
 class CacheURLFetchStrategy(URLFetchStrategy):
     """The resource associated with a cache URL may be out of date."""
+
     def __init__(self, *args, **kwargs):
         super(CacheURLFetchStrategy, self).__init__(*args, **kwargs)
 
@@ -836,6 +837,7 @@ def for_package_version(pkg, version):
 
 
 class FsCache(object):
+
     def __init__(self, root):
         self.root = os.path.abspath(root)
 
diff --git a/lib/spack/spack/file_cache.py b/lib/spack/spack/file_cache.py
new file mode 100644
index 0000000000..0a66166fd8
--- /dev/null
+++ b/lib/spack/spack/file_cache.py
@@ -0,0 +1,185 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+import os
+import shutil
+
+from llnl.util.filesystem import *
+from llnl.util.lock import *
+
+from spack.error import SpackError
+
+
+class FileCache(object):
+    """This class manages cached data in the filesystem.
+
+    - Cache files are fetched and stored by unique keys.  Keys can be relative
+      paths, so that thre can be some hierarchy in the cache.
+
+    - The FileCache handles locking cache files for reading and writing, so
+      client code need not manage locks for cache entries.
+
+    """
+
+    def __init__(self, root):
+        """Create a file cache object.
+
+        This will create the cache directory if it does not exist yet.
+
+        """
+        self.root = root.rstrip(os.path.sep)
+        if not os.path.exists(self.root):
+            mkdirp(self.root)
+
+        self._locks = {}
+
+    def destroy(self):
+        """Remove all files under the cache root."""
+        for f in os.listdir(self.root):
+            path = join_path(self.root, f)
+            if os.path.isdir(path):
+                shutil.rmtree(path, True)
+            else:
+                os.remove(path)
+
+    def cache_path(self, key):
+        """Path to the file in the cache for a particular key."""
+        return join_path(self.root, key)
+
+    def _lock_path(self, key):
+        """Path to the file in the cache for a particular key."""
+        keyfile = os.path.basename(key)
+        keydir = os.path.dirname(key)
+
+        return join_path(self.root, keydir, '.' + keyfile + '.lock')
+
+    def _get_lock(self, key):
+        """Create a lock for a key, if necessary, and return a lock object."""
+        if key not in self._locks:
+            lock_file = self._lock_path(key)
+            if not os.path.exists(lock_file):
+                touch(lock_file)
+            self._locks[key] = Lock(lock_file)
+        return self._locks[key]
+
+    def init_entry(self, key):
+        """Ensure we can access a cache file. Create a lock for it if needed.
+
+        Return whether the cache file exists yet or not.
+        """
+        cache_path = self.cache_path(key)
+
+        exists = os.path.exists(cache_path)
+        if exists:
+            if not os.path.isfile(cache_path):
+                raise CacheError("Cache file is not a file: %s" % cache_path)
+
+            if not os.access(cache_path, os.R_OK | os.W_OK):
+                raise CacheError("Cannot access cache file: %s" % cache_path)
+        else:
+            # if the file is hierarchical, make parent directories
+            parent = os.path.dirname(cache_path)
+            if parent.rstrip(os.path.sep) != self.root:
+                mkdirp(parent)
+
+            if not os.access(parent, os.R_OK | os.W_OK):
+                raise CacheError("Cannot access cache directory: %s" % parent)
+
+            # ensure lock is created for this key
+            self._get_lock(key)
+        return exists
+
+    def read_transaction(self, key):
+        """Get a read transaction on a file cache item.
+
+        Returns a ReadTransaction context manager and opens the cache file for
+        reading.  You can use it like this:
+
+           with spack.user_cache.read_transaction(key) as cache_file:
+               cache_file.read()
+
+        """
+        return ReadTransaction(
+            self._get_lock(key), lambda: open(self.cache_path(key)))
+
+    def write_transaction(self, key):
+        """Get a write transaction on a file cache item.
+
+        Returns a WriteTransaction context manager that opens a temporary file
+        for writing.  Once the context manager finishes, if nothing went wrong,
+        moves the file into place on top of the old file atomically.
+
+        """
+        class WriteContextManager(object):
+
+            def __enter__(cm):
+                cm.orig_filename = self.cache_path(key)
+                cm.orig_file = None
+                if os.path.exists(cm.orig_filename):
+                    cm.orig_file = open(cm.orig_filename, 'r')
+
+                cm.tmp_filename = self.cache_path(key) + '.tmp'
+                cm.tmp_file = open(cm.tmp_filename, 'w')
+
+                return cm.orig_file, cm.tmp_file
+
+            def __exit__(cm, type, value, traceback):
+                if cm.orig_file:
+                    cm.orig_file.close()
+                cm.tmp_file.close()
+
+                if value:
+                    # remove tmp on exception & raise it
+                    shutil.rmtree(cm.tmp_filename, True)
+                    raise value
+                else:
+                    os.rename(cm.tmp_filename, cm.orig_filename)
+
+        return WriteTransaction(self._get_lock(key), WriteContextManager)
+
+    def mtime(self, key):
+        """Return modification time of cache file, or 0 if it does not exist.
+
+        Time is in units returned by os.stat in the mtime field, which is
+        platform-dependent.
+
+        """
+        if not self.init_entry(key):
+            return 0
+        else:
+            sinfo = os.stat(self.cache_path(key))
+            return sinfo.st_mtime
+
+    def remove(self, key):
+        lock = self._get_lock(key)
+        try:
+            lock.acquire_write()
+            os.unlink(self.cache_path(key))
+        finally:
+            lock.release_write()
+        os.unlink(self._lock_path(key))
+
+
+class CacheError(SpackError):
+    pass
diff --git a/lib/spack/spack/graph.py b/lib/spack/spack/graph.py
index 063e4647b6..b875e9da99 100644
--- a/lib/spack/spack/graph.py
+++ b/lib/spack/spack/graph.py
@@ -61,7 +61,6 @@ Note that ``graph_ascii`` assumes a single spec while ``graph_dot``
 can take a number of specs as input.
 
 """
-__all__ = ['topological_sort', 'graph_ascii', 'AsciiGraph', 'graph_dot']
 
 from heapq import *
 
@@ -71,6 +70,8 @@ from llnl.util.tty.color import *
 import spack
 from spack.spec import Spec
 
+__all__ = ['topological_sort', 'graph_ascii', 'AsciiGraph', 'graph_dot']
+
 
 def topological_sort(spec, **kwargs):
     """Topological sort for specs.
@@ -94,6 +95,7 @@ def topological_sort(spec, **kwargs):
     nodes = spec.index()
 
     topo_order = []
+    par = dict((name, parents(nodes[name])) for name in nodes.keys())
     remaining = [name for name in nodes.keys() if not parents(nodes[name])]
     heapify(remaining)
 
@@ -102,12 +104,12 @@ def topological_sort(spec, **kwargs):
         topo_order.append(name)
 
         node = nodes[name]
-        for dep in children(node).values():
-            del parents(dep)[node.name]
-            if not parents(dep):
+        for dep in children(node):
+            par[dep.name].remove(node)
+            if not par[dep.name]:
                 heappush(remaining, dep.name)
 
-    if any(parents(s) for s in spec.traverse()):
+    if any(par.get(s.name, []) for s in spec.traverse()):
         raise ValueError("Spec has cycles!")
     else:
         return topo_order
@@ -132,7 +134,9 @@ def find(seq, predicate):
 states = ('node', 'collapse', 'merge-right', 'expand-right', 'back-edge')
 NODE, COLLAPSE, MERGE_RIGHT, EXPAND_RIGHT, BACK_EDGE = states
 
+
 class AsciiGraph(object):
+
     def __init__(self):
         # These can be set after initialization or after a call to
         # graph() to change behavior.
@@ -153,18 +157,15 @@ class AsciiGraph(object):
         self._prev_state = None       # State of previous line
         self._prev_index = None       # Index of expansion point of prev line
 
-
     def _indent(self):
         self._out.write(self.indent * ' ')
 
-
     def _write_edge(self, string, index, sub=0):
         """Write a colored edge to the output stream."""
         name = self._frontier[index][sub]
         edge = "@%s{%s}" % (self._name_to_color[name], string)
         self._out.write(edge)
 
-
     def _connect_deps(self, i, deps, label=None):
         """Connect dependencies to existing edges in the frontier.
 
@@ -199,7 +200,8 @@ class AsciiGraph(object):
             collapse = True
             if self._prev_state == EXPAND_RIGHT:
                 # Special case where previous line expanded and i is off by 1.
-                self._back_edge_line([], j, i+1, True, label + "-1.5 " + str((i+1,j)))
+                self._back_edge_line([], j, i + 1, True,
+                                     label + "-1.5 " + str((i + 1, j)))
                 collapse = False
 
             else:
@@ -207,19 +209,20 @@ class AsciiGraph(object):
                 if self._prev_state == NODE and self._prev_index < i:
                     i += 1
 
-                if i-j > 1:
+                if i - j > 1:
                     # We need two lines to connect if distance > 1
-                    self._back_edge_line([], j,  i, True, label + "-1 " + str((i,j)))
+                    self._back_edge_line([], j,  i, True,
+                                         label + "-1 " + str((i, j)))
                     collapse = False
 
-            self._back_edge_line([j], -1, -1, collapse, label + "-2 " + str((i,j)))
+            self._back_edge_line([j], -1, -1, collapse,
+                                 label + "-2 " + str((i, j)))
             return True
 
         elif deps:
             self._frontier.insert(i, deps)
             return False
 
-
     def _set_state(self, state, index, label=None):
         if state not in states:
             raise ValueError("Invalid graph state!")
@@ -233,7 +236,6 @@ class AsciiGraph(object):
             self._out.write("%-20s" % (str(label) if label else ''))
             self._out.write("%s" % self._frontier)
 
-
     def _back_edge_line(self, prev_ends, end, start, collapse, label=None):
         """Write part of a backwards edge in the graph.
 
@@ -287,27 +289,26 @@ class AsciiGraph(object):
         self._indent()
 
         for p in prev_ends:
-            advance(p,         lambda: [("| ", self._pos)] )
-            advance(p+1,       lambda: [("|/", self._pos)] )
+            advance(p,         lambda: [("| ", self._pos)])
+            advance(p + 1,     lambda: [("|/", self._pos)])
 
         if end >= 0:
-            advance(end + 1,   lambda: [("| ", self._pos)] )
-            advance(start - 1, lambda: [("|",  self._pos), ("_", end)] )
+            advance(end + 1,   lambda: [("| ", self._pos)])
+            advance(start - 1, lambda: [("|",  self._pos), ("_", end)])
         else:
-            advance(start - 1, lambda: [("| ", self._pos)] )
+            advance(start - 1, lambda: [("| ", self._pos)])
 
         if start >= 0:
-            advance(start,     lambda: [("|",  self._pos), ("/", end)] )
+            advance(start,     lambda: [("|",  self._pos), ("/", end)])
 
         if collapse:
-            advance(flen,      lambda: [(" /", self._pos)] )
+            advance(flen,      lambda: [(" /", self._pos)])
         else:
-            advance(flen,      lambda: [("| ", self._pos)] )
+            advance(flen,      lambda: [("| ", self._pos)])
 
         self._set_state(BACK_EDGE, end, label)
         self._out.write("\n")
 
-
     def _node_line(self, index, name):
         """Writes a line with a node at index."""
         self._indent()
@@ -316,14 +317,13 @@ class AsciiGraph(object):
 
         self._out.write("%s " % self.node_character)
 
-        for c in range(index+1, len(self._frontier)):
+        for c in range(index + 1, len(self._frontier)):
             self._write_edge("| ", c)
 
         self._out.write(" %s" % name)
         self._set_state(NODE, index)
         self._out.write("\n")
 
-
     def _collapse_line(self, index):
         """Write a collapsing line after a node was added at index."""
         self._indent()
@@ -335,36 +335,33 @@ class AsciiGraph(object):
         self._set_state(COLLAPSE, index)
         self._out.write("\n")
 
-
     def _merge_right_line(self, index):
         """Edge at index is same as edge to right.  Merge directly with '\'"""
         self._indent()
         for c in range(index):
             self._write_edge("| ", c)
         self._write_edge("|", index)
-        self._write_edge("\\", index+1)
-        for c in range(index+1, len(self._frontier)):
-            self._write_edge("| ", c )
+        self._write_edge("\\", index + 1)
+        for c in range(index + 1, len(self._frontier)):
+            self._write_edge("| ", c)
 
         self._set_state(MERGE_RIGHT, index)
         self._out.write("\n")
 
-
     def _expand_right_line(self, index):
         self._indent()
         for c in range(index):
             self._write_edge("| ", c)
 
         self._write_edge("|", index)
-        self._write_edge("\\", index+1)
+        self._write_edge("\\", index + 1)
 
-        for c in range(index+2, len(self._frontier)):
+        for c in range(index + 2, len(self._frontier)):
             self._write_edge(" \\", c)
 
         self._set_state(EXPAND_RIGHT, index)
         self._out.write("\n")
 
-
     def write(self, spec, **kwargs):
         """Write out an ascii graph of the provided spec.
 
@@ -398,7 +395,7 @@ class AsciiGraph(object):
         # Colors associated with each node in the DAG.
         # Edges are colored by the node they point to.
         self._name_to_color = dict((name, self.colors[i % len(self.colors)])
-                                  for i, name in enumerate(topo_order))
+                                   for i, name in enumerate(topo_order))
 
         # Frontier tracks open edges of the graph as it's written out.
         self._frontier = [[spec.name]]
@@ -407,7 +404,8 @@ class AsciiGraph(object):
             i = find(self._frontier, lambda f: len(f) > 1)
 
             if i >= 0:
-                # Expand frontier until there are enough columns for all children.
+                # Expand frontier until there are enough columns for all
+                # children.
 
                 # Figure out how many back connections there are and
                 # sort them so we do them in order
@@ -424,8 +422,9 @@ class AsciiGraph(object):
                     prev_ends = []
                     for j, (b, d) in enumerate(back):
                         self._frontier[i].remove(d)
-                        if i-b > 1:
-                            self._back_edge_line(prev_ends, b, i, False, 'left-1')
+                        if i - b > 1:
+                            self._back_edge_line(prev_ends, b, i, False,
+                                                 'left-1')
                             del prev_ends[:]
                         prev_ends.append(b)
 
@@ -439,12 +438,13 @@ class AsciiGraph(object):
                 elif len(self._frontier[i]) > 1:
                     # Expand forward after doing all back connections
 
-                    if (i+1 < len(self._frontier) and len(self._frontier[i+1]) == 1
-                        and self._frontier[i+1][0] in self._frontier[i]):
+                    if (i + 1 < len(self._frontier) and
+                            len(self._frontier[i + 1]) == 1 and
+                            self._frontier[i + 1][0] in self._frontier[i]):
                         # We need to connect to the element to the right.
                         # Keep lines straight by connecting directly and
                         # avoiding unnecessary expand/contract.
-                        name = self._frontier[i+1][0]
+                        name = self._frontier[i + 1][0]
                         self._frontier[i].remove(name)
                         self._merge_right_line(i)
 
@@ -458,9 +458,8 @@ class AsciiGraph(object):
                         self._frontier.pop(i)
                         self._connect_deps(i, deps, "post-expand")
 
-
                 # Handle any remaining back edges to the right
-                j = i+1
+                j = i + 1
                 while j < len(self._frontier):
                     deps = self._frontier.pop(j)
                     if not self._connect_deps(j, deps, "back-from-right"):
@@ -477,9 +476,10 @@ class AsciiGraph(object):
 
                 # Replace node with its dependencies
                 self._frontier.pop(i)
-                if node.dependencies:
-                    deps = sorted((d for d in node.dependencies), reverse=True)
-                    self._connect_deps(i, deps, "new-deps") # anywhere.
+                if node.dependencies():
+                    deps = sorted((d.name for d in node.dependencies()),
+                                  reverse=True)
+                    self._connect_deps(i, deps, "new-deps")  # anywhere.
 
                 elif self._frontier:
                     self._collapse_line(i)
@@ -501,7 +501,6 @@ def graph_ascii(spec, **kwargs):
     graph.write(spec, color=color, out=out)
 
 
-
 def graph_dot(*specs, **kwargs):
     """Generate a graph in dot format of all provided specs.
 
diff --git a/lib/spack/spack/hooks/__init__.py b/lib/spack/spack/hooks/__init__.py
index 902e488eca..c7c84defa0 100644
--- a/lib/spack/spack/hooks/__init__.py
+++ b/lib/spack/spack/hooks/__init__.py
@@ -45,6 +45,7 @@ from llnl.util.lang import memoized, list_modules
 from llnl.util.filesystem import join_path
 import spack
 
+
 @memoized
 def all_hook_modules():
     modules = []
@@ -58,6 +59,7 @@ def all_hook_modules():
 
 
 class HookRunner(object):
+
     def __init__(self, hook_name):
         self.hook_name = hook_name
 
diff --git a/lib/spack/spack/hooks/extensions.py b/lib/spack/spack/hooks/extensions.py
index bcbd68dfa0..070b309a43 100644
--- a/lib/spack/spack/hooks/extensions.py
+++ b/lib/spack/spack/hooks/extensions.py
@@ -23,8 +23,6 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 
-import spack
-
 
 def pre_uninstall(pkg):
     assert(pkg.spec.concrete)
diff --git a/lib/spack/spack/hooks/sbang.py b/lib/spack/spack/hooks/sbang.py
index 3a957c6e0e..02c1ce3816 100644
--- a/lib/spack/spack/hooks/sbang.py
+++ b/lib/spack/spack/hooks/sbang.py
@@ -23,6 +23,7 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
+import stat
 import re
 
 import llnl.util.tty as tty
@@ -62,10 +63,21 @@ def filter_shebang(path):
     if re.search(r'^#!(/[^/]*)*lua\b', original):
         original = re.sub(r'^#', '--', original)
 
+    # Change non-writable files to be writable if needed.
+    saved_mode = None
+    if not os.access(path, os.W_OK):
+        st = os.stat(path)
+        saved_mode = st.st_mode
+        os.chmod(path, saved_mode | stat.S_IWRITE)
+
     with open(path, 'w') as new_file:
         new_file.write(new_sbang_line)
         new_file.write(original)
 
+    # Restore original permissions.
+    if saved_mode is not None:
+        os.chmod(path, saved_mode)
+
     tty.warn("Patched overlong shebang in %s" % path)
 
 
diff --git a/lib/spack/spack/mirror.py b/lib/spack/spack/mirror.py
index 0bbcfba6b4..f053e4405f 100644
--- a/lib/spack/spack/mirror.py
+++ b/lib/spack/spack/mirror.py
@@ -40,9 +40,8 @@ import spack.error
 import spack.url as url
 import spack.fetch_strategy as fs
 from spack.spec import Spec
-from spack.stage import Stage
 from spack.version import *
-from spack.util.compression import extension, allowed_archive
+from spack.util.compression import allowed_archive
 
 
 def mirror_archive_filename(spec, fetcher):
@@ -52,10 +51,10 @@ def mirror_archive_filename(spec, fetcher):
 
     if isinstance(fetcher, fs.URLFetchStrategy):
         if fetcher.expand_archive:
-            # If we fetch this version with a URLFetchStrategy, use URL's archive type
+            # If we fetch with a URLFetchStrategy, use URL's archive type
             ext = url.downloaded_file_extension(fetcher.url)
         else:
-            # If the archive shouldn't be expanded, don't check for its extension.
+            # If the archive shouldn't be expanded, don't check extension.
             ext = None
     else:
         # Otherwise we'll make a .tar.gz ourselves
@@ -106,7 +105,9 @@ def get_matching_versions(specs, **kwargs):
 
 def suggest_archive_basename(resource):
     """
-    Return a tentative basename for an archive. Raise an exception if the name is among the allowed archive types.
+    Return a tentative basename for an archive.
+
+    Raises an exception if the name is not an allowed archive type.
 
     :param fetcher:
     :return:
@@ -170,7 +171,7 @@ def create(path, specs, **kwargs):
         'error': []
     }
 
-    # Iterate through packages and download all the safe tarballs for each of them
+    # Iterate through packages and download all safe tarballs for each
     for spec in version_specs:
         add_single_spec(spec, mirror_root, categories, **kwargs)
 
@@ -190,12 +191,15 @@ def add_single_spec(spec, mirror_root, categories, **kwargs):
                 fetcher = stage.fetcher
                 if ii == 0:
                     # create a subdirectory for the current package@version
-                    archive_path = os.path.abspath(join_path(mirror_root, mirror_archive_path(spec, fetcher)))
+                    archive_path = os.path.abspath(join_path(
+                        mirror_root, mirror_archive_path(spec, fetcher)))
                     name = spec.format("$_$@")
                 else:
                     resource = stage.resource
-                    archive_path = join_path(subdir, suggest_archive_basename(resource))
-                    name = "{resource} ({pkg}).".format(resource=resource.name, pkg=spec.format("$_$@"))
+                    archive_path = join_path(
+                        subdir, suggest_archive_basename(resource))
+                    name = "{resource} ({pkg}).".format(
+                        resource=resource.name, pkg=spec.format("$_$@"))
                 subdir = os.path.dirname(archive_path)
                 mkdirp(subdir)
 
@@ -217,15 +221,18 @@ def add_single_spec(spec, mirror_root, categories, **kwargs):
             categories['present'].append(spec)
         else:
             categories['mirrored'].append(spec)
+
     except Exception as e:
         if spack.debug:
             sys.excepthook(*sys.exc_info())
         else:
-            tty.warn("Error while fetching %s" % spec.format('$_$@'), e.message)
+            tty.warn("Error while fetching %s"
+                     % spec.format('$_$@'), e.message)
         categories['error'].append(spec)
 
 
 class MirrorError(spack.error.SpackError):
     """Superclass of all mirror-creation related errors."""
+
     def __init__(self, msg, long_msg=None):
         super(MirrorError, self).__init__(msg, long_msg)
diff --git a/lib/spack/spack/modules.py b/lib/spack/spack/modules.py
index 72656b8ae0..debc6752b4 100644
--- a/lib/spack/spack/modules.py
+++ b/lib/spack/spack/modules.py
@@ -272,14 +272,26 @@ class EnvModule(object):
 
     @property
     def tokens(self):
+        """Tokens that can be substituted in environment variable values
+        and naming schemes
+        """
         tokens = {
             'name': self.spec.name,
             'version': self.spec.version,
-            'compiler': self.spec.compiler
+            'compiler': self.spec.compiler,
+            'prefix': self.spec.package.prefix
         }
         return tokens
 
     @property
+    def upper_tokens(self):
+        """Tokens that can be substituted in environment variable names"""
+        upper_tokens = {
+            'name': self.spec.name.replace('-', '_').upper()
+        }
+        return upper_tokens
+
+    @property
     def use_name(self):
         """
         Subclasses should implement this to return the name the module command
@@ -438,11 +450,17 @@ class EnvModule(object):
 
     def process_environment_command(self, env):
         for command in env:
+            # Token expansion from configuration file
+            name = command.args.get('name', '').format(**self.upper_tokens)
+            value = str(command.args.get('value', '')).format(**self.tokens)
+            command.update_args(name=name, value=value)
+            # Format the line int the module file
             try:
                 yield self.environment_modifications_formats[type(
                     command)].format(**command.args)
             except KeyError:
-                message = 'Cannot handle command of type {command} : skipping request'  # NOQA: ignore=E501
+                message = ('Cannot handle command of type {command}: '
+                           'skipping request')
                 details = '{context} at {filename}:{lineno}'
                 tty.warn(message.format(command=type(command)))
                 tty.warn(details.format(**command.args))
@@ -471,12 +489,14 @@ class Dotkit(EnvModule):
     path = join_path(spack.share_path, 'dotkit')
     environment_modifications_formats = {
         PrependPath: 'dk_alter {name} {value}\n',
+        RemovePath: 'dk_unalter {name} {value}\n',
         SetEnv: 'dk_setenv {name} {value}\n'
     }
 
     autoload_format = 'dk_op {module_file}\n'
 
-    default_naming_format = '{name}-{version}-{compiler.name}-{compiler.version}'  # NOQA: ignore=E501
+    default_naming_format = \
+        '{name}-{version}-{compiler.name}-{compiler.version}'
 
     @property
     def file_name(self):
@@ -502,7 +522,8 @@ class Dotkit(EnvModule):
 
     def prerequisite(self, spec):
         tty.warn('prerequisites:  not supported by dotkit module files')
-        tty.warn('\tYou may want to check  ~/.spack/modules.yaml')
+        tty.warn('\tYou may want to check %s/modules.yaml'
+                 % spack.user_config_path)
         return ''
 
 
@@ -510,9 +531,9 @@ class TclModule(EnvModule):
     name = 'tcl'
     path = join_path(spack.share_path, "modules")
     environment_modifications_formats = {
-        PrependPath: 'prepend-path --delim "{delim}" {name} \"{value}\"\n',
-        AppendPath: 'append-path   --delim "{delim}" {name} \"{value}\"\n',
-        RemovePath: 'remove-path   --delim "{delim}" {name} \"{value}\"\n',
+        PrependPath: 'prepend-path --delim "{separator}" {name} \"{value}\"\n',
+        AppendPath: 'append-path   --delim "{separator}" {name} \"{value}\"\n',
+        RemovePath: 'remove-path   --delim "{separator}" {name} \"{value}\"\n',
         SetEnv: 'setenv {name} \"{value}\"\n',
         UnsetEnv: 'unsetenv {name}\n'
     }
@@ -524,7 +545,8 @@ class TclModule(EnvModule):
 
     prerequisite_format = 'prereq {module_file}\n'
 
-    default_naming_format = '{name}-{version}-{compiler.name}-{compiler.version}'  # NOQA: ignore=E501
+    default_naming_format = \
+        '{name}-{version}-{compiler.name}-{compiler.version}'
 
     @property
     def file_name(self):
@@ -535,7 +557,7 @@ class TclModule(EnvModule):
         timestamp = datetime.datetime.now()
         # TCL Modulefile header
         header = '#%Module1.0\n'
-        header += '## Module file created by spack (https://github.com/LLNL/spack) on %s\n' % timestamp  # NOQA: ignore=E501
+        header += '## Module file created by spack (https://github.com/LLNL/spack) on %s\n' % timestamp
         header += '##\n'
         header += '## %s\n' % self.spec.short_spec
         header += '##\n'
@@ -565,10 +587,12 @@ class TclModule(EnvModule):
                 for naming_dir, conflict_dir in zip(
                         self.naming_scheme.split('/'), item.split('/')):
                     if naming_dir != conflict_dir:
-                        message = 'conflict scheme does not match naming scheme [{spec}]\n\n'  # NOQA: ignore=E501
+                        message = 'conflict scheme does not match naming '
+                        message += 'scheme [{spec}]\n\n'
                         message += 'naming scheme   : "{nformat}"\n'
                         message += 'conflict scheme : "{cformat}"\n\n'
-                        message += '** You may want to check your `modules.yaml` configuration file **\n'  # NOQA: ignore=E501
+                        message += '** You may want to check your '
+                        message += '`modules.yaml` configuration file **\n'
                         tty.error(message.format(spec=self.spec,
                                                  nformat=self.naming_scheme,
                                                  cformat=item))
diff --git a/lib/spack/spack/multimethod.py b/lib/spack/spack/multimethod.py
index 0818f9092f..d1d1f32445 100644
--- a/lib/spack/spack/multimethod.py
+++ b/lib/spack/spack/multimethod.py
@@ -43,15 +43,13 @@ avoids overly complicated rat nests of if statements.  Obviously,
 depending on the scenario, regular old conditionals might be clearer,
 so package authors should use their judgement.
 """
-import sys
 import functools
-import collections
 
 from llnl.util.lang import *
 
 import spack.architecture
 import spack.error
-from spack.spec import parse_anonymous_spec, Spec
+from spack.spec import parse_anonymous_spec
 
 
 class SpecMultiMethod(object):
@@ -89,13 +87,13 @@ class SpecMultiMethod(object):
 
        See the docs for decorators below for more details.
     """
+
     def __init__(self, default=None):
         self.method_list = []
         self.default = default
         if default:
             functools.update_wrapper(self, default)
 
-
     def register(self, spec, method):
         """Register a version of a method for a particular sys_type."""
         self.method_list.append((spec, method))
@@ -105,12 +103,10 @@ class SpecMultiMethod(object):
         else:
             assert(self.__name__ == method.__name__)
 
-
     def __get__(self, obj, objtype):
         """This makes __call__ support instance methods."""
         return functools.partial(self.__call__, obj)
 
-
     def __call__(self, package_self, *args, **kwargs):
         """Find the first method with a spec that matches the
            package's spec.  If none is found, call the default
@@ -127,7 +123,6 @@ class SpecMultiMethod(object):
                 type(package_self), self.__name__, spec,
                 [m[0] for m in self.method_list])
 
-
     def __str__(self):
         return "SpecMultiMethod {\n\tdefault: %s,\n\tspecs: %s\n}" % (
             self.default, self.method_list)
@@ -195,11 +190,13 @@ class when(object):
        platform-specific versions.  There's not much we can do to get
        around this because of the way decorators work.
     """
+
     def __init__(self, spec):
         pkg = get_calling_module_name()
         if spec is True:
             spec = pkg
-        self.spec = parse_anonymous_spec(spec, pkg) if spec is not False else None
+        self.spec = (parse_anonymous_spec(spec, pkg)
+                     if spec is not False else None)
 
     def __call__(self, method):
         # Get the first definition of the method in the calling scope
@@ -218,12 +215,14 @@ class when(object):
 
 class MultiMethodError(spack.error.SpackError):
     """Superclass for multimethod dispatch errors"""
+
     def __init__(self, message):
         super(MultiMethodError, self).__init__(message)
 
 
 class NoSuchMethodError(spack.error.SpackError):
     """Raised when we can't find a version of a multi-method."""
+
     def __init__(self, cls, method_name, spec, possible_specs):
         super(NoSuchMethodError, self).__init__(
             "Package %s does not support %s called with %s.  Options are: %s"
diff --git a/lib/spack/spack/operating_systems/cnl.py b/lib/spack/spack/operating_systems/cnl.py
index c160a60be8..78807865b3 100644
--- a/lib/spack/spack/operating_systems/cnl.py
+++ b/lib/spack/spack/operating_systems/cnl.py
@@ -7,29 +7,33 @@ import spack.spec
 from spack.util.multiproc import parmap
 import spack.compilers
 
+
 class Cnl(OperatingSystem):
     """ Compute Node Linux (CNL) is the operating system used for the Cray XC
     series super computers. It is a very stripped down version of GNU/Linux.
     Any compilers found through this operating system will be used with
-    modules. If updated, user must make sure that version and name are 
+    modules. If updated, user must make sure that version and name are
     updated to indicate that OS has been upgraded (or downgraded)
     """
+
     def __init__(self):
         name = 'CNL'
         version = '10'
         super(Cnl, self).__init__(name, version)
 
+    def __str__(self):
+        return self.name
 
     def find_compilers(self, *paths):
         types = spack.compilers.all_compiler_types()
-        compiler_lists = parmap(lambda cmp_cls: self.find_compiler(cmp_cls, *paths), types)
+        compiler_lists = parmap(
+            lambda cmp_cls: self.find_compiler(cmp_cls, *paths), types)
 
         # ensure all the version calls we made are cached in the parent
         # process, as well.  This speeds up Spack a lot.
-        clist = reduce(lambda x,y: x+y, compiler_lists)
+        clist = reduce(lambda x, y: x + y, compiler_lists)
         return clist
 
-
     def find_compiler(self, cmp_cls, *paths):
         compilers = []
         if cmp_cls.PrgEnv:
@@ -45,13 +49,16 @@ class Cnl(OperatingSystem):
             if paths:
                 module_paths = ':' + ':'.join(p for p in paths)
                 os.environ['MODULEPATH'] = module_paths
-        
-            output = modulecmd('avail', cmp_cls.PrgEnv_compiler, output=str, error=str)
-            matches = re.findall(r'(%s)/([\d\.]+[\d])' % cmp_cls.PrgEnv_compiler, output)
+
+            output = modulecmd(
+                'avail', cmp_cls.PrgEnv_compiler, output=str, error=str)
+            matches = re.findall(
+                r'(%s)/([\d\.]+[\d])' % cmp_cls.PrgEnv_compiler, output)
             for name, version in matches:
                 v = version
-                comp = cmp_cls(spack.spec.CompilerSpec(name + '@' + v), self,
-                           ['cc', 'CC', 'ftn'], [cmp_cls.PrgEnv, name +'/' + v])
+                comp = cmp_cls(
+                    spack.spec.CompilerSpec(name + '@' + v), self,
+                    ['cc', 'CC', 'ftn'], [cmp_cls.PrgEnv, name + '/' + v])
 
                 compilers.append(comp)
 
diff --git a/lib/spack/spack/operating_systems/linux_distro.py b/lib/spack/spack/operating_systems/linux_distro.py
index 2e3c72719b..6d70ae80b6 100644
--- a/lib/spack/spack/operating_systems/linux_distro.py
+++ b/lib/spack/spack/operating_systems/linux_distro.py
@@ -2,6 +2,7 @@ import re
 import platform as py_platform
 from spack.architecture import OperatingSystem
 
+
 class LinuxDistro(OperatingSystem):
     """ This class will represent the autodetected operating system
         for a Linux System. Since there are many different flavors of
@@ -9,6 +10,7 @@ class LinuxDistro(OperatingSystem):
         autodetection using the python module platform and the method
         platform.dist()
     """
+
     def __init__(self):
         distname, version, _ = py_platform.linux_distribution(
             full_distribution_name=False)
diff --git a/lib/spack/spack/operating_systems/mac_os.py b/lib/spack/spack/operating_systems/mac_os.py
index f35b3ca577..3e5ab9b2e9 100644
--- a/lib/spack/spack/operating_systems/mac_os.py
+++ b/lib/spack/spack/operating_systems/mac_os.py
@@ -1,6 +1,7 @@
 import platform as py_platform
 from spack.architecture import OperatingSystem
 
+
 class MacOs(OperatingSystem):
     """This class represents the macOS operating system. This will be
     auto detected using the python platform.mac_ver. The macOS
diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index ea798e8eaa..0d9067a955 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -39,6 +39,7 @@ import inspect
 import os
 import platform
 import re
+import sys
 import textwrap
 import time
 from StringIO import StringIO
@@ -64,7 +65,7 @@ from spack import directory_layout
 from spack.stage import Stage, ResourceStage, StageComposite
 from spack.util.compression import allowed_archive
 from spack.util.environment import dump_environment
-from spack.util.executable import ProcessError, which
+from spack.util.executable import ProcessError
 from spack.version import *
 
 """Allowed URL schemes for spack packages."""
@@ -330,12 +331,10 @@ class PackageBase(object):
 
     Most software comes in nicely packaged tarballs, like this one:
         http://www.cmake.org/files/v2.8/cmake-2.8.10.2.tar.gz
-
     Taking a page from homebrew, spack deduces pretty much everything it
     needs to know from the URL above.  If you simply type this:
 
         spack create http://www.cmake.org/files/v2.8/cmake-2.8.10.2.tar.gz
-
     Spack will download the tarball, generate an md5 hash, figure out the
     version and the name of the package from the URL, and create a new
     package file for you with all the names and attributes set correctly.
@@ -785,50 +784,12 @@ class PackageBase(object):
         exts = spack.install_layout.extension_map(self.extendee_spec)
         return (self.name in exts) and (exts[self.name] == self.spec)
 
-    def preorder_traversal(self, visited=None, **kwargs):
-        """This does a preorder traversal of the package's dependence DAG."""
-        virtual = kwargs.get("virtual", False)
-
-        if visited is None:
-            visited = set()
-
-        if self.name in visited:
-            return
-        visited.add(self.name)
-
-        if not virtual:
-            yield self
-
-        for name in sorted(self.dependencies.keys()):
-            dep_spec = self.get_dependency(name)
-            spec = dep_spec.spec
-
-            # Currently, we do not descend into virtual dependencies, as this
-            # makes doing a sensible traversal much harder.  We just assume
-            # that ANY of the virtual deps will work, which might not be true
-            # (due to conflicts or unsatisfiable specs).  For now this is ok,
-            # but we might want to reinvestigate if we start using a lot of
-            # complicated virtual dependencies
-            # TODO: reinvestigate this.
-            if spec.virtual:
-                if virtual:
-                    yield spec
-                continue
-
-            for pkg in spack.repo.get(name).preorder_traversal(visited,
-                                                               **kwargs):
-                yield pkg
-
     def provides(self, vpkg_name):
         """
         True if this package provides a virtual package with the specified name
         """
         return any(s.name == vpkg_name for s in self.provided)
 
-    def virtual_dependencies(self, visited=None):
-        for spec in sorted(set(self.preorder_traversal(virtual=True))):
-            yield spec
-
     @property
     def installed(self):
         return os.path.isdir(self.prefix)
@@ -898,13 +859,13 @@ class PackageBase(object):
 
             # Ask the user whether to skip the checksum if we're
             # interactive, but just fail if non-interactive.
-            checksum_msg = "Add a checksum or use --no-checksum to skip this check."  # NOQA: ignore=E501
+            ck_msg = "Add a checksum or use --no-checksum to skip this check."
             ignore_checksum = False
             if sys.stdout.isatty():
                 ignore_checksum = tty.get_yes_or_no("  Fetch anyway?",
                                                     default=False)
                 if ignore_checksum:
-                    tty.msg("Fetching with no checksum.", checksum_msg)
+                    tty.msg("Fetching with no checksum.", ck_msg)
 
             if not ignore_checksum:
                 raise FetchError("Will not fetch %s" %
@@ -1396,7 +1357,15 @@ class PackageBase(object):
 
     def do_uninstall(self, force=False):
         if not self.installed:
-            raise InstallError(str(self.spec) + " is not installed.")
+            # prefix may not exist, but DB may be inconsistent. Try to fix by
+            # removing, but omit hooks.
+            specs = spack.installed_db.query(self.spec, installed=True)
+            if specs:
+                spack.installed_db.remove(specs[0])
+                tty.msg("Removed stale DB entry for %s" % self.spec.short_spec)
+                return
+            else:
+                raise InstallError(str(self.spec) + " is not installed.")
 
         if not force:
             dependents = self.installed_dependents
@@ -1495,9 +1464,10 @@ class PackageBase(object):
                     continue
                 for dep in aspec.traverse(deptype='run'):
                     if self.spec == dep:
+                        msg = ("Cannot deactivate %s because %s is activated "
+                               "and depends on it.")
                         raise ActivationError(
-                            "Cannot deactivate %s because %s is activated and depends on it."  # NOQA: ignore=E501
-                            % (self.spec.short_spec, aspec.short_spec))
+                            msg % (self.spec.short_spec, aspec.short_spec))
 
         self.extendee_spec.package.deactivate(self, **self.extendee_args)
 
@@ -1726,6 +1696,7 @@ def use_cray_compiler_names():
     os.environ['FC'] = 'ftn'
     os.environ['F77'] = 'ftn'
 
+
 def flatten_dependencies(spec, flat_dir):
     """Make each dependency of spec present in dir via symlink."""
     for dep in spec.traverse(root=False):
@@ -1890,12 +1861,14 @@ class ExtensionError(PackageError):
 
 
 class ExtensionConflictError(ExtensionError):
+
     def __init__(self, path):
         super(ExtensionConflictError, self).__init__(
             "Extension blocked by file: %s" % path)
 
 
 class ActivationError(ExtensionError):
+
     def __init__(self, msg, long_msg=None):
         super(ActivationError, self).__init__(msg, long_msg)
 
diff --git a/lib/spack/spack/parse.py b/lib/spack/spack/parse.py
index 8adf957e7f..1b88db2d7c 100644
--- a/lib/spack/spack/parse.py
+++ b/lib/spack/spack/parse.py
@@ -29,6 +29,7 @@ import spack.error
 
 class Token:
     """Represents tokens; generated from input by lexer and fed to parse()."""
+
     def __init__(self, type, value='', start=0, end=0):
         self.type = type
         self.value = value
@@ -51,11 +52,13 @@ class Token:
 
 class Lexer(object):
     """Base class for Lexers that keep track of line numbers."""
+
     def __init__(self, lexicon):
         self.scanner = re.Scanner(lexicon)
 
     def token(self, type, value=''):
-        return Token(type, value, self.scanner.match.start(0), self.scanner.match.end(0))
+        return Token(type, value,
+                     self.scanner.match.start(0), self.scanner.match.end(0))
 
     def lex(self, text):
         tokens, remainder = self.scanner.scan(text)
@@ -66,10 +69,11 @@ class Lexer(object):
 
 class Parser(object):
     """Base class for simple recursive descent parsers."""
+
     def __init__(self, lexer):
-        self.tokens = iter([])   # iterators over tokens, handled in order.  Starts empty.
-        self.token = Token(None) # last accepted token starts at beginning of file
-        self.next = None         # next token
+        self.tokens = iter([])    # iterators over tokens, handled in order.
+        self.token = Token(None)  # last accepted token
+        self.next = None          # next token
         self.lexer = lexer
         self.text = None
 
@@ -82,11 +86,12 @@ class Parser(object):
 
     def push_tokens(self, iterable):
         """Adds all tokens in some iterable to the token stream."""
-        self.tokens = itertools.chain(iter(iterable), iter([self.next]), self.tokens)
+        self.tokens = itertools.chain(
+            iter(iterable), iter([self.next]), self.tokens)
         self.gettok()
 
     def accept(self, id):
-        """Puts the next symbol in self.token if we like it.  Then calls gettok()"""
+        """Put the next symbol in self.token if accepted, then call gettok()"""
         if self.next and self.next.is_a(id):
             self.token = self.next
             self.gettok()
@@ -124,9 +129,9 @@ class Parser(object):
         return self.do_parse()
 
 
-
 class ParseError(spack.error.SpackError):
     """Raised when we don't hit an error while parsing."""
+
     def __init__(self, message, string, pos):
         super(ParseError, self).__init__(message)
         self.string = string
@@ -135,5 +140,6 @@ class ParseError(spack.error.SpackError):
 
 class LexError(ParseError):
     """Raised when we don't know how to lex something."""
+
     def __init__(self, message, string, pos):
         super(LexError, self).__init__(message, string, pos)
diff --git a/lib/spack/spack/patch.py b/lib/spack/spack/patch.py
index c2e181be2f..0bd9f5d29d 100644
--- a/lib/spack/spack/patch.py
+++ b/lib/spack/spack/patch.py
@@ -24,7 +24,6 @@
 ##############################################################################
 import os
 
-import llnl.util.tty as tty
 from llnl.util.filesystem import join_path
 
 import spack
@@ -59,7 +58,6 @@ class Patch(object):
             if not os.path.isfile(self.path):
                 raise NoSuchPatchFileError(pkg_name, self.path)
 
-
     def apply(self, stage):
         """Fetch this patch, if necessary, and apply it to the source
            code in the supplied stage.
@@ -84,9 +82,9 @@ class Patch(object):
                 patch_stage.destroy()
 
 
-
 class NoSuchPatchFileError(spack.error.SpackError):
     """Raised when user specifies a patch file that doesn't exist."""
+
     def __init__(self, package, path):
         super(NoSuchPatchFileError, self).__init__(
             "No such patch file for package %s: %s" % (package, path))
diff --git a/lib/spack/spack/platforms/bgq.py b/lib/spack/spack/platforms/bgq.py
index e0eb76f336..91afdd04db 100644
--- a/lib/spack/spack/platforms/bgq.py
+++ b/lib/spack/spack/platforms/bgq.py
@@ -1,6 +1,7 @@
 import os
 from spack.architecture import Platform, Target
 
+
 class Bgq(Platform):
     priority    = 30
     front_end   = 'power7'
@@ -15,4 +16,3 @@ class Bgq(Platform):
     @classmethod
     def detect(self):
         return os.path.exists('/bgsys')
-    
diff --git a/lib/spack/spack/platforms/cray.py b/lib/spack/spack/platforms/cray.py
new file mode 100644
index 0000000000..0059b49ff1
--- /dev/null
+++ b/lib/spack/spack/platforms/cray.py
@@ -0,0 +1,105 @@
+import os
+import re
+import spack.config
+import llnl.util.tty as tty
+from spack.util.executable import which
+from spack.architecture import Platform, Target, NoPlatformError
+from spack.operating_systems.linux_distro import LinuxDistro
+from spack.operating_systems.cnl import Cnl
+from llnl.util.filesystem import join_path
+
+# Craype- module prefixes that are not valid CPU targets.
+NON_TARGETS = ('hugepages', 'network', 'target', 'accel', 'xtpe')
+
+
+def _target_from_clean_env(name):
+    '''Return the default back_end target as loaded in a clean login session.
+
+    A bash subshell is launched with a wiped environment and the list of loaded
+    modules is parsed for the first acceptable CrayPE target.
+    '''
+    # Based on the incantation:
+    # echo "$(env - USER=$USER /bin/bash -l -c 'module list -lt')"
+    targets = []
+    if name != 'front_end':
+        env = which('env')
+        env.add_default_arg('-')
+        # CAUTION - $USER is generally needed to initialize the environment.
+        # There may be other variables needed for general success.
+        output = env('USER=%s' % os.environ['USER'],
+                     '/bin/bash', '--noprofile', '--norc', '-c',
+                     '. /etc/profile; module list -lt',
+                     output=str, error=str)
+        default_modules = [i for i in output.splitlines()
+                           if len(i.split()) == 1]
+        tty.debug("Found default modules:",
+                  *["      " + mod for mod in default_modules])
+        pattern = 'craype-(?!{0})(\S*)'.format('|'.join(NON_TARGETS))
+        for mod in default_modules:
+            if 'craype-' in mod:
+                targets.extend(re.findall(pattern, mod))
+    return targets[0] if targets else None
+
+
+class Cray(Platform):
+    priority = 10
+
+    def __init__(self):
+        ''' Create a Cray system platform.
+
+        Target names should use craype target names but not include the
+        'craype-' prefix. Uses first viable target from:
+          self
+          envars [SPACK_FRONT_END, SPACK_BACK_END]
+          configuration file "targets.yaml" with keys 'front_end', 'back_end'
+          scanning /etc/bash/bashrc.local for back_end only
+        '''
+        super(Cray, self).__init__('cray')
+
+        # Get targets from config or make best guess from environment:
+        conf = spack.config.get_config('targets')
+        for name in ('front_end', 'back_end'):
+            _target = getattr(self, name, None)
+            if _target is None:
+                _target = os.environ.get('SPACK_' + name.upper())
+            if _target is None:
+                _target = conf.get(name)
+            if _target is None:
+                _target = _target_from_clean_env(name)
+            setattr(self, name, _target)
+
+            if _target is not None:
+                self.add_target(name, Target(_target, 'craype-' + _target))
+                self.add_target(_target, Target(_target, 'craype-' + _target))
+
+        if self.back_end is not None:
+            self.default = self.back_end
+            self.add_target(
+                'default', Target(self.default, 'craype-' + self.default))
+        else:
+            raise NoPlatformError()
+
+        front_distro = LinuxDistro()
+        back_distro = Cnl()
+
+        self.default_os = str(back_distro)
+        self.back_os = self.default_os
+        self.front_os = str(front_distro)
+
+        self.add_operating_system(self.back_os, back_distro)
+        self.add_operating_system(self.front_os, front_distro)
+
+    @classmethod
+    def setup_platform_environment(self, pkg, env):
+        """ Change the linker to default dynamic to be more
+            similar to linux/standard linker behavior
+        """
+        env.set('CRAYPE_LINK_TYPE', 'dynamic')
+        cray_wrapper_names = join_path(spack.build_env_path, 'cray')
+        if os.path.isdir(cray_wrapper_names):
+            env.prepend_path('PATH', cray_wrapper_names)
+            env.prepend_path('SPACK_ENV_PATH', cray_wrapper_names)
+
+    @classmethod
+    def detect(self):
+        return os.environ.get('CRAYPE_VERSION') is not None
diff --git a/lib/spack/spack/platforms/cray_xc.py b/lib/spack/spack/platforms/cray_xc.py
deleted file mode 100644
index e3c7761a94..0000000000
--- a/lib/spack/spack/platforms/cray_xc.py
+++ /dev/null
@@ -1,59 +0,0 @@
-import os
-from spack.architecture import Platform, Target
-from spack.operating_systems.linux_distro import LinuxDistro
-from spack.operating_systems.cnl import Cnl
-from spack.util.executable import which
-
-
-class CrayXc(Platform):
-    priority    = 20
-    front_end   = 'sandybridge'
-    back_end    = 'ivybridge'
-    default     = 'ivybridge'
-
-    back_os     = "CNL10"
-    default_os  = "CNL10"
-
-    def __init__(self):
-        ''' Since cori doesn't have ivybridge as a front end it's better
-            if we use CRAY_CPU_TARGET as the default. This will ensure
-            that if we're on a XC-40 or XC-30 then we can detect the target
-        '''
-        super(CrayXc, self).__init__('cray_xc')
-
-        # Handle the default here so we can check for a key error
-        if 'CRAY_CPU_TARGET' in os.environ:
-            self.default = os.environ['CRAY_CPU_TARGET']
-
-        # Change the defaults to haswell if we're on an XC40
-        if self.default == 'haswell':
-            self.front_end = self.default
-            self.back_end = self.default
-
-        # Could switch to use modules and fe targets for front end
-        # Currently using compilers by path for front end.
-        self.add_target('sandybridge', Target('sandybridge'))
-        self.add_target('ivybridge',
-                        Target('ivybridge', 'craype-ivybridge'))
-        self.add_target('haswell',
-                        Target('haswell', 'craype-haswell'))
-
-        # Front end of the cray platform is a linux distro.
-        linux_dist = LinuxDistro()
-        self.front_os = str(linux_dist)
-        self.add_operating_system(str(linux_dist), linux_dist)
-        self.add_operating_system('CNL10', Cnl())
-
-    @classmethod
-    def detect(self):
-        try:
-            cc_verbose = which('ftn')
-            text = cc_verbose('-craype-verbose',
-                              output=str, error=str,
-                              ignore_errors=True).split()
-            if '-D__CRAYXC' in text:
-                return True
-            else:
-                return False
-        except:
-            return False
diff --git a/lib/spack/spack/platforms/darwin.py b/lib/spack/spack/platforms/darwin.py
index d47dd640f9..974ce3a3f9 100644
--- a/lib/spack/spack/platforms/darwin.py
+++ b/lib/spack/spack/platforms/darwin.py
@@ -2,6 +2,7 @@ import subprocess
 from spack.architecture import Platform, Target
 from spack.operating_systems.mac_os import MacOs
 
+
 class Darwin(Platform):
     priority    = 89
     front_end   = 'x86_64'
@@ -21,6 +22,6 @@ class Darwin(Platform):
 
     @classmethod
     def detect(self):
-        platform = subprocess.Popen(['uname', '-a'], stdout = subprocess.PIPE)
+        platform = subprocess.Popen(['uname', '-a'], stdout=subprocess.PIPE)
         platform, _ = platform.communicate()
         return 'darwin' in platform.strip().lower()
diff --git a/lib/spack/spack/platforms/linux.py b/lib/spack/spack/platforms/linux.py
index 4d3f59c320..38d2cdbfec 100644
--- a/lib/spack/spack/platforms/linux.py
+++ b/lib/spack/spack/platforms/linux.py
@@ -3,6 +3,7 @@ import platform
 from spack.architecture import Platform, Target
 from spack.operating_systems.linux_distro import LinuxDistro
 
+
 class Linux(Platform):
     priority    = 90
 
@@ -26,6 +27,6 @@ class Linux(Platform):
 
     @classmethod
     def detect(self):
-        platform = subprocess.Popen(['uname', '-a'], stdout = subprocess.PIPE)
+        platform = subprocess.Popen(['uname', '-a'], stdout=subprocess.PIPE)
         platform, _ = platform.communicate()
         return 'linux' in platform.strip().lower()
diff --git a/lib/spack/spack/platforms/test.py b/lib/spack/spack/platforms/test.py
index 8fa2585a7a..c918211555 100644
--- a/lib/spack/spack/platforms/test.py
+++ b/lib/spack/spack/platforms/test.py
@@ -1,4 +1,27 @@
-import subprocess
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
 from spack.architecture import Platform, Target
 from spack.operating_systems.linux_distro import LinuxDistro
 from spack.operating_systems.cnl import Cnl
@@ -9,7 +32,7 @@ class Test(Platform):
     front_end   = 'x86_32'
     back_end    = 'x86_64'
     default     = 'x86_64'
-    
+
     back_os = 'CNL10'
     default_os = 'CNL10'
 
diff --git a/lib/spack/spack/preferred_packages.py b/lib/spack/spack/preferred_packages.py
index 1b94f03de7..45a41c8e2b 100644
--- a/lib/spack/spack/preferred_packages.py
+++ b/lib/spack/spack/preferred_packages.py
@@ -156,7 +156,14 @@ class PreferredPackages(object):
         """Return True iff the named package has a list of preferred
            providers"""
         return bool(self._order_for_package(pkgname, 'providers',
-                    provider_str, False))
+                                            provider_str, False))
+
+    def spec_preferred_variants(self, pkgname):
+        """Return a VariantMap of preferred variants and their values"""
+        variants = self.preferred.get(pkgname, {}).get('variants', '')
+        if not isinstance(variants, basestring):
+            variants = " ".join(variants)
+        return spack.spec.Spec("%s %s" % (pkgname, variants)).variants
 
     def version_compare(self, pkgname, a, b):
         """Return less-than-0, 0, or greater than 0 if version a of pkgname is
diff --git a/lib/spack/spack/virtual.py b/lib/spack/spack/provider_index.py
index bb8333f023..3f9cd285e7 100644
--- a/lib/spack/spack/virtual.py
+++ b/lib/spack/spack/provider_index.py
@@ -25,8 +25,14 @@
 """
 The ``virtual`` module contains utility classes for virtual dependencies.
 """
-import spack.spec
-import itertools
+from itertools import product as iproduct
+from pprint import pformat
+
+import yaml
+from yaml.error import MarkedYAMLError
+
+import spack
+
 
 class ProviderIndex(object):
     """This is a dict of dicts used for finding providers of particular
@@ -44,13 +50,30 @@ class ProviderIndex(object):
 
        Calling providers_for(spec) will find specs that provide a
        matching implementation of MPI.
+
     """
-    def __init__(self, specs, **kwargs):
-        # TODO: come up with another name for this.  This "restricts" values to
-        # the verbatim impu specs (i.e., it doesn't pre-apply package's constraints, and
-        # keeps things as broad as possible, so it's really the wrong name)
-        self.restrict = kwargs.setdefault('restrict', False)
 
+    def __init__(self, specs=None, restrict=False):
+        """Create a new ProviderIndex.
+
+        Optional arguments:
+
+        specs
+            List (or sequence) of specs.  If provided, will call
+            `update` on this ProviderIndex with each spec in the list.
+
+        restrict
+            "restricts" values to the verbatim input specs; do not
+            pre-apply package's constraints.
+
+            TODO: rename this.  It is intended to keep things as broad
+            as possible without overly restricting results, so it is
+            not the best name.
+        """
+        if specs is None:
+            specs = []
+
+        self.restrict = restrict
         self.providers = {}
 
         for spec in specs:
@@ -62,9 +85,8 @@ class ProviderIndex(object):
 
             self.update(spec)
 
-
     def update(self, spec):
-        if type(spec) != spack.spec.Spec:
+        if not isinstance(spec, spack.spec.Spec):
             spec = spack.spec.Spec(spec)
 
         if not spec.name:
@@ -75,12 +97,13 @@ class ProviderIndex(object):
 
         pkg = spec.package
         for provided_spec, provider_spec in pkg.provided.iteritems():
-            provider_spec.compiler_flags = spec.compiler_flags.copy()#We want satisfaction other than flags
+            # We want satisfaction other than flags
+            provider_spec.compiler_flags = spec.compiler_flags.copy()
             if provider_spec.satisfies(spec, deps=False):
                 provided_name = provided_spec.name
 
                 provider_map = self.providers.setdefault(provided_name, {})
-                if not provided_spec in provider_map:
+                if provided_spec not in provider_map:
                     provider_map[provided_spec] = set()
 
                 if self.restrict:
@@ -102,7 +125,6 @@ class ProviderIndex(object):
                     constrained.constrain(provider_spec)
                     provider_map[provided_spec].add(constrained)
 
-
     def providers_for(self, *vpkg_specs):
         """Gives specs of all packages that provide virtual packages
            with the supplied specs."""
@@ -114,26 +136,25 @@ class ProviderIndex(object):
 
             # Add all the providers that satisfy the vpkg spec.
             if vspec.name in self.providers:
-                for provider_spec, spec_set in self.providers[vspec.name].items():
-                    if provider_spec.satisfies(vspec, deps=False):
+                for p_spec, spec_set in self.providers[vspec.name].items():
+                    if p_spec.satisfies(vspec, deps=False):
                         providers.update(spec_set)
 
         # Return providers in order
         return sorted(providers)
 
-
     # TODO: this is pretty darned nasty, and inefficient, but there
     # are not that many vdeps in most specs.
     def _cross_provider_maps(self, lmap, rmap):
         result = {}
-        for lspec, rspec in itertools.product(lmap, rmap):
+        for lspec, rspec in iproduct(lmap, rmap):
             try:
                 constrained = lspec.constrained(rspec)
             except spack.spec.UnsatisfiableSpecError:
                 continue
 
             # lp and rp are left and right provider specs.
-            for lp_spec, rp_spec in itertools.product(lmap[lspec], rmap[rspec]):
+            for lp_spec, rp_spec in iproduct(lmap[lspec], rmap[rspec]):
                 if lp_spec.name == rp_spec.name:
                     try:
                         const = lp_spec.constrained(rp_spec, deps=False)
@@ -142,12 +163,10 @@ class ProviderIndex(object):
                         continue
         return result
 
-
     def __contains__(self, name):
         """Whether a particular vpkg name is in the index."""
         return name in self.providers
 
-
     def satisfies(self, other):
         """Check that providers of virtual specs are compatible."""
         common = set(self.providers) & set(other.providers)
@@ -164,3 +183,111 @@ class ProviderIndex(object):
                 result[name] = crossed
 
         return all(c in result for c in common)
+
+    def to_yaml(self, stream=None):
+        provider_list = self._transform(
+            lambda vpkg, pset: [
+                vpkg.to_node_dict(), [p.to_node_dict() for p in pset]], list)
+
+        yaml.dump({'provider_index': {'providers': provider_list}},
+                  stream=stream)
+
+    @staticmethod
+    def from_yaml(stream):
+        try:
+            yfile = yaml.load(stream)
+        except MarkedYAMLError, e:
+            raise spack.spec.SpackYAMLError(
+                "error parsing YAML ProviderIndex cache:", str(e))
+
+        if not isinstance(yfile, dict):
+            raise spack.spec.SpackYAMLError(
+                "YAML ProviderIndex was not a dict.")
+
+        if 'provider_index' not in yfile:
+            raise spack.spec.SpackYAMLError(
+                "YAML ProviderIndex does not start with 'provider_index'")
+
+        index = ProviderIndex()
+        providers = yfile['provider_index']['providers']
+        index.providers = _transform(
+            providers,
+            lambda vpkg, plist: (
+                spack.spec.Spec.from_node_dict(vpkg),
+                set(spack.spec.Spec.from_node_dict(p) for p in plist)))
+        return index
+
+    def merge(self, other):
+        """Merge `other` ProviderIndex into this one."""
+        other = other.copy()   # defensive copy.
+
+        for pkg in other.providers:
+            if pkg not in self.providers:
+                self.providers[pkg] = other.providers[pkg]
+                continue
+
+            spdict, opdict = self.providers[pkg], other.providers[pkg]
+            for provided_spec in opdict:
+                if provided_spec not in spdict:
+                    spdict[provided_spec] = opdict[provided_spec]
+                    continue
+
+                spdict[provided_spec] += opdict[provided_spec]
+
+    def remove_provider(self, pkg_name):
+        """Remove a provider from the ProviderIndex."""
+        empty_pkg_dict = []
+        for pkg, pkg_dict in self.providers.items():
+            empty_pset = []
+            for provided, pset in pkg_dict.items():
+                same_name = set(p for p in pset if p.fullname == pkg_name)
+                pset.difference_update(same_name)
+
+                if not pset:
+                    empty_pset.append(provided)
+
+            for provided in empty_pset:
+                del pkg_dict[provided]
+
+            if not pkg_dict:
+                empty_pkg_dict.append(pkg)
+
+        for pkg in empty_pkg_dict:
+            del self.providers[pkg]
+
+    def copy(self):
+        """Deep copy of this ProviderIndex."""
+        clone = ProviderIndex()
+        clone.providers = self._transform(
+            lambda vpkg, pset: (vpkg, set((p.copy() for p in pset))))
+        return clone
+
+    def __eq__(self, other):
+        return self.providers == other.providers
+
+    def _transform(self, transform_fun, out_mapping_type=dict):
+        return _transform(self.providers, transform_fun, out_mapping_type)
+
+    def __str__(self):
+        return pformat(
+            _transform(self.providers,
+                       lambda k, v: (k, list(v))))
+
+
+def _transform(providers, transform_fun, out_mapping_type=dict):
+    """Syntactic sugar for transforming a providers dict.
+
+    transform_fun takes a (vpkg, pset) mapping and runs it on each
+    pair in nested dicts.
+
+    """
+    def mapiter(mappings):
+        if isinstance(mappings, dict):
+            return mappings.iteritems()
+        else:
+            return iter(mappings)
+
+    return dict(
+        (name, out_mapping_type([
+            transform_fun(vpkg, pset) for vpkg, pset in mapiter(mappings)]))
+        for name, mappings in providers.items())
diff --git a/lib/spack/spack/repository.py b/lib/spack/spack/repository.py
index 2c160a5f45..2d8dc39648 100644
--- a/lib/spack/spack/repository.py
+++ b/lib/spack/spack/repository.py
@@ -23,6 +23,9 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
+import stat
+import shutil
+import errno
 import exceptions
 import sys
 import inspect
@@ -30,15 +33,18 @@ import imp
 import re
 import traceback
 from bisect import bisect_left
+from types import ModuleType
+
 import yaml
 
 import llnl.util.tty as tty
 from llnl.util.filesystem import *
 
+import spack
 import spack.error
 import spack.config
 import spack.spec
-from spack.virtual import ProviderIndex
+from spack.provider_index import ProviderIndex
 from spack.util.naming import *
 
 #
@@ -51,6 +57,7 @@ repo_namespace     = 'spack.pkg'
 # These names describe how repos should be laid out in the filesystem.
 #
 repo_config_name   = 'repo.yaml'   # Top-level filename for repo config.
+repo_index_name    = 'index.yaml'  # Top-level filename for repository index.
 packages_dir_name  = 'packages'    # Top-level repo directory containing pkgs.
 package_file_name  = 'package.py'  # Filename for packages in a repository.
 
@@ -61,6 +68,7 @@ NOT_PROVIDED = object()
 def _autospec(function):
     """Decorator that automatically converts the argument of a single-arg
        function to a Spec."""
+
     def converter(self, spec_like, *args, **kwargs):
         if not isinstance(spec_like, spack.spec.Spec):
             spec_like = spack.spec.Spec(spec_like)
@@ -68,12 +76,22 @@ def _autospec(function):
     return converter
 
 
-def _make_namespace_module(ns):
-    module = imp.new_module(ns)
-    module.__file__ = "(spack namespace)"
-    module.__path__ = []
-    module.__package__ = ns
-    return module
+class SpackNamespace(ModuleType):
+    """ Allow lazy loading of modules."""
+
+    def __init__(self, namespace):
+        super(SpackNamespace, self).__init__(namespace)
+        self.__file__ = "(spack namespace)"
+        self.__path__ = []
+        self.__name__ = namespace
+        self.__package__ = namespace
+        self.__modules = {}
+
+    def __getattr__(self, name):
+        """Getattr lazily loads modules if they're not already loaded."""
+        submodule = self.__package__ + '.' + name
+        setattr(self, name, __import__(submodule))
+        return getattr(self, name)
 
 
 def substitute_spack_prefix(path):
@@ -96,6 +114,7 @@ class RepoPath(object):
        combined results of the Repos in its list instead of on a
        single package repository.
     """
+
     def __init__(self, *repo_dirs, **kwargs):
         # super-namespace for all packages in the RepoPath
         self.super_namespace = kwargs.get('namespace', repo_namespace)
@@ -104,7 +123,7 @@ class RepoPath(object):
         self.by_namespace = NamespaceTrie()
         self.by_path = {}
 
-        self._all_package_names = []
+        self._all_package_names = None
         self._provider_index = None
 
         # If repo_dirs is empty, just use the configuration
@@ -125,7 +144,6 @@ class RepoPath(object):
                          "To remove the bad repository, run this command:",
                          "    spack repo rm %s" % root)
 
-
     def swap(self, other):
         """Convenience function to make swapping repostiories easier.
 
@@ -143,7 +161,6 @@ class RepoPath(object):
             setattr(self, attr, getattr(other, attr))
             setattr(other, attr, tmp)
 
-
     def _add(self, repo):
         """Add a repository to the namespace and path indexes.
 
@@ -157,36 +174,28 @@ class RepoPath(object):
         if repo.namespace in self.by_namespace:
             raise DuplicateRepoError(
                 "Package repos '%s' and '%s' both provide namespace %s"
-                % (repo.root, self.by_namespace[repo.namespace].root, repo.namespace))
+                % (repo.root, self.by_namespace[repo.namespace].root,
+                   repo.namespace))
 
         # Add repo to the pkg indexes
         self.by_namespace[repo.full_namespace] = repo
         self.by_path[repo.root] = repo
 
-        # add names to the cached name list
-        new_pkgs = set(repo.all_package_names())
-        new_pkgs.update(set(self._all_package_names))
-        self._all_package_names = sorted(new_pkgs, key=lambda n:n.lower())
-
-
     def put_first(self, repo):
         """Add repo first in the search path."""
         self._add(repo)
         self.repos.insert(0, repo)
 
-
     def put_last(self, repo):
         """Add repo last in the search path."""
         self._add(repo)
         self.repos.append(repo)
 
-
     def remove(self, repo):
         """Remove a repo from the search path."""
         if repo in self.repos:
             self.repos.remove(repo)
 
-
     def get_repo(self, namespace, default=NOT_PROVIDED):
         """Get a repository by namespace.
         Arguments
@@ -206,38 +215,45 @@ class RepoPath(object):
             return default
         return self.by_namespace[fullspace]
 
-
     def first_repo(self):
         """Get the first repo in precedence order."""
         return self.repos[0] if self.repos else None
 
-
     def all_package_names(self):
         """Return all unique package names in all repositories."""
+        if self._all_package_names is None:
+            all_pkgs = set()
+            for repo in self.repos:
+                for name in repo.all_package_names():
+                    all_pkgs.add(name)
+            self._all_package_names = sorted(all_pkgs, key=lambda n: n.lower())
         return self._all_package_names
 
-
     def all_packages(self):
         for name in self.all_package_names():
             yield self.get(name)
 
+    @property
+    def provider_index(self):
+        """Merged ProviderIndex from all Repos in the RepoPath."""
+        if self._provider_index is None:
+            self._provider_index = ProviderIndex()
+            for repo in reversed(self.repos):
+                self._provider_index.merge(repo.provider_index)
+
+        return self._provider_index
 
     @_autospec
     def providers_for(self, vpkg_spec):
-        if self._provider_index is None:
-            self._provider_index = ProviderIndex(self.all_package_names())
-
-        providers = self._provider_index.providers_for(vpkg_spec)
+        providers = self.provider_index.providers_for(vpkg_spec)
         if not providers:
             raise UnknownPackageError(vpkg_spec.name)
         return providers
 
-
     @_autospec
     def extensions_for(self, extendee_spec):
         return [p for p in self.all_packages() if p.extends(extendee_spec)]
 
-
     def find_module(self, fullname, path=None):
         """Implements precedence for overlaid namespaces.
 
@@ -264,7 +280,6 @@ class RepoPath(object):
 
         return None
 
-
     def load_module(self, fullname):
         """Handles loading container namespaces when necessary.
 
@@ -273,18 +288,14 @@ class RepoPath(object):
         if fullname in sys.modules:
             return sys.modules[fullname]
 
-        # partition fullname into prefix and module name.
-        namespace, dot, module_name = fullname.rpartition('.')
-
         if not self.by_namespace.is_prefix(fullname):
             raise ImportError("No such Spack repo: %s" % fullname)
 
-        module = _make_namespace_module(namespace)
+        module = SpackNamespace(fullname)
         module.__loader__ = self
         sys.modules[fullname] = module
         return module
 
-
     @_autospec
     def repo_for_pkg(self, spec):
         """Given a spec, get the repository for its package."""
@@ -306,7 +317,6 @@ class RepoPath(object):
         # that can operate on packages that don't exist yet.
         return self.first_repo()
 
-
     @_autospec
     def get(self, spec, new=False):
         """Find a repo that contains the supplied spec's package.
@@ -315,12 +325,10 @@ class RepoPath(object):
         """
         return self.repo_for_pkg(spec).get(spec)
 
-
     def get_pkg_class(self, pkg_name):
         """Find a class for the spec's package and return the class object."""
         return self.repo_for_pkg(pkg_name).get_pkg_class(pkg_name)
 
-
     @_autospec
     def dump_provenance(self, spec, path):
         """Dump provenance information for a spec to a particular path.
@@ -330,24 +338,19 @@ class RepoPath(object):
         """
         return self.repo_for_pkg(spec).dump_provenance(spec, path)
 
-
     def dirname_for_package_name(self, pkg_name):
         return self.repo_for_pkg(pkg_name).dirname_for_package_name(pkg_name)
 
-
     def filename_for_package_name(self, pkg_name):
         return self.repo_for_pkg(pkg_name).filename_for_package_name(pkg_name)
 
-
     def exists(self, pkg_name):
         return any(repo.exists(pkg_name) for repo in self.repos)
 
-
     def __contains__(self, pkg_name):
         return self.exists(pkg_name)
 
 
-
 class Repo(object):
     """Class representing a package repository in the filesystem.
 
@@ -360,6 +363,7 @@ class Repo(object):
         A Python namespace where the repository's packages should live.
 
     """
+
     def __init__(self, root, namespace=repo_namespace):
         """Instantiate a package repository from a filesystem path.
 
@@ -381,12 +385,14 @@ class Repo(object):
 
         # check and raise BadRepoError on fail.
         def check(condition, msg):
-            if not condition: raise BadRepoError(msg)
+            if not condition:
+                raise BadRepoError(msg)
 
         # Validate repository layout.
-        self.config_file   = join_path(self.root, repo_config_name)
+        self.config_file = join_path(self.root, repo_config_name)
         check(os.path.isfile(self.config_file),
               "No %s found in '%s'" % (repo_config_name, root))
+
         self.packages_path = join_path(self.root, packages_dir_name)
         check(os.path.isdir(self.packages_path),
               "No directory '%s' found in '%s'" % (repo_config_name, root))
@@ -398,12 +404,14 @@ class Repo(object):
 
         self.namespace = config['namespace']
         check(re.match(r'[a-zA-Z][a-zA-Z0-9_.]+', self.namespace),
-              ("Invalid namespace '%s' in repo '%s'. "  % (self.namespace, self.root)) +
+              ("Invalid namespace '%s' in repo '%s'. "
+               % (self.namespace, self.root)) +
               "Namespaces must be valid python identifiers separated by '.'")
 
         # Set up 'full_namespace' to include the super-namespace
         if self.super_namespace:
-            self.full_namespace = "%s.%s" % (self.super_namespace, self.namespace)
+            self.full_namespace = "%s.%s" % (
+                self.super_namespace, self.namespace)
         else:
             self.full_namespace = self.namespace
 
@@ -414,12 +422,21 @@ class Repo(object):
         self._modules = {}
         self._classes = {}
         self._instances = {}
+
+        # list of packages that are newer than the index.
+        self._needs_update = []
+
+        # Index of virtual dependencies
         self._provider_index = None
+
+        # Cached list of package names.
         self._all_package_names = None
 
         # make sure the namespace for packages in this repo exists.
         self._create_namespace()
 
+        # Unique filename for cache of virtual dependency providers
+        self._cache_file = 'providers/%s-index.yaml' % self.namespace
 
     def _create_namespace(self):
         """Create this repo's namespace module and insert it into sys.modules.
@@ -429,10 +446,11 @@ class Repo(object):
 
         """
         parent = None
-        for l in range(1, len(self._names)+1):
+        for l in range(1, len(self._names) + 1):
             ns = '.'.join(self._names[:l])
-            if not ns in sys.modules:
-                module = _make_namespace_module(ns)
+
+            if ns not in sys.modules:
+                module = SpackNamespace(ns)
                 module.__loader__ = self
                 sys.modules[ns] = module
 
@@ -442,14 +460,14 @@ class Repo(object):
                 # This ensures that we can do things like:
                 #    import spack.pkg.builtin.mpich as mpich
                 if parent:
-                    modname = self._names[l-1]
-                    if not hasattr(parent, modname):
-                        setattr(parent, modname, module)
+                    modname = self._names[l - 1]
+                    setattr(parent, modname, module)
             else:
-                # no need to set up a module, but keep track of the parent.
+                # no need to set up a module
                 module = sys.modules[ns]
-            parent = module
 
+            # but keep track of the parent in this loop
+            parent = module
 
     def real_name(self, import_name):
         """Allow users to import Spack packages using Python identifiers.
@@ -476,13 +494,11 @@ class Repo(object):
                 return name
         return None
 
-
     def is_prefix(self, fullname):
         """True if fullname is a prefix of this Repo's namespace."""
         parts = fullname.split('.')
         return self._names[:len(parts)] == parts
 
-
     def find_module(self, fullname, path=None):
         """Python find_module import hook.
 
@@ -498,7 +514,6 @@ class Repo(object):
 
         return None
 
-
     def load_module(self, fullname):
         """Python importer load hook.
 
@@ -510,7 +525,7 @@ class Repo(object):
         namespace, dot, module_name = fullname.rpartition('.')
 
         if self.is_prefix(fullname):
-            module = _make_namespace_module(fullname)
+            module = SpackNamespace(fullname)
 
         elif namespace == self.full_namespace:
             real_name = self.real_name(module_name)
@@ -523,8 +538,12 @@ class Repo(object):
 
         module.__loader__ = self
         sys.modules[fullname] = module
-        return module
+        if namespace != fullname:
+            parent = sys.modules[namespace]
+            if not hasattr(parent, module_name):
+                setattr(parent, module_name, module)
 
+        return module
 
     def _read_config(self):
         """Check for a YAML config file in this db's root directory."""
@@ -533,40 +552,39 @@ class Repo(object):
                 yaml_data = yaml.load(reponame_file)
 
                 if (not yaml_data or 'repo' not in yaml_data or
-                    not isinstance(yaml_data['repo'], dict)):
-                    tty.die("Invalid %s in repository %s"
-                            % (repo_config_name, self.root))
+                        not isinstance(yaml_data['repo'], dict)):
+                    tty.die("Invalid %s in repository %s" % (
+                        repo_config_name, self.root))
 
                 return yaml_data['repo']
 
-        except exceptions.IOError, e:
+        except exceptions.IOError:
             tty.die("Error reading %s when opening %s"
                     % (self.config_file, self.root))
 
-
     @_autospec
     def get(self, spec, new=False):
         if spec.virtual:
             raise UnknownPackageError(spec.name)
 
         if spec.namespace and spec.namespace != self.namespace:
-            raise UnknownPackageError("Repository %s does not contain package %s"
-                                      % (self.namespace, spec.fullname))
+            raise UnknownPackageError(
+                "Repository %s does not contain package %s"
+                % (self.namespace, spec.fullname))
 
         key = hash(spec)
         if new or key not in self._instances:
             package_class = self.get_pkg_class(spec.name)
             try:
-                copy = spec.copy() # defensive copy.  Package owns its spec.
+                copy = spec.copy()  # defensive copy.  Package owns its spec.
                 self._instances[key] = package_class(copy)
-            except Exception, e:
+            except Exception:
                 if spack.debug:
                     sys.excepthook(*sys.exc_info())
                 raise FailedConstructorError(spec.fullname, *sys.exc_info())
 
         return self._instances[key]
 
-
     @_autospec
     def dump_provenance(self, spec, path):
         """Dump provenance information for a spec to a particular path.
@@ -579,8 +597,9 @@ class Repo(object):
             raise UnknownPackageError(spec.name)
 
         if spec.namespace and spec.namespace != self.namespace:
-            raise UnknownPackageError("Repository %s does not contain package %s."
-                                      % (self.namespace, spec.fullname))
+            raise UnknownPackageError(
+                "Repository %s does not contain package %s."
+                % (self.namespace, spec.fullname))
 
         # Install any patch files needed by packages.
         mkdirp(path)
@@ -595,34 +614,61 @@ class Repo(object):
         # Install the package.py file itself.
         install(self.filename_for_package_name(spec), path)
 
-
     def purge(self):
         """Clear entire package instance cache."""
         self._instances.clear()
 
+    def _update_provider_index(self):
+        # Check modification dates of all packages
+        self._fast_package_check()
 
-    @_autospec
-    def providers_for(self, vpkg_spec):
+        def read():
+            with open(self.index_file) as f:
+                self._provider_index = ProviderIndex.from_yaml(f)
+
+        # Read the old ProviderIndex, or make a new one.
+        key = self._cache_file
+        index_existed = spack.user_cache.init_entry(key)
+        if index_existed and not self._needs_update:
+            with spack.user_cache.read_transaction(key) as f:
+                self._provider_index = ProviderIndex.from_yaml(f)
+        else:
+            with spack.user_cache.write_transaction(key) as (old, new):
+                if old:
+                    self._provider_index = ProviderIndex.from_yaml(old)
+                else:
+                    self._provider_index = ProviderIndex()
+
+                for pkg_name in self._needs_update:
+                    namespaced_name = '%s.%s' % (self.namespace, pkg_name)
+                    self._provider_index.remove_provider(namespaced_name)
+                    self._provider_index.update(namespaced_name)
+
+                self._provider_index.to_yaml(new)
+
+    @property
+    def provider_index(self):
+        """A provider index with names *specific* to this repo."""
         if self._provider_index is None:
-            self._provider_index = ProviderIndex(self.all_package_names())
+            self._update_provider_index()
+        return self._provider_index
 
-        providers = self._provider_index.providers_for(vpkg_spec)
+    @_autospec
+    def providers_for(self, vpkg_spec):
+        providers = self.provider_index.providers_for(vpkg_spec)
         if not providers:
             raise UnknownPackageError(vpkg_spec.name)
         return providers
 
-
     @_autospec
     def extensions_for(self, extendee_spec):
         return [p for p in self.all_packages() if p.extends(extendee_spec)]
 
-
     def _check_namespace(self, spec):
         """Check that the spec's namespace is the same as this repository's."""
         if spec.namespace and spec.namespace != self.namespace:
             raise UnknownNamespaceError(spec.namespace)
 
-
     @_autospec
     def dirname_for_package_name(self, spec):
         """Get the directory name for a particular package.  This is the
@@ -630,7 +676,6 @@ class Repo(object):
         self._check_namespace(spec)
         return join_path(self.packages_path, spec.name)
 
-
     @_autospec
     def filename_for_package_name(self, spec):
         """Get the filename for the module we should load for a particular
@@ -645,48 +690,95 @@ class Repo(object):
         pkg_dir = self.dirname_for_package_name(spec.name)
         return join_path(pkg_dir, package_file_name)
 
+    def _fast_package_check(self):
+        """List packages in the repo and check whether index is up to date.
 
-    def all_package_names(self):
-        """Returns a sorted list of all package names in the Repo."""
+        Both of these opreations require checking all `package.py`
+        files so we do them at the same time.  We list the repo
+        directory and look at package.py files, and we compare the
+        index modification date with the ost recently modified package
+        file, storing the result.
+
+        The implementation here should try to minimize filesystem
+        calls.  At the moment, it is O(number of packages) and makes
+        about one stat call per package.  This is resonably fast, and
+        avoids actually importing packages in Spack, which is slow.
+
+        """
         if self._all_package_names is None:
             self._all_package_names = []
 
+            # Get index modification time.
+            index_mtime = spack.user_cache.mtime(self._cache_file)
+
             for pkg_name in os.listdir(self.packages_path):
                 # Skip non-directories in the package root.
                 pkg_dir = join_path(self.packages_path, pkg_name)
-                if not os.path.isdir(pkg_dir):
-                    continue
-
-                # Skip directories without a package.py in them.
-                pkg_file = join_path(self.packages_path, pkg_name, package_file_name)
-                if not os.path.isfile(pkg_file):
-                    continue
 
                 # Warn about invalid names that look like packages.
                 if not valid_module_name(pkg_name):
-                    tty.warn("Skipping package at %s. '%s' is not a valid Spack module name."
-                             % (pkg_dir, pkg_name))
+                    msg = ("Skipping package at %s. "
+                           "'%s' is not a valid Spack module name.")
+                    tty.warn(msg % (pkg_dir, pkg_name))
+                    continue
+
+                # construct the file name from the directory
+                pkg_file = join_path(
+                    self.packages_path, pkg_name, package_file_name)
+
+                # Use stat here to avoid lots of calls to the filesystem.
+                try:
+                    sinfo = os.stat(pkg_file)
+                except OSError as e:
+                    if e.errno == errno.ENOENT:
+                        # No package.py file here.
+                        continue
+                    elif e.errno == errno.EACCES:
+                        tty.warn("Can't read package file %s." % pkg_file)
+                        continue
+                    raise e
+
+                # if it's not a file, skip it.
+                if stat.S_ISDIR(sinfo.st_mode):
                     continue
 
                 # All checks passed.  Add it to the list.
                 self._all_package_names.append(pkg_name)
+
+                # record the package if it is newer than the index.
+                if sinfo.st_mtime > index_mtime:
+                    self._needs_update.append(pkg_name)
+
             self._all_package_names.sort()
 
         return self._all_package_names
 
+    def all_package_names(self):
+        """Returns a sorted list of all package names in the Repo."""
+        self._fast_package_check()
+        return self._all_package_names
 
     def all_packages(self):
+        """Iterator over all packages in the repository.
+
+        Use this with care, because loading packages is slow.
+
+        """
         for name in self.all_package_names():
             yield self.get(name)
 
-
     def exists(self, pkg_name):
         """Whether a package with the supplied name exists."""
-        # This does a binary search in the sorted list.
-        idx = bisect_left(self.all_package_names(), pkg_name)
-        return (idx < len(self._all_package_names) and
-                self._all_package_names[idx] == pkg_name)
+        if self._all_package_names:
+            # This does a binary search in the sorted list.
+            idx = bisect_left(self.all_package_names(), pkg_name)
+            return (idx < len(self._all_package_names) and
+                    self._all_package_names[idx] == pkg_name)
 
+        # If we haven't generated the full package list, don't.
+        # Just check whether the file exists.
+        filename = self.filename_for_package_name(pkg_name)
+        return os.path.exists(filename)
 
     def _get_pkg_module(self, pkg_name):
         """Create a module for a particular package.
@@ -719,7 +811,6 @@ class Repo(object):
 
         return self._modules[pkg_name]
 
-
     def get_pkg_class(self, pkg_name):
         """Get the class for the package out of its module.
 
@@ -727,6 +818,11 @@ class Repo(object):
         package. Then extracts the package class from the module
         according to Spack's naming convention.
         """
+        namespace, _, pkg_name = pkg_name.rpartition('.')
+        if namespace and (namespace != self.namespace):
+            raise InvalidNamespaceError('Invalid namespace for %s repo: %s'
+                                        % (self.namespace, namespace))
+
         class_name = mod_to_class(pkg_name)
         module = self._get_pkg_module(pkg_name)
 
@@ -736,15 +832,12 @@ class Repo(object):
 
         return cls
 
-
     def __str__(self):
         return "[Repo '%s' at '%s']" % (self.namespace, self.root)
 
-
     def __repr__(self):
         return self.__str__()
 
-
     def __contains__(self, pkg_name):
         return self.exists(pkg_name)
 
@@ -753,30 +846,37 @@ def create_repo(root, namespace=None):
     """Create a new repository in root with the specified namespace.
 
        If the namespace is not provided, use basename of root.
-       Return the canonicalized path and the namespace of the created repository.
+       Return the canonicalized path and namespace of the created repository.
     """
     root = canonicalize_path(root)
     if not namespace:
         namespace = os.path.basename(root)
 
     if not re.match(r'\w[\.\w-]*', namespace):
-        raise InvalidNamespaceError("'%s' is not a valid namespace." % namespace)
+        raise InvalidNamespaceError(
+            "'%s' is not a valid namespace." % namespace)
 
     existed = False
     if os.path.exists(root):
         if os.path.isfile(root):
-            raise BadRepoError('File %s already exists and is not a directory' % root)
+            raise BadRepoError('File %s already exists and is not a directory'
+                               % root)
         elif os.path.isdir(root):
             if not os.access(root, os.R_OK | os.W_OK):
-                raise BadRepoError('Cannot create new repo in %s: cannot access directory.' % root)
+                raise BadRepoError(
+                    'Cannot create new repo in %s: cannot access directory.'
+                    % root)
             if os.listdir(root):
-                raise BadRepoError('Cannot create new repo in %s: directory is not empty.' % root)
+                raise BadRepoError(
+                    'Cannot create new repo in %s: directory is not empty.'
+                    % root)
         existed = True
 
     full_path = os.path.realpath(root)
     parent = os.path.dirname(full_path)
     if not os.access(parent, os.R_OK | os.W_OK):
-        raise BadRepoError("Cannot create repository in %s: can't access parent!" % root)
+        raise BadRepoError(
+            "Cannot create repository in %s: can't access parent!" % root)
 
     try:
         config_path = os.path.join(root, repo_config_name)
@@ -827,6 +927,7 @@ class PackageLoadError(spack.error.SpackError):
 
 class UnknownPackageError(PackageLoadError):
     """Raised when we encounter a package spack doesn't have."""
+
     def __init__(self, name, repo=None):
         msg = None
         if repo:
@@ -839,6 +940,7 @@ class UnknownPackageError(PackageLoadError):
 
 class UnknownNamespaceError(PackageLoadError):
     """Raised when we encounter an unknown namespace"""
+
     def __init__(self, namespace):
         super(UnknownNamespaceError, self).__init__(
             "Unknown namespace: %s" % namespace)
@@ -846,6 +948,7 @@ class UnknownNamespaceError(PackageLoadError):
 
 class FailedConstructorError(PackageLoadError):
     """Raised when a package's class constructor fails."""
+
     def __init__(self, name, exc_type, exc_obj, exc_tb):
         super(FailedConstructorError, self).__init__(
             "Class constructor failed for package '%s'." % name,
diff --git a/lib/spack/spack/resource.py b/lib/spack/spack/resource.py
index 24b675f8da..1d4d448298 100644
--- a/lib/spack/spack/resource.py
+++ b/lib/spack/spack/resource.py
@@ -31,9 +31,11 @@ package to enable optional features.
 
 
 class Resource(object):
+    """Represents an optional resource to be fetched by a package.
+
+    Aggregates a name, a fetcher, a destination and a placement.
     """
-    Represents an optional resource. Aggregates a name, a fetcher, a destination and a placement
-    """
+
     def __init__(self, name, fetcher, destination, placement):
         self.name = name
         self.fetcher = fetcher
diff --git a/lib/spack/spack/schema/__init__.py b/lib/spack/spack/schema/__init__.py
new file mode 100644
index 0000000000..de45ea921f
--- /dev/null
+++ b/lib/spack/spack/schema/__init__.py
@@ -0,0 +1,33 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+"""This module contains jsonschema files for all of Spack's YAML formats.
+"""
+from llnl.util.lang import list_modules
+
+# Automatically bring in all sub-modules
+__all__ = []
+for mod in list_modules(__path__[0]):
+    __import__('%s.%s' % (__name__, mod))
+    __all__.append(mod)
diff --git a/lib/spack/spack/schema/compilers.py b/lib/spack/spack/schema/compilers.py
new file mode 100644
index 0000000000..2ffac03a66
--- /dev/null
+++ b/lib/spack/spack/schema/compilers.py
@@ -0,0 +1,80 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+"""Schema for compiler configuration files."""
+
+
+schema = {
+    '$schema': 'http://json-schema.org/schema#',
+    'title': 'Spack compiler configuration file schema',
+    'type': 'object',
+    'additionalProperties': False,
+    'patternProperties': {
+        'compilers:?': {  # optional colon for overriding site config.
+            'type': 'array',
+            'items': {
+                'compiler': {
+                    'type': 'object',
+                    'additionalProperties': False,
+                    'required': [
+                        'paths', 'spec', 'modules', 'operating_system'],
+                    'properties': {
+                        'paths': {
+                            'type': 'object',
+                            'required': ['cc', 'cxx', 'f77', 'fc'],
+                            'additionalProperties': False,
+                            'properties': {
+                                'cc':  {'anyOf': [{'type': 'string'},
+                                                  {'type': 'null'}]},
+                                'cxx': {'anyOf': [{'type': 'string'},
+                                                  {'type': 'null'}]},
+                                'f77': {'anyOf': [{'type': 'string'},
+                                                  {'type': 'null'}]},
+                                'fc':  {'anyOf': [{'type': 'string'},
+                                                  {'type': 'null'}]},
+                                'cflags': {'anyOf': [{'type': 'string'},
+                                                     {'type': 'null'}]},
+                                'cxxflags': {'anyOf': [{'type': 'string'},
+                                                       {'type': 'null'}]},
+                                'fflags': {'anyOf': [{'type': 'string'},
+                                                     {'type': 'null'}]},
+                                'cppflags': {'anyOf': [{'type': 'string'},
+                                                       {'type': 'null'}]},
+                                'ldflags': {'anyOf': [{'type': 'string'},
+                                                      {'type': 'null'}]},
+                                'ldlibs': {'anyOf': [{'type': 'string'},
+                                                     {'type': 'null'}]}}},
+                        'spec': {'type': 'string'},
+                        'operating_system': {'type': 'string'},
+                        'alias': {'anyOf': [{'type': 'string'},
+                                            {'type': 'null'}]},
+                        'modules': {'anyOf': [{'type': 'string'},
+                                              {'type': 'null'},
+                                              {'type': 'array'}]}
+                    },
+                },
+            },
+        },
+    },
+}
diff --git a/lib/spack/spack/schema/mirrors.py b/lib/spack/spack/schema/mirrors.py
new file mode 100644
index 0000000000..ff599b9c7d
--- /dev/null
+++ b/lib/spack/spack/schema/mirrors.py
@@ -0,0 +1,44 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+"""Schema for mirror configuration files."""
+
+
+schema = {
+    '$schema': 'http://json-schema.org/schema#',
+    'title': 'Spack mirror configuration file schema',
+    'type': 'object',
+    'additionalProperties': False,
+    'patternProperties': {
+        r'mirrors:?': {
+            'type': 'object',
+            'default': {},
+            'additionalProperties': False,
+            'patternProperties': {
+                r'\w[\w-]*': {
+                    'type': 'string'},
+            },
+        },
+    },
+}
diff --git a/lib/spack/spack/schema/modules.py b/lib/spack/spack/schema/modules.py
new file mode 100644
index 0000000000..f8066919f1
--- /dev/null
+++ b/lib/spack/spack/schema/modules.py
@@ -0,0 +1,158 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+"""Schema for mirror configuration files."""
+
+
+schema = {
+    '$schema': 'http://json-schema.org/schema#',
+    'title': 'Spack module file configuration file schema',
+    'type': 'object',
+    'additionalProperties': False,
+    'definitions': {
+        'array_of_strings': {
+            'type': 'array',
+            'default': [],
+            'items': {
+                'type': 'string'
+            }
+        },
+        'dictionary_of_strings': {
+            'type': 'object',
+            'patternProperties': {
+                r'\w[\w-]*': {  # key
+                    'type': 'string'
+                }
+            }
+        },
+        'dependency_selection': {
+            'type': 'string',
+            'enum': ['none', 'direct', 'all']
+        },
+        'module_file_configuration': {
+            'type': 'object',
+            'default': {},
+            'additionalProperties': False,
+            'properties': {
+                'filter': {
+                    'type': 'object',
+                    'default': {},
+                    'additionalProperties': False,
+                    'properties': {
+                        'environment_blacklist': {
+                            'type': 'array',
+                            'default': [],
+                            'items': {
+                                'type': 'string'
+                            }
+                        }
+                    }
+                },
+                'autoload': {
+                    '$ref': '#/definitions/dependency_selection'},
+                'prerequisites': {
+                    '$ref': '#/definitions/dependency_selection'},
+                'conflict': {
+                    '$ref': '#/definitions/array_of_strings'},
+                'load': {
+                    '$ref': '#/definitions/array_of_strings'},
+                'suffixes': {
+                    '$ref': '#/definitions/dictionary_of_strings'},
+                'environment': {
+                    'type': 'object',
+                    'default': {},
+                    'additionalProperties': False,
+                    'properties': {
+                        'set': {
+                            '$ref': '#/definitions/dictionary_of_strings'},
+                        'unset': {
+                            '$ref': '#/definitions/array_of_strings'},
+                        'prepend_path': {
+                            '$ref': '#/definitions/dictionary_of_strings'},
+                        'append_path': {
+                            '$ref': '#/definitions/dictionary_of_strings'}
+                    }
+                }
+            }
+        },
+        'module_type_configuration': {
+            'type': 'object',
+            'default': {},
+            'anyOf': [
+                {'properties': {
+                    'hash_length': {
+                        'type': 'integer',
+                        'minimum': 0,
+                        'default': 7
+                    },
+                    'whitelist': {
+                        '$ref': '#/definitions/array_of_strings'},
+                    'blacklist': {
+                        '$ref': '#/definitions/array_of_strings'},
+                    'naming_scheme': {
+                        'type': 'string'  # Can we be more specific here?
+                    }
+                }},
+                {'patternProperties': {
+                    r'\w[\w-]*': {
+                        '$ref': '#/definitions/module_file_configuration'
+                    }
+                }}
+            ]
+        }
+    },
+    'patternProperties': {
+        r'modules:?': {
+            'type': 'object',
+            'default': {},
+            'additionalProperties': False,
+            'properties': {
+                'prefix_inspections': {
+                    'type': 'object',
+                    'patternProperties': {
+                        # prefix-relative path to be inspected for existence
+                        r'\w[\w-]*': {
+                            '$ref': '#/definitions/array_of_strings'}}},
+                'enable': {
+                    'type': 'array',
+                    'default': [],
+                    'items': {
+                        'type': 'string',
+                        'enum': ['tcl', 'dotkit']}},
+                'tcl': {
+                    'allOf': [
+                        # Base configuration
+                        {'$ref': '#/definitions/module_type_configuration'},
+                        {}  # Specific tcl extensions
+                    ]},
+                'dotkit': {
+                    'allOf': [
+                        # Base configuration
+                        {'$ref': '#/definitions/module_type_configuration'},
+                        {}  # Specific dotkit extensions
+                    ]},
+            }
+        },
+    },
+}
diff --git a/lib/spack/spack/schema/packages.py b/lib/spack/spack/schema/packages.py
new file mode 100644
index 0000000000..e19f3f533b
--- /dev/null
+++ b/lib/spack/spack/schema/packages.py
@@ -0,0 +1,86 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+"""Schema for packages.yaml configuration files."""
+
+
+schema = {
+    '$schema': 'http://json-schema.org/schema#',
+    'title': 'Spack package configuration file schema',
+    'type': 'object',
+    'additionalProperties': False,
+    'patternProperties': {
+        r'packages:?': {
+            'type': 'object',
+            'default': {},
+            'additionalProperties': False,
+            'patternProperties': {
+                r'\w[\w-]*': {  # package name
+                    'type': 'object',
+                    'default': {},
+                    'additionalProperties': False,
+                    'properties': {
+                        'version': {
+                            'type': 'array',
+                            'default': [],
+                            # version strings
+                            'items': {'anyOf': [{'type': 'string'},
+                                                {'type': 'number'}]}},
+                        'compiler': {
+                            'type': 'array',
+                            'default': [],
+                            'items': {'type': 'string'}},  # compiler specs
+                        'buildable': {
+                            'type':  'boolean',
+                            'default': True,
+                        },
+                        'modules': {
+                            'type': 'object',
+                            'default': {},
+                        },
+                        'providers': {
+                            'type':  'object',
+                            'default': {},
+                            'additionalProperties': False,
+                            'patternProperties': {
+                                r'\w[\w-]*': {
+                                    'type': 'array',
+                                    'default': [],
+                                    'items': {'type': 'string'}, }, }, },
+                        'paths': {
+                            'type': 'object',
+                            'default': {},
+                        },
+                        'variants': {
+                            'oneOf': [
+                                {'type': 'string'},
+                                {'type': 'array',
+                                 'items': {'type': 'string'}}],
+                        },
+                    },
+                },
+            },
+        },
+    },
+}
diff --git a/lib/spack/spack/schema/repos.py b/lib/spack/spack/schema/repos.py
new file mode 100644
index 0000000000..9f01942422
--- /dev/null
+++ b/lib/spack/spack/schema/repos.py
@@ -0,0 +1,41 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+"""Schema for repository configuration files."""
+
+
+schema = {
+    '$schema': 'http://json-schema.org/schema#',
+    'title': 'Spack repository configuration file schema',
+    'type': 'object',
+    'additionalProperties': False,
+    'patternProperties': {
+        r'repos:?': {
+            'type': 'array',
+            'default': [],
+            'items': {
+                'type': 'string'},
+        },
+    },
+}
diff --git a/lib/spack/spack/schema/targets.py b/lib/spack/spack/schema/targets.py
new file mode 100644
index 0000000000..312474cab4
--- /dev/null
+++ b/lib/spack/spack/schema/targets.py
@@ -0,0 +1,45 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+"""Schema for target configuration files."""
+
+
+schema = {
+    '$schema': 'http://json-schema.org/schema#',
+    'title': 'Spack target configuration file schema',
+    'type': 'object',
+    'additionalProperties': False,
+    'patternProperties': {
+        r'targets:?': {
+            'type': 'object',
+            'default': {},
+            'additionalProperties': False,
+            'patternProperties': {
+                r'\w[\w-]*': {  # target name
+                    'type': 'string',
+                },
+            },
+        },
+    },
+}
diff --git a/lib/spack/spack/spec.py b/lib/spack/spack/spec.py
index e694f2b2da..0d72d454c6 100644
--- a/lib/spack/spack/spec.py
+++ b/lib/spack/spack/spec.py
@@ -95,32 +95,33 @@ thing.  Spack uses ~variant in directory names and in the canonical form of
 specs to avoid ambiguity.  Both are provided because ~ can cause shell
 expansion when it is the first character in an id typed on the command line.
 """
-import sys
-import hashlib
 import base64
+import hashlib
 import imp
+import sys
 from StringIO import StringIO
 from operator import attrgetter
+
 import yaml
 from yaml.error import MarkedYAMLError
 
 import llnl.util.tty as tty
+from llnl.util.filesystem import join_path
 from llnl.util.lang import *
 from llnl.util.tty.color import *
-from llnl.util.filesystem import join_path
 
 import spack
 import spack.architecture
-import spack.parse
-import spack.error
 import spack.compilers as compilers
-
-from spack.version import *
-from spack.util.string import *
-from spack.util.prefix import Prefix
-from spack.util.naming import mod_to_class
-from spack.virtual import ProviderIndex
+import spack.error
+import spack.parse
 from spack.build_environment import get_path_from_module, load_module
+from spack.util.naming import mod_to_class
+from spack.util.prefix import Prefix
+from spack.util.string import *
+from spack.version import *
+from spack.provider_index import ProviderIndex
+
 
 # Valid pattern for an identifier in Spack
 identifier_re = r'\w[\w-]*'
@@ -155,25 +156,17 @@ _any_version = VersionList([':'])
 # Special types of dependencies.
 alldeps = ('build', 'link', 'run')
 nolink = ('build', 'run')
-
-
-def index_specs(specs):
-    """Take a list of specs and return a dict of lists.  Dict is
-       keyed by spec name and lists include all specs with the
-       same name.
-    """
-    spec_dict = {}
-    for spec in specs:
-        if spec.name not in spec_dict:
-            spec_dict[spec.name] = []
-        spec_dict[spec.name].append(spec)
-    return spec_dict
+special_types = {
+    'alldeps': alldeps,
+    'nolink': nolink,
+}
 
 
 def colorize_spec(spec):
     """Returns a spec colorized according to the colors specified in
        color_formats."""
     class insert_color:
+
         def __init__(self):
             self.last = None
 
@@ -194,6 +187,7 @@ class CompilerSpec(object):
     """The CompilerSpec field represents the compiler or range of compiler
        versions that a package should be built with.  CompilerSpecs have a
        name and a version list. """
+
     def __init__(self, *args):
         nargs = len(args)
         if nargs == 1:
@@ -304,6 +298,7 @@ class DependencySpec(object):
     - spec: the spack.spec.Spec description of a dependency.
     - deptypes: strings representing the type of dependency this is.
     """
+
     def __init__(self, spec, deptypes):
         self.spec = spec
         self.deptypes = deptypes
@@ -325,6 +320,7 @@ class VariantSpec(object):
        on the particular package being built, and each named variant can
        be enabled or disabled.
     """
+
     def __init__(self, name, value):
         self.name = name
         self.value = value
@@ -449,16 +445,15 @@ class FlagMap(HashableMap):
         return clone
 
     def _cmp_key(self):
-        return ''.join(str(key) + ' '.join(str(v) for v in value)
-                       for key, value in sorted(self.items()))
+        return tuple((k, tuple(v)) for k, v in sorted(self.iteritems()))
 
     def __str__(self):
         sorted_keys = filter(
             lambda flag: self[flag] != [], sorted(self.keys()))
         cond_symbol = ' ' if len(sorted_keys) > 0 else ''
-        return cond_symbol + ' '.join(str(key) + '=\"' + ' '.join(str(f)
-                                      for f in self[key]) + '\"'
-                                      for key in sorted_keys)
+        return cond_symbol + ' '.join(
+            str(key) + '=\"' + ' '.join(
+                str(f) for f in self[key]) + '\"' for key in sorted_keys)
 
 
 class DependencyMap(HashableMap):
@@ -471,7 +466,7 @@ class DependencyMap(HashableMap):
 
     def __str__(self):
         return ''.join(
-            ["^" + str(self[name].spec) for name in sorted(self.keys())])
+            ["^" + self[name].format() for name in sorted(self.keys())])
 
 
 @key_ordering
@@ -542,7 +537,8 @@ class Spec(object):
             return alldeps
         # Force deptype to be a set object so that we can do set intersections.
         if isinstance(deptype, str):
-            return (deptype,)
+            # Support special deptypes.
+            return special_types.get(deptype, (deptype,))
         return deptype
 
     def _find_deps(self, where, deptype):
@@ -725,7 +721,7 @@ class Spec(object):
         """Internal package call gets only the class object for a package.
            Use this to just get package metadata.
         """
-        return spack.repo.get_pkg_class(self.name)
+        return spack.repo.get_pkg_class(self.fullname)
 
     @property
     def virtual(self):
@@ -871,7 +867,7 @@ class Spec(object):
             for name in sorted(successors):
                 child = successors[name]
                 children = child.spec.traverse_with_deptype(
-                    visited, d=d + 1, deptype=deptype_query,
+                    visited, d=d + 1, deptype=deptype,
                     deptype_query=deptype_query,
                     _self_deptype=child.deptypes, **kwargs)
                 for elt in children:
@@ -914,37 +910,36 @@ class Spec(object):
             return b32_hash
 
     def to_node_dict(self):
+        d = {}
+
         params = dict((name, v.value) for name, v in self.variants.items())
         params.update(dict((name, value)
-                      for name, value in self.compiler_flags.items()))
-        deps = self.dependencies_dict(deptype=('link', 'run'))
-        d = {
-            'parameters': params,
-            'arch': self.architecture,
-            'dependencies': dict(
+                           for name, value in self.compiler_flags.items()))
+
+        if params:
+            d['parameters'] = params
+
+        if self.dependencies():
+            deps = self.dependencies_dict(deptype=('link', 'run'))
+            d['dependencies'] = dict(
                 (name, {
                     'hash': dspec.spec.dag_hash(),
                     'type': [str(s) for s in dspec.deptypes]})
                 for name, dspec in deps.items())
-        }
 
-        # Older concrete specs do not have a namespace.  Omit for
-        # consistent hashing.
-        if not self.concrete or self.namespace:
+        if self.namespace:
             d['namespace'] = self.namespace
 
         if self.architecture:
             # TODO: Fix the target.to_dict to account for the tuple
             # Want it to be a dict of dicts
             d['arch'] = self.architecture.to_dict()
-        else:
-            d['arch'] = None
 
         if self.compiler:
             d.update(self.compiler.to_dict())
-        else:
-            d['compiler'] = None
-        d.update(self.versions.to_dict())
+
+        if self.versions:
+            d.update(self.versions.to_dict())
 
         return {self.name: d}
 
@@ -964,17 +959,18 @@ class Spec(object):
 
         spec = Spec(name)
         spec.namespace = node.get('namespace', None)
-        spec.versions = VersionList.from_dict(node)
+        spec._hash = node.get('hash', None)
 
-        if 'hash' in node:
-            spec._hash = node['hash']
+        if 'version' in node or 'versions' in node:
+            spec.versions = VersionList.from_dict(node)
 
-        spec.architecture = spack.architecture.arch_from_dict(node['arch'])
+        if 'arch' in node:
+            spec.architecture = spack.architecture.arch_from_dict(node['arch'])
 
-        if node['compiler'] is None:
-            spec.compiler = None
-        else:
+        if 'compiler' in node:
             spec.compiler = CompilerSpec.from_dict(node)
+        else:
+            spec.compiler = None
 
         if 'parameters' in node:
             for name, value in node['parameters'].items():
@@ -982,14 +978,12 @@ class Spec(object):
                     spec.compiler_flags[name] = value
                 else:
                     spec.variants[name] = VariantSpec(name, value)
+
         elif 'variants' in node:
             for name, value in node['variants'].items():
                 spec.variants[name] = VariantSpec(name, value)
             for name in FlagMap.valid_compiler_flags():
                 spec.compiler_flags[name] = []
-        else:
-            raise SpackRecordError(
-                "Did not find a valid format for variants in YAML file")
 
         # Don't read dependencies here; from_node_dict() is used by
         # from_yaml() to read the root *and* each dependency spec.
@@ -1031,7 +1025,7 @@ class Spec(object):
         """
         try:
             yfile = yaml.load(stream)
-        except MarkedYAMLError, e:
+        except MarkedYAMLError as e:
             raise SpackYAMLError("error parsing YAML spec:", str(e))
 
         nodes = yfile['spec']
@@ -1047,6 +1041,10 @@ class Spec(object):
         for node in nodes:
             # get dependency dict from the node.
             name = next(iter(node))
+
+            if 'dependencies' not in node[name]:
+                continue
+
             yaml_deps = node[name]['dependencies']
             for dname, dhash, dtypes in Spec.read_yaml_dep_specs(yaml_deps):
                 # Fill in dependencies by looking them up by name in deps dict
@@ -1345,7 +1343,7 @@ class Spec(object):
 
             return flat_deps
 
-        except UnsatisfiableSpecError, e:
+        except UnsatisfiableSpecError as e:
             # Here, the DAG contains two instances of the same package
             # with inconsistent constraints.  Users cannot produce
             # inconsistent specs like this on the command line: the
@@ -1380,7 +1378,7 @@ class Spec(object):
                     dep = Spec(name)
                 try:
                     dep.constrain(dep_spec)
-                except UnsatisfiableSpecError, e:
+                except UnsatisfiableSpecError as e:
                     e.message = ("Conflicting conditional dependencies on"
                                  "package %s for spec %s" % (self.name, self))
                     raise e
@@ -1466,7 +1464,7 @@ class Spec(object):
         try:
             changed |= spec_deps[dep.name].spec.constrain(dep)
 
-        except UnsatisfiableSpecError, e:
+        except UnsatisfiableSpecError as e:
             e.message = "Invalid spec: '%s'. "
             e.message += "Package %s requires %s %s, but spec asked for %s"
             e.message %= (spec_deps[dep.name].spec, dep.name,
@@ -1577,7 +1575,7 @@ class Spec(object):
            UnsupportedCompilerError.
         """
         for spec in self.traverse():
-            # Don't get a package for a virtual name.
+            # raise an UnknownPackageError if the spec's package isn't real.
             if (not spec.virtual) and spec.name:
                 spack.repo.get(spec.fullname)
 
@@ -1604,8 +1602,8 @@ class Spec(object):
             raise UnsatisfiableSpecNameError(self.name, other.name)
 
         if (other.namespace is not None and
-           self.namespace is not None and
-           other.namespace != self.namespace):
+                self.namespace is not None and
+                other.namespace != self.namespace):
             raise UnsatisfiableSpecNameError(self.fullname, other.fullname)
 
         if not self.versions.overlaps(other.versions):
@@ -1759,8 +1757,8 @@ class Spec(object):
 
         # namespaces either match, or other doesn't require one.
         if (other.namespace is not None and
-            self.namespace is not None and
-           self.namespace != other.namespace):
+                self.namespace is not None and
+                self.namespace != other.namespace):
             return False
         if self.versions and other.versions:
             if not self.versions.satisfies(other.versions, strict=strict):
@@ -1855,7 +1853,7 @@ class Spec(object):
         # compatible with mpich2)
         for spec in self.virtual_dependencies():
             if (spec.name in other_index and
-               not other_index.providers_for(spec)):
+                    not other_index.providers_for(spec)):
                 return False
 
         for spec in other.virtual_dependencies():
@@ -2351,6 +2349,7 @@ _lexer = SpecLexer()
 
 
 class SpecParser(spack.parse.Parser):
+
     def __init__(self):
         super(SpecParser, self).__init__(_lexer)
         self.previous = None
@@ -2400,7 +2399,7 @@ class SpecParser(spack.parse.Parser):
                     # errors now?
                     specs.append(self.spec(None, True))
 
-        except spack.parse.ParseError, e:
+        except spack.parse.ParseError as e:
             raise SpecParseError(e)
 
         # If the spec has an os or a target and no platform, give it
@@ -2834,15 +2833,9 @@ class SpackYAMLError(spack.error.SpackError):
         super(SpackYAMLError, self).__init__(msg, str(yaml_error))
 
 
-class SpackRecordError(spack.error.SpackError):
-
-    def __init__(self, msg):
-        super(SpackRecordError, self).__init__(msg)
-
-
 class AmbiguousHashError(SpecError):
 
     def __init__(self, msg, *specs):
         super(AmbiguousHashError, self).__init__(msg)
         for spec in specs:
-            print '    ', spec.format('$.$@$%@+$+$=$#')
+            print('    ', spec.format('$.$@$%@+$+$=$#'))
diff --git a/lib/spack/spack/stage.py b/lib/spack/spack/stage.py
index b08cce43b8..7676cb9ab6 100644
--- a/lib/spack/spack/stage.py
+++ b/lib/spack/spack/stage.py
@@ -37,6 +37,7 @@ import spack
 import spack.config
 import spack.fetch_strategy as fs
 import spack.error
+from spack.version import *
 
 STAGE_PREFIX = 'spack-stage-'
 
@@ -51,10 +52,12 @@ class Stage(object):
     lifecycle looks like this:
 
     ```
-    with Stage() as stage:      # Context manager creates and destroys the stage directory
+    with Stage() as stage:      # Context manager creates and destroys the
+                                # stage directory
         stage.fetch()           # Fetch a source archive into the stage.
         stage.expand_archive()  # Expand the source archive.
-        <install>               # Build and install the archive. (handled by user of Stage)
+        <install>               # Build and install the archive. (handled by
+                                # user of Stage)
     ```
 
     When used as a context manager, the stage is automatically
@@ -71,7 +74,8 @@ class Stage(object):
         stage.create()          # Explicitly create the stage directory.
         stage.fetch()           # Fetch a source archive into the stage.
         stage.expand_archive()  # Expand the source archive.
-        <install>               # Build and install the archive. (handled by user of Stage)
+        <install>               # Build and install the archive. (handled by
+                                # user of Stage)
     finally:
         stage.destroy()         # Explicitly destroy the stage directory.
     ```
@@ -120,13 +124,17 @@ class Stage(object):
         elif isinstance(url_or_fetch_strategy, fs.FetchStrategy):
             self.fetcher = url_or_fetch_strategy
         else:
-            raise ValueError("Can't construct Stage without url or fetch strategy")
+            raise ValueError(
+                "Can't construct Stage without url or fetch strategy")
         self.fetcher.set_stage(self)
-        self.default_fetcher = self.fetcher  # self.fetcher can change with mirrors.
-        self.skip_checksum_for_mirror = True  # used for mirrored archives of repositories.
+        # self.fetcher can change with mirrors.
+        self.default_fetcher = self.fetcher
+        # used for mirrored archives of repositories.
+        self.skip_checksum_for_mirror = True
 
-        # TODO : this uses a protected member of tempfile, but seemed the only way to get a temporary name
-        # TODO : besides, the temporary link name won't be the same as the temporary stage area in tmp_root
+        # TODO : this uses a protected member of tempfile, but seemed the only
+        # TODO : way to get a temporary name besides, the temporary link name
+        # TODO : won't be the same as the temporary stage area in tmp_root
         self.name = name
         if name is None:
             self.name = STAGE_PREFIX + next(tempfile._get_candidate_names())
@@ -143,7 +151,6 @@ class Stage(object):
         # Flag to decide whether to delete the stage folder on exit or not
         self.keep = keep
 
-
     def __enter__(self):
         """
         Entering a stage context will create the stage directory
@@ -154,7 +161,6 @@ class Stage(object):
         self.create()
         return self
 
-
     def __exit__(self, exc_type, exc_val, exc_tb):
         """
         Exiting from a stage context will delete the stage directory unless:
@@ -173,12 +179,10 @@ class Stage(object):
         if exc_type is None and not self.keep:
             self.destroy()
 
-
     def _need_to_create_path(self):
         """Makes sure nothing weird has happened since the last time we
            looked at path.  Returns True if path already exists and is ok.
-           Returns False if path needs to be created.
-        """
+           Returns False if path needs to be created."""
         # Path doesn't exist yet.  Will need to create it.
         if not os.path.exists(self.path):
             return True
@@ -196,7 +200,8 @@ class Stage(object):
             if spack.use_tmp_stage:
                 # If we're using a tmp dir, it's a link, and it points at the
                 # right spot, then keep it.
-                if (real_path.startswith(real_tmp) and os.path.exists(real_path)):
+                if (real_path.startswith(real_tmp) and
+                        os.path.exists(real_path)):
                     return False
                 else:
                     # otherwise, just unlink it and start over.
@@ -204,7 +209,8 @@ class Stage(object):
                     return True
 
             else:
-                # If we're not tmp mode, then it's a link and we want a directory.
+                # If we're not tmp mode, then it's a link and we want a
+                # directory.
                 os.unlink(self.path)
                 return True
 
@@ -215,10 +221,12 @@ class Stage(object):
         """Possible archive file paths."""
         paths = []
         if isinstance(self.fetcher, fs.URLFetchStrategy):
-            paths.append(os.path.join(self.path, os.path.basename(self.fetcher.url)))
+            paths.append(os.path.join(
+                self.path, os.path.basename(self.fetcher.url)))
 
         if self.mirror_path:
-            paths.append(os.path.join(self.path, os.path.basename(self.mirror_path)))
+            paths.append(os.path.join(
+                self.path, os.path.basename(self.mirror_path)))
 
         return paths
 
@@ -227,10 +235,12 @@ class Stage(object):
         """Path to the source archive within this stage directory."""
         paths = []
         if isinstance(self.fetcher, fs.URLFetchStrategy):
-            paths.append(os.path.join(self.path, os.path.basename(self.fetcher.url)))
+            paths.append(os.path.join(
+                self.path, os.path.basename(self.fetcher.url)))
 
         if self.mirror_path:
-            paths.append(os.path.join(self.path, os.path.basename(self.mirror_path)))
+            paths.append(os.path.join(
+                self.path, os.path.basename(self.mirror_path)))
 
         for path in paths:
             if os.path.exists(path):
@@ -262,7 +272,8 @@ class Stage(object):
         return None
 
     def chdir(self):
-        """Changes directory to the stage path.  Or dies if it is not set up."""
+        """Changes directory to the stage path. Or dies if it is not set
+        up."""
         if os.path.isdir(self.path):
             os.chdir(self.path)
         else:
@@ -304,7 +315,26 @@ class Stage(object):
             # Add URL strategies for all the mirrors with the digest
             for url in urls:
                 fetchers.insert(0, fs.URLFetchStrategy(url, digest))
-            fetchers.insert(0, spack.cache.fetcher(self.mirror_path, digest))
+            fetchers.insert(0, spack.fetch_cache.fetcher(self.mirror_path,
+                                                         digest))
+
+            # Look for the archive in list_url
+            package_name = os.path.dirname(self.mirror_path)
+            pkg = spack.repo.get(package_name)
+            if pkg.list_url is not None and pkg.url is not None:
+                try:
+                    archive_version = spack.url.parse_version(
+                        self.default_fetcher.url)
+                    versions = pkg.fetch_remote_versions()
+                    try:
+                        url_from_list = versions[Version(archive_version)]
+                        fetchers.append(fs.URLFetchStrategy(
+                            url_from_list, digest))
+                    except KeyError:
+                        tty.msg("Can not find version %s in url_list" %
+                                archive_version)
+                except:
+                    tty.msg("Could not determine url from list_url.")
 
         for fetcher in fetchers:
             try:
@@ -321,11 +351,11 @@ class Stage(object):
             self.fetcher = self.default_fetcher
             raise fs.FetchError(errMessage, None)
 
-
     def check(self):
         """Check the downloaded archive against a checksum digest.
            No-op if this stage checks code out of a repository."""
-        if self.fetcher is not self.default_fetcher and self.skip_checksum_for_mirror:
+        if self.fetcher is not self.default_fetcher and \
+           self.skip_checksum_for_mirror:
             tty.warn("Fetching from mirror without a checksum!",
                      "This package is normally checked out from a version "
                      "control system, but it has been archived on a spack "
@@ -335,16 +365,13 @@ class Stage(object):
         else:
             self.fetcher.check()
 
-
     def cache_local(self):
-        spack.cache.store(self.fetcher, self.mirror_path)
-
+        spack.fetch_cache.store(self.fetcher, self.mirror_path)
 
     def expand_archive(self):
         """Changes to the stage directory and attempt to expand the downloaded
-           archive.  Fail if the stage is not set up or if the archive is not yet
-           downloaded.
-        """
+        archive.  Fail if the stage is not set up or if the archive is not yet
+        downloaded."""
         archive_dir = self.source_path
         if not archive_dir:
             self.fetcher.expand()
@@ -386,8 +413,8 @@ class Stage(object):
         # Create the top-level stage directory
         mkdirp(spack.stage_path)
         remove_dead_links(spack.stage_path)
-        # If a tmp_root exists then create a directory there and then link it in the stage area,
-        # otherwise create the stage directory in self.path
+        # If a tmp_root exists then create a directory there and then link it
+        # in the stage area, otherwise create the stage directory in self.path
         if self._need_to_create_path():
             if self.tmp_root:
                 tmp_dir = tempfile.mkdtemp('', STAGE_PREFIX, self.tmp_root)
@@ -409,6 +436,7 @@ class Stage(object):
 
 
 class ResourceStage(Stage):
+
     def __init__(self, url_or_fetch_strategy, root, resource, **kwargs):
         super(ResourceStage, self).__init__(url_or_fetch_strategy, **kwargs)
         self.root_stage = root
@@ -418,12 +446,15 @@ class ResourceStage(Stage):
         super(ResourceStage, self).expand_archive()
         root_stage = self.root_stage
         resource = self.resource
-        placement = os.path.basename(self.source_path) if resource.placement is None else resource.placement
+        placement = os.path.basename(self.source_path) \
+            if resource.placement is None \
+            else resource.placement
         if not isinstance(placement, dict):
             placement = {'': placement}
         # Make the paths in the dictionary absolute and link
         for key, value in placement.iteritems():
-            target_path = join_path(root_stage.source_path, resource.destination)
+            target_path = join_path(
+                root_stage.source_path, resource.destination)
             destination_path = join_path(target_path, value)
             source_path = join_path(self.source_path, key)
 
@@ -437,21 +468,23 @@ class ResourceStage(Stage):
 
             if not os.path.exists(destination_path):
                 # Create a symlink
-                tty.info('Moving resource stage\n\tsource : {stage}\n\tdestination : {destination}'.format(
-                    stage=source_path, destination=destination_path
-                ))
+                tty.info('Moving resource stage\n\tsource : '
+                         '{stage}\n\tdestination : {destination}'.format(
+                             stage=source_path, destination=destination_path
+                         ))
                 shutil.move(source_path, destination_path)
 
 
-@pattern.composite(method_list=['fetch', 'create', 'check', 'expand_archive',  'restage', 'destroy', 'cache_local'])
+@pattern.composite(method_list=['fetch', 'create', 'check', 'expand_archive',
+                                'restage', 'destroy', 'cache_local'])
 class StageComposite:
-    """
-    Composite for Stage type objects. The first item in this composite is considered to be the root package, and
-    operations that return a value are forwarded to it.
-    """
+    """Composite for Stage type objects. The first item in this composite is
+    considered to be the root package, and operations that return a value are
+    forwarded to it."""
     #
     # __enter__ and __exit__ delegate to all stages in the composite.
     #
+
     def __enter__(self):
         for item in self:
             item.__enter__()
@@ -496,8 +529,11 @@ class DIYStage(object):
             raise ChdirError("Setup failed: no such directory: " + self.path)
 
     # DIY stages do nothing as context managers.
-    def __enter__(self): pass
-    def __exit__(self, exc_type, exc_val, exc_tb): pass
+    def __enter__(self):
+        pass
+
+    def __exit__(self, exc_type, exc_val, exc_tb):
+        pass
 
     def chdir_to_source(self):
         self.chdir()
diff --git a/lib/spack/spack/test/__init__.py b/lib/spack/spack/test/__init__.py
index a849d5f350..db683917b5 100644
--- a/lib/spack/spack/test/__init__.py
+++ b/lib/spack/spack/test/__init__.py
@@ -23,6 +23,7 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import sys
+import os
 
 import llnl.util.tty as tty
 import nose
@@ -32,16 +33,53 @@ from llnl.util.tty.colify import colify
 from spack.test.tally_plugin import Tally
 """Names of tests to be included in Spack's test suite"""
 
+# All the tests Spack knows about.
+# Keep these one per line so that it's easy to see changes in diffs.
 test_names = [
-    'architecture', 'versions', 'url_parse', 'url_substitution', 'packages',
-    'stage', 'spec_syntax', 'spec_semantics', 'spec_dag', 'concretize',
-    'multimethod', 'install', 'package_sanity', 'config', 'directory_layout',
-    'pattern', 'python_version', 'git_fetch', 'svn_fetch', 'hg_fetch',
-    'mirror', 'modules', 'url_extrapolate', 'cc', 'link_tree', 'spec_yaml',
-    'optional_deps', 'make_executable', 'build_system_guess', 'lock',
-    'database', 'namespace_trie', 'yaml', 'sbang', 'environment', 'cmd.find',
-    'cmd.uninstall', 'cmd.test_install', 'cmd.test_compiler_cmd',
-    'cmd.module'
+    'architecture',
+    'build_system_guess',
+    'cc',
+    'cmd.find',
+    'cmd.module',
+    'cmd.test_install',
+    'cmd.uninstall',
+    'concretize',
+    'concretize_preferences',
+    'config',
+    'database',
+    'directory_layout',
+    'environment',
+    'file_cache',
+    'git_fetch',
+    'hg_fetch',
+    'install',
+    'link_tree',
+    'lock',
+    'make_executable',
+    'mirror',
+    'modules',
+    'multimethod',
+    'namespace_trie',
+    'optional_deps',
+    'package_sanity',
+    'packages',
+    'pattern',
+    'python_version',
+    'sbang',
+    'spec_dag',
+    'spec_semantics',
+    'spec_syntax',
+    'spec_yaml',
+    'stage',
+    'svn_fetch',
+    'url_extrapolate',
+    'url_parse',
+    'url_substitution',
+    'versions',
+    'provider_index',
+    'yaml',
+    # This test needs to be last until global compiler cache is fixed.
+    'cmd.test_compiler_cmd',
 ]
 
 
@@ -53,6 +91,10 @@ def list_tests():
 def run(names, outputDir, verbose=False):
     """Run tests with the supplied names.  Names should be a list.  If
        it's empty, run ALL of Spack's tests."""
+    # Print output to stdout if verbose is 1.
+    if verbose:
+        os.environ['NOSE_NOCAPTURE'] = '1'
+
     if not names:
         names = test_names
     else:
diff --git a/lib/spack/spack/test/architecture.py b/lib/spack/spack/test/architecture.py
index 09bdb021af..22ddd4c97e 100644
--- a/lib/spack/spack/test/architecture.py
+++ b/lib/spack/spack/test/architecture.py
@@ -31,7 +31,7 @@ import platform as py_platform
 import spack
 import spack.architecture
 from spack.spec import *
-from spack.platforms.cray_xc import CrayXc
+from spack.platforms.cray import Cray
 from spack.platforms.linux import Linux
 from spack.platforms.bgq import Bgq
 from spack.platforms.darwin import Darwin
@@ -40,6 +40,7 @@ from spack.test.mock_packages_test import *
 
 
 class ArchitectureTest(MockPackagesTest):
+
     def setUp(self):
         super(ArchitectureTest, self).setUp()
         self.platform = spack.architecture.platform()
@@ -76,7 +77,7 @@ class ArchitectureTest(MockPackagesTest):
     def test_platform(self):
         output_platform_class = spack.architecture.platform()
         if os.path.exists('/opt/cray/craype'):
-            my_platform_class = CrayXc()
+            my_platform_class = Cray()
         elif os.path.exists('/bgsys'):
             my_platform_class = Bgq()
         elif 'Linux' in py_platform.system():
@@ -86,6 +87,29 @@ class ArchitectureTest(MockPackagesTest):
 
         self.assertEqual(str(output_platform_class), str(my_platform_class))
 
+    def test_boolness(self):
+        # Make sure architecture reports that it's False when nothing's set.
+        arch = spack.architecture.Arch()
+        self.assertFalse(arch)
+
+        # Dummy architecture parts
+        plat = spack.architecture.platform()
+        plat_os = plat.operating_system('default_os')
+        plat_target = plat.target('default_target')
+
+        # Make sure architecture reports that it's True when anything is set.
+        arch = spack.architecture.Arch()
+        arch.platform = plat
+        self.assertTrue(arch)
+
+        arch = spack.architecture.Arch()
+        arch.platform_os = plat_os
+        self.assertTrue(arch)
+
+        arch = spack.architecture.Arch()
+        arch.target = plat_target
+        self.assertTrue(arch)
+
     def test_user_front_end_input(self):
         """Test when user inputs just frontend that both the frontend target
             and frontend operating system match
diff --git a/lib/spack/spack/test/cc.py b/lib/spack/spack/test/cc.py
index ea2b164462..f3e4bb31d2 100644
--- a/lib/spack/spack/test/cc.py
+++ b/lib/spack/spack/test/cc.py
@@ -45,7 +45,8 @@ test_command = [
     '-llib1', '-llib2',
     'arg4',
     '-Wl,--end-group',
-    '-Xlinker', '-rpath', '-Xlinker', '/third/rpath', '-Xlinker', '-rpath', '-Xlinker', '/fourth/rpath',
+    '-Xlinker', '-rpath', '-Xlinker', '/third/rpath', '-Xlinker',
+    '-rpath', '-Xlinker', '/fourth/rpath',
     '-llib3', '-llib4',
     'arg5', 'arg6']
 
@@ -67,7 +68,7 @@ class CompilerTest(unittest.TestCase):
         os.environ['SPACK_FC'] = self.realcc
 
         os.environ['SPACK_PREFIX'] = self.prefix
-        os.environ['SPACK_ENV_PATH']="test"
+        os.environ['SPACK_ENV_PATH'] = "test"
         os.environ['SPACK_DEBUG_LOG_DIR'] = "."
         os.environ['SPACK_COMPILER_SPEC'] = "gcc@4.4.7"
         os.environ['SPACK_SHORT_SPEC'] = "foo@1.2"
@@ -97,16 +98,13 @@ class CompilerTest(unittest.TestCase):
         if 'SPACK_DEPENDENCIES' in os.environ:
             del os.environ['SPACK_DEPENDENCIES']
 
-
     def tearDown(self):
         shutil.rmtree(self.tmp_deps, True)
 
-
     def check_cc(self, command, args, expected):
         os.environ['SPACK_TEST_COMMAND'] = command
         self.assertEqual(self.cc(*args, output=str).strip(), expected)
 
-
     def check_cxx(self, command, args, expected):
         os.environ['SPACK_TEST_COMMAND'] = command
         self.assertEqual(self.cxx(*args, output=str).strip(), expected)
@@ -115,46 +113,46 @@ class CompilerTest(unittest.TestCase):
         os.environ['SPACK_TEST_COMMAND'] = command
         self.assertEqual(self.fc(*args, output=str).strip(), expected)
 
-
     def check_ld(self, command, args, expected):
         os.environ['SPACK_TEST_COMMAND'] = command
         self.assertEqual(self.ld(*args, output=str).strip(), expected)
 
-
     def check_cpp(self, command, args, expected):
         os.environ['SPACK_TEST_COMMAND'] = command
         self.assertEqual(self.cpp(*args, output=str).strip(), expected)
 
-
     def test_vcheck_mode(self):
         self.check_cc('dump-mode', ['-I/include', '--version'], "vcheck")
         self.check_cc('dump-mode', ['-I/include', '-V'], "vcheck")
         self.check_cc('dump-mode', ['-I/include', '-v'], "vcheck")
         self.check_cc('dump-mode', ['-I/include', '-dumpversion'], "vcheck")
         self.check_cc('dump-mode', ['-I/include', '--version', '-c'], "vcheck")
-        self.check_cc('dump-mode', ['-I/include', '-V', '-o', 'output'], "vcheck")
-
+        self.check_cc('dump-mode', ['-I/include',
+                                    '-V', '-o', 'output'], "vcheck")
 
     def test_cpp_mode(self):
         self.check_cc('dump-mode', ['-E'], "cpp")
         self.check_cpp('dump-mode', [], "cpp")
 
-
     def test_as_mode(self):
         self.check_cc('dump-mode', ['-S'], "as")
 
-
     def test_ccld_mode(self):
         self.check_cc('dump-mode', [], "ccld")
         self.check_cc('dump-mode', ['foo.c', '-o', 'foo'], "ccld")
-        self.check_cc('dump-mode', ['foo.c', '-o', 'foo', '-Wl,-rpath,foo'], "ccld")
-        self.check_cc('dump-mode', ['foo.o', 'bar.o', 'baz.o', '-o', 'foo', '-Wl,-rpath,foo'], "ccld")
-
+        self.check_cc('dump-mode', ['foo.c', '-o',
+                                    'foo', '-Wl,-rpath,foo'], "ccld")
+        self.check_cc(
+            'dump-mode',
+            ['foo.o', 'bar.o', 'baz.o', '-o', 'foo', '-Wl,-rpath,foo'],
+            "ccld")
 
     def test_ld_mode(self):
         self.check_ld('dump-mode', [], "ld")
-        self.check_ld('dump-mode', ['foo.o', 'bar.o', 'baz.o', '-o', 'foo', '-Wl,-rpath,foo'], "ld")
-
+        self.check_ld(
+            'dump-mode',
+            ['foo.o', 'bar.o', 'baz.o', '-o', 'foo', '-Wl,-rpath,foo'],
+            "ld")
 
     def test_flags(self):
         os.environ['SPACK_LDFLAGS'] = '-L foo'
@@ -176,10 +174,11 @@ class CompilerTest(unittest.TestCase):
         # Test cppflags added properly in cpp mode
         self.check_cpp('dump-args', test_command,
                        "cpp " +
-                      '-g -O1 ' +
-                      ' '.join(test_command))
+                       '-g -O1 ' +
+                       ' '.join(test_command))
 
-        # Test ldflags, cppflags, and language specific flags are added in proper order
+        # Test ldflags, cppflags, and language specific flags are added in
+        # proper order
         self.check_cc('dump-args', test_command,
                       self.realcc + ' ' +
                       '-Wl,-rpath,' + self.prefix + '/lib ' +
@@ -191,14 +190,14 @@ class CompilerTest(unittest.TestCase):
                       '-lfoo')
 
         self.check_cxx('dump-args', test_command,
-                      self.realcc + ' ' +
-                      '-Wl,-rpath,' + self.prefix + '/lib ' +
-                      '-Wl,-rpath,' + self.prefix + '/lib64 ' +
-                      '-g -O1 ' +
-                      '-Werror ' +
-                      '-L foo ' +
-                      ' '.join(test_command) + ' ' +
-                      '-lfoo')
+                       self.realcc + ' ' +
+                       '-Wl,-rpath,' + self.prefix + '/lib ' +
+                       '-Wl,-rpath,' + self.prefix + '/lib64 ' +
+                       '-g -O1 ' +
+                       '-Werror ' +
+                       '-L foo ' +
+                       ' '.join(test_command) + ' ' +
+                       '-lfoo')
 
         self.check_fc('dump-args', test_command,
                       self.realcc + ' ' +
@@ -210,9 +209,8 @@ class CompilerTest(unittest.TestCase):
                       ' '.join(test_command) + ' ' +
                       '-lfoo')
 
-        os.environ['SPACK_LDFLAGS']=''
-        os.environ['SPACK_LDLIBS']=''
-
+        os.environ['SPACK_LDFLAGS'] = ''
+        os.environ['SPACK_LDLIBS'] = ''
 
     def test_dep_rpath(self):
         """Ensure RPATHs for root package are added."""
@@ -222,7 +220,6 @@ class CompilerTest(unittest.TestCase):
                       '-Wl,-rpath,' + self.prefix + '/lib64 ' +
                       ' '.join(test_command))
 
-
     def test_dep_include(self):
         """Ensure a single dependency include directory is added."""
         os.environ['SPACK_DEPENDENCIES'] = self.dep4
@@ -233,7 +230,6 @@ class CompilerTest(unittest.TestCase):
                       '-I' + self.dep4 + '/include ' +
                       ' '.join(test_command))
 
-
     def test_dep_lib(self):
         """Ensure a single dependency RPATH is added."""
         os.environ['SPACK_DEPENDENCIES'] = self.dep2
@@ -245,7 +241,6 @@ class CompilerTest(unittest.TestCase):
                       '-Wl,-rpath,' + self.dep2 + '/lib64 ' +
                       ' '.join(test_command))
 
-
     def test_all_deps(self):
         """Ensure includes and RPATHs for all deps are added. """
         os.environ['SPACK_DEPENDENCIES'] = ':'.join([
@@ -274,7 +269,6 @@ class CompilerTest(unittest.TestCase):
 
                       ' '.join(test_command))
 
-
     def test_ld_deps(self):
         """Ensure no (extra) -I args or -Wl, are passed in ld mode."""
         os.environ['SPACK_DEPENDENCIES'] = ':'.join([
diff --git a/lib/spack/spack/test/cmd/module.py b/lib/spack/spack/test/cmd/module.py
index 36a4a73fe6..3a0ce32e6c 100644
--- a/lib/spack/spack/test/cmd/module.py
+++ b/lib/spack/spack/test/cmd/module.py
@@ -33,16 +33,17 @@ import spack.test.mock_database
 class TestModule(spack.test.mock_database.MockDatabase):
 
     def _get_module_files(self, args):
-        return [
-            modules.module_types[args.module_type](spec).file_name for spec in args.specs  # NOQA: ignore=E501
-        ]
+        return [modules.module_types[args.module_type](spec).file_name
+                for spec in args.specs]
 
     def test_module_common_operations(self):
         parser = argparse.ArgumentParser()
         module.setup_parser(parser)
+
         # Try to remove a non existing module [tcl]
         args = parser.parse_args(['rm', 'doesnotexist'])
         self.assertRaises(SystemExit, module.module, parser, args)
+
         # Remove existing modules [tcl]
         args = parser.parse_args(['rm', '-y', 'mpileaks'])
         module_files = self._get_module_files(args)
@@ -51,22 +52,28 @@ class TestModule(spack.test.mock_database.MockDatabase):
         module.module(parser, args)
         for item in module_files:
             self.assertFalse(os.path.exists(item))
+
         # Add them back [tcl]
         args = parser.parse_args(['refresh', '-y', 'mpileaks'])
         module.module(parser, args)
         for item in module_files:
             self.assertTrue(os.path.exists(item))
+
         # TODO : test the --delete-tree option
         # TODO : this requires having a separate directory for test modules
+
         # Try to find a module with multiple matches
         args = parser.parse_args(['find', 'mpileaks'])
         self.assertRaises(SystemExit, module.module, parser, args)
+
         # Try to find a module with no matches
         args = parser.parse_args(['find', 'doesnotexist'])
         self.assertRaises(SystemExit, module.module, parser, args)
+
         # Try to find a module
         args = parser.parse_args(['find', 'libelf'])
         module.module(parser, args)
+
         # Remove existing modules [dotkit]
         args = parser.parse_args(['rm', '-y', '-m', 'dotkit', 'mpileaks'])
         module_files = self._get_module_files(args)
@@ -75,6 +82,7 @@ class TestModule(spack.test.mock_database.MockDatabase):
         module.module(parser, args)
         for item in module_files:
             self.assertFalse(os.path.exists(item))
+
         # Add them back [dotkit]
         args = parser.parse_args(['refresh', '-y', '-m', 'dotkit', 'mpileaks'])
         module.module(parser, args)
diff --git a/lib/spack/spack/test/cmd/test_compiler_cmd.py b/lib/spack/spack/test/cmd/test_compiler_cmd.py
index d89814154b..fa806ee6f4 100644
--- a/lib/spack/spack/test/cmd/test_compiler_cmd.py
+++ b/lib/spack/spack/test/cmd/test_compiler_cmd.py
@@ -12,7 +12,9 @@ from spack.test.mock_packages_test import *
 
 test_version = '4.5-spacktest'
 
+
 class MockArgs(object):
+
     def __init__(self, add_paths=[], scope=None, compiler_spec=None, all=None):
         self.add_paths = add_paths
         self.scope = scope
@@ -52,14 +54,12 @@ done
 class CompilerCmdTest(MockPackagesTest):
     """ Test compiler commands for add and remove """
 
-
     def test_compiler_remove(self):
         args = MockArgs(all=True, compiler_spec='gcc@4.5.0')
         spack.cmd.compiler.compiler_remove(args)
         compilers = spack.compilers.all_compilers()
         self.assertTrue(spack.spec.CompilerSpec("gcc@4.5.0") not in compilers)
 
-
     def test_compiler_add(self):
         # compilers available by default.
         old_compilers = set(spack.compilers.all_compilers())
@@ -75,7 +75,8 @@ class CompilerCmdTest(MockPackagesTest):
             new_compilers = set(spack.compilers.all_compilers())
             new_compiler = new_compilers - old_compilers
             self.assertTrue(new_compiler)
-            self.assertTrue(new_compiler.pop().version == Version(test_version))
+            self.assertTrue(new_compiler.pop().version ==
+                            Version(test_version))
 
         finally:
             shutil.rmtree(compiler_dir, ignore_errors=True)
diff --git a/lib/spack/spack/test/cmd/test_install.py b/lib/spack/spack/test/cmd/test_install.py
index a94d3c8bba..39287d5d6d 100644
--- a/lib/spack/spack/test/cmd/test_install.py
+++ b/lib/spack/spack/test/cmd/test_install.py
@@ -22,18 +22,24 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
+import StringIO
 import collections
-from contextlib import contextmanager
+import os
+import unittest
+import contextlib
 
-import StringIO
+import spack
+import spack.cmd
 
 FILE_REGISTRY = collections.defaultdict(StringIO.StringIO)
 
+
 # Monkey-patch open to write module files to a StringIO instance
-@contextmanager
+@contextlib.contextmanager
 def mock_open(filename, mode):
     if not mode == 'wb':
-        raise RuntimeError('test.test_install : unexpected opening mode for monkey-patched open')
+        message = 'test.test_install : unexpected opening mode for mock_open'
+        raise RuntimeError(message)
 
     FILE_REGISTRY[filename] = StringIO.StringIO()
 
@@ -44,19 +50,14 @@ def mock_open(filename, mode):
         FILE_REGISTRY[filename] = handle.getvalue()
         handle.close()
 
-import os
-import itertools
-import unittest
-
-import spack
-import spack.cmd
 
-
-# The use of __import__ is necessary to maintain a name with hyphen (which cannot be an identifier in python)
+# The use of __import__ is necessary to maintain a name with hyphen (which
+# cannot be an identifier in python)
 test_install = __import__("spack.cmd.test-install", fromlist=['test_install'])
 
 
 class MockSpec(object):
+
     def __init__(self, name, version, hashStr=None):
         self._dependencies = {}
         self.name = name
@@ -88,10 +89,6 @@ class MockSpec(object):
         for _, spec in self._dependencies.items():
             yield spec.spec
         yield self
-        #from_iterable = itertools.chain.from_iterable
-        #allDeps = from_iterable(i.traverse()
-        #                        for i in self.dependencies())
-        #return set(itertools.chain([self], allDeps))
 
     def dag_hash(self):
         return self.hash
@@ -102,6 +99,7 @@ class MockSpec(object):
 
 
 class MockPackage(object):
+
     def __init__(self, spec, buildLogPath):
         self.name = spec.name
         self.spec = spec
@@ -113,6 +111,7 @@ class MockPackage(object):
 
 
 class MockPackageDb(object):
+
     def __init__(self, init=None):
         self.specToPkg = {}
         if init:
@@ -133,6 +132,7 @@ pkgY = MockPackage(specY, 'logY')
 
 
 class MockArgs(object):
+
     def __init__(self, package):
         self.package = package
         self.jobs = None
@@ -168,7 +168,7 @@ class TestInstallTest(unittest.TestCase):
         test_install.open = mock_open
 
         # Clean FILE_REGISTRY
-        FILE_REGISTRY = collections.defaultdict(StringIO.StringIO)
+        FILE_REGISTRY.clear()
 
         pkgX.installed = False
         pkgY.installed = False
@@ -194,7 +194,7 @@ class TestInstallTest(unittest.TestCase):
         spack.repo = self.saved_db
 
     def test_installing_both(self):
-        test_install.test_install(None, MockArgs('X') )
+        test_install.test_install(None, MockArgs('X'))
         self.assertEqual(len(FILE_REGISTRY), 1)
         for _, content in FILE_REGISTRY.items():
             self.assertTrue('tests="2"' in content)
@@ -210,4 +210,5 @@ class TestInstallTest(unittest.TestCase):
             self.assertTrue('tests="2"' in content)
             self.assertTrue('failures="0"' in content)
             self.assertTrue('errors="0"' in content)
-            self.assertEqual(sum('skipped' in line for line in content.split('\n')), 2)
+            self.assertEqual(
+                sum('skipped' in line for line in content.split('\n')), 2)
diff --git a/lib/spack/spack/test/cmd/uninstall.py b/lib/spack/spack/test/cmd/uninstall.py
index 9fffaace40..4ccb9ddbf4 100644
--- a/lib/spack/spack/test/cmd/uninstall.py
+++ b/lib/spack/spack/test/cmd/uninstall.py
@@ -28,6 +28,7 @@ from spack.cmd.uninstall import uninstall
 
 
 class MockArgs(object):
+
     def __init__(self, packages, all=False, force=False, dependents=False):
         self.packages = packages
         self.all = all
@@ -37,6 +38,7 @@ class MockArgs(object):
 
 
 class TestUninstall(spack.test.mock_database.MockDatabase):
+
     def test_uninstall(self):
         parser = None
         # Multiple matches
diff --git a/lib/spack/spack/test/concretize.py b/lib/spack/spack/test/concretize.py
index ae3ceecfc8..8ecbddbda2 100644
--- a/lib/spack/spack/test/concretize.py
+++ b/lib/spack/spack/test/concretize.py
@@ -29,6 +29,7 @@ from spack.version import ver
 from spack.concretize import find_spec
 from spack.test.mock_packages_test import *
 
+
 class ConcretizeTest(MockPackagesTest):
 
     def check_spec(self, abstract, concrete):
@@ -59,7 +60,6 @@ class ConcretizeTest(MockPackagesTest):
         if abstract.architecture and abstract.architecture.concrete:
             self.assertEqual(abstract.architecture, concrete.architecture)
 
-
     def check_concretize(self, abstract_spec):
         abstract = Spec(abstract_spec)
         concrete = abstract.concretized()
@@ -70,29 +70,24 @@ class ConcretizeTest(MockPackagesTest):
 
         return concrete
 
-
     def test_concretize_no_deps(self):
         self.check_concretize('libelf')
         self.check_concretize('libelf@0.8.13')
 
-
     def test_concretize_dag(self):
         self.check_concretize('callpath')
         self.check_concretize('mpileaks')
         self.check_concretize('libelf')
 
-
     def test_concretize_variant(self):
         self.check_concretize('mpich+debug')
         self.check_concretize('mpich~debug')
         self.check_concretize('mpich debug=2')
         self.check_concretize('mpich')
 
-
     def test_conretize_compiler_flags(self):
         self.check_concretize('mpich cppflags="-O3"')
 
-
     def test_concretize_preferred_version(self):
         spec = self.check_concretize('python')
         self.assertEqual(spec.versions, ver('2.7.11'))
@@ -100,7 +95,6 @@ class ConcretizeTest(MockPackagesTest):
         spec = self.check_concretize('python@3.5.1')
         self.assertEqual(spec.versions, ver('3.5.1'))
 
-
     def test_concretize_with_virtual(self):
         self.check_concretize('mpileaks ^mpi')
         self.check_concretize('mpileaks ^mpi@:1.1')
@@ -111,7 +105,6 @@ class ConcretizeTest(MockPackagesTest):
         self.check_concretize('mpileaks ^mpi@:1')
         self.check_concretize('mpileaks ^mpi@1.2:2')
 
-
     def test_concretize_with_restricted_virtual(self):
         self.check_concretize('mpileaks ^mpich2')
 
@@ -142,58 +135,55 @@ class ConcretizeTest(MockPackagesTest):
         concrete = self.check_concretize('mpileaks   ^mpich2@1.3.1:1.4')
         self.assertTrue(concrete['mpich2'].satisfies('mpich2@1.3.1:1.4'))
 
-
     def test_concretize_with_provides_when(self):
         """Make sure insufficient versions of MPI are not in providers list when
            we ask for some advanced version.
         """
-        self.assertTrue(not any(spec.satisfies('mpich2@:1.0')
-                                for spec in spack.repo.providers_for('mpi@2.1')))
-
-        self.assertTrue(not any(spec.satisfies('mpich2@:1.1')
-                                for spec in spack.repo.providers_for('mpi@2.2')))
-
-        self.assertTrue(not any(spec.satisfies('mpich2@:1.1')
-                                for spec in spack.repo.providers_for('mpi@2.2')))
+        self.assertTrue(
+            not any(spec.satisfies('mpich2@:1.0')
+                    for spec in spack.repo.providers_for('mpi@2.1')))
 
-        self.assertTrue(not any(spec.satisfies('mpich@:1')
-                                for spec in spack.repo.providers_for('mpi@2')))
+        self.assertTrue(
+            not any(spec.satisfies('mpich2@:1.1')
+                    for spec in spack.repo.providers_for('mpi@2.2')))
 
-        self.assertTrue(not any(spec.satisfies('mpich@:1')
-                                for spec in spack.repo.providers_for('mpi@3')))
+        self.assertTrue(
+            not any(spec.satisfies('mpich@:1')
+                    for spec in spack.repo.providers_for('mpi@2')))
 
-        self.assertTrue(not any(spec.satisfies('mpich2')
-                                for spec in spack.repo.providers_for('mpi@3')))
+        self.assertTrue(
+            not any(spec.satisfies('mpich@:1')
+                    for spec in spack.repo.providers_for('mpi@3')))
 
+        self.assertTrue(
+            not any(spec.satisfies('mpich2')
+                    for spec in spack.repo.providers_for('mpi@3')))
 
     def test_concretize_two_virtuals(self):
         """Test a package with multiple virtual dependencies."""
-        s = Spec('hypre').concretize()
-
+        Spec('hypre').concretize()
 
     def test_concretize_two_virtuals_with_one_bound(self):
         """Test a package with multiple virtual dependencies and one preset."""
-        s = Spec('hypre ^openblas').concretize()
-
+        Spec('hypre ^openblas').concretize()
 
     def test_concretize_two_virtuals_with_two_bound(self):
-        """Test a package with multiple virtual dependencies and two of them preset."""
-        s = Spec('hypre ^openblas ^netlib-lapack').concretize()
-
+        """Test a package with multiple virtual deps and two of them preset."""
+        Spec('hypre ^openblas ^netlib-lapack').concretize()
 
     def test_concretize_two_virtuals_with_dual_provider(self):
         """Test a package with multiple virtual dependencies and force a provider
            that provides both."""
-        s = Spec('hypre ^openblas-with-lapack').concretize()
-
+        Spec('hypre ^openblas-with-lapack').concretize()
 
     def test_concretize_two_virtuals_with_dual_provider_and_a_conflict(self):
-        """Test a package with multiple virtual dependencies and force a provider
-           that provides both, and another conflicting package that provides one."""
+        """Test a package with multiple virtual dependencies and force a
+           provider that provides both, and another conflicting package that
+           provides one.
+        """
         s = Spec('hypre ^openblas-with-lapack ^netlib-lapack')
         self.assertRaises(spack.spec.MultipleProviderError, s.concretize)
 
-
     def test_virtual_is_fully_expanded_for_callpath(self):
         # force dependence on fake "zmpi" by asking for MPI 10.0
         spec = Spec('callpath ^mpi@10.0')
@@ -210,7 +200,6 @@ class ConcretizeTest(MockPackagesTest):
 
         self.assertTrue('fake' in spec._dependencies['zmpi'].spec)
 
-
     def test_virtual_is_fully_expanded_for_mpileaks(self):
         spec = Spec('mpileaks ^mpi@10.0')
         self.assertTrue('mpi' in spec._dependencies)
@@ -220,23 +209,24 @@ class ConcretizeTest(MockPackagesTest):
 
         self.assertTrue('zmpi' in spec._dependencies)
         self.assertTrue('callpath' in spec._dependencies)
-        self.assertTrue('zmpi' in spec._dependencies['callpath'].
-                                  spec._dependencies)
-        self.assertTrue('fake' in spec._dependencies['callpath'].
-                                  spec._dependencies['zmpi'].
-                                  spec._dependencies)
-
-        self.assertTrue(all(not 'mpi' in d._dependencies for d in spec.traverse()))
+        self.assertTrue(
+            'zmpi' in spec._dependencies['callpath']
+            .spec._dependencies)
+        self.assertTrue(
+            'fake' in spec._dependencies['callpath']
+            .spec._dependencies['zmpi']
+            .spec._dependencies)
+
+        self.assertTrue(
+            all('mpi' not in d._dependencies for d in spec.traverse()))
         self.assertTrue('zmpi' in spec)
         self.assertTrue('mpi' in spec)
 
-
     def test_my_dep_depends_on_provider_of_my_virtual_dep(self):
         spec = Spec('indirect_mpich')
         spec.normalize()
         spec.concretize()
 
-
     def test_compiler_inheritance(self):
         spec = Spec('mpileaks')
         spec.normalize()
@@ -248,26 +238,26 @@ class ConcretizeTest(MockPackagesTest):
         self.assertTrue(spec['libdwarf'].compiler.satisfies('clang'))
         self.assertTrue(spec['libelf'].compiler.satisfies('clang'))
 
-
     def test_external_package(self):
         spec = Spec('externaltool%gcc')
         spec.concretize()
 
-        self.assertEqual(spec['externaltool'].external, '/path/to/external_tool')
+        self.assertEqual(
+            spec['externaltool'].external, '/path/to/external_tool')
         self.assertFalse('externalprereq' in spec)
         self.assertTrue(spec['externaltool'].compiler.satisfies('gcc'))
 
-
     def test_external_package_module(self):
         # No tcl modules on darwin/linux machines
         # TODO: improved way to check for this.
-        if (spack.architecture.platform().name == 'darwin' or
-            spack.architecture.platform().name == 'linux'):
+        platform = spack.architecture.platform().name
+        if (platform == 'darwin' or platform == 'linux'):
             return
 
         spec = Spec('externalmodule')
         spec.concretize()
-        self.assertEqual(spec['externalmodule'].external_module, 'external-module')
+        self.assertEqual(
+            spec['externalmodule'].external_module, 'external-module')
         self.assertFalse('externalprereq' in spec)
         self.assertTrue(spec['externalmodule'].compiler.satisfies('gcc'))
 
@@ -280,16 +270,16 @@ class ConcretizeTest(MockPackagesTest):
             got_error = True
         self.assertTrue(got_error)
 
-
     def test_external_and_virtual(self):
         spec = Spec('externaltest')
         spec.concretize()
-        self.assertEqual(spec['externaltool'].external, '/path/to/external_tool')
-        self.assertEqual(spec['stuff'].external, '/path/to/external_virtual_gcc')
+        self.assertEqual(
+            spec['externaltool'].external, '/path/to/external_tool')
+        self.assertEqual(
+            spec['stuff'].external, '/path/to/external_virtual_gcc')
         self.assertTrue(spec['externaltool'].compiler.satisfies('gcc'))
         self.assertTrue(spec['stuff'].compiler.satisfies('gcc'))
 
-
     def test_find_spec_parents(self):
         """Tests the spec finding logic used by concretization. """
         s = Spec('a +foo',
@@ -300,7 +290,6 @@ class ConcretizeTest(MockPackagesTest):
 
         self.assertEqual('a', find_spec(s['b'], lambda s: '+foo' in s).name)
 
-
     def test_find_spec_children(self):
         s = Spec('a',
                  Spec('b +foo',
@@ -315,7 +304,6 @@ class ConcretizeTest(MockPackagesTest):
                  Spec('e +foo'))
         self.assertEqual('c', find_spec(s['b'], lambda s: '+foo' in s).name)
 
-
     def test_find_spec_sibling(self):
         s = Spec('a',
                  Spec('b +foo',
@@ -333,7 +321,6 @@ class ConcretizeTest(MockPackagesTest):
                       Spec('f +foo')))
         self.assertEqual('f', find_spec(s['b'], lambda s: '+foo' in s).name)
 
-
     def test_find_spec_self(self):
         s = Spec('a',
                  Spec('b +foo',
@@ -342,7 +329,6 @@ class ConcretizeTest(MockPackagesTest):
                  Spec('e'))
         self.assertEqual('b', find_spec(s['b'], lambda s: '+foo' in s).name)
 
-
     def test_find_spec_none(self):
         s = Spec('a',
                  Spec('b',
@@ -351,7 +337,6 @@ class ConcretizeTest(MockPackagesTest):
                  Spec('e'))
         self.assertEqual(None, find_spec(s['b'], lambda s: '+foo' in s))
 
-
     def test_compiler_child(self):
         s = Spec('mpileaks%clang ^dyninst%gcc')
         s.concretize()
diff --git a/lib/spack/spack/test/concretize_preferences.py b/lib/spack/spack/test/concretize_preferences.py
new file mode 100644
index 0000000000..2c8bedc33f
--- /dev/null
+++ b/lib/spack/spack/test/concretize_preferences.py
@@ -0,0 +1,106 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+import spack
+import spack.architecture
+from spack.test.mock_packages_test import *
+from tempfile import mkdtemp
+
+
+class ConcretizePreferencesTest(MockPackagesTest):
+    """Test concretization preferences are being applied correctly.
+    """
+
+    def setUp(self):
+        """Create config section to store concretization preferences
+        """
+        super(ConcretizePreferencesTest, self).setUp()
+        self.tmp_dir = mkdtemp('.tmp', 'spack-config-test-')
+        spack.config.ConfigScope('concretize',
+                                 os.path.join(self.tmp_dir, 'concretize'))
+
+    def tearDown(self):
+        super(ConcretizePreferencesTest, self).tearDown()
+        shutil.rmtree(self.tmp_dir, True)
+        spack.pkgsort = spack.PreferredPackages()
+
+    def concretize(self, abstract_spec):
+        return Spec(abstract_spec).concretized()
+
+    def update_packages(self, pkgname, section, value):
+        """Update config and reread package list"""
+        conf = {pkgname: {section: value}}
+        spack.config.update_config('packages', conf, 'concretize')
+        spack.pkgsort = spack.PreferredPackages()
+
+    def assert_variant_values(self, spec, **variants):
+        concrete = self.concretize(spec)
+        for variant, value in variants.items():
+            self.assertEqual(concrete.variants[variant].value, value)
+
+    def test_preferred_variants(self):
+        """Test preferred variants are applied correctly
+        """
+        self.update_packages('mpileaks', 'variants',
+                             '~debug~opt+shared+static')
+        self.assert_variant_values('mpileaks', debug=False, opt=False,
+                                   shared=True, static=True)
+
+        self.update_packages('mpileaks', 'variants',
+                             ['+debug', '+opt', '~shared', '-static'])
+        self.assert_variant_values('mpileaks', debug=True, opt=True,
+                                   shared=False, static=False)
+
+    def test_preferred_compilers(self):
+        """Test preferred compilers are applied correctly
+        """
+        self.update_packages('mpileaks', 'compiler', ['clang@3.3'])
+        spec = self.concretize('mpileaks')
+        self.assertEqual(spec.compiler, spack.spec.CompilerSpec('clang@3.3'))
+
+        self.update_packages('mpileaks', 'compiler', ['gcc@4.5.0'])
+        spec = self.concretize('mpileaks')
+        self.assertEqual(spec.compiler, spack.spec.CompilerSpec('gcc@4.5.0'))
+
+    def test_preferred_versions(self):
+        """Test preferred package versions are applied correctly
+        """
+        self.update_packages('mpileaks', 'version', ['2.3'])
+        spec = self.concretize('mpileaks')
+        self.assertEqual(spec.version, spack.spec.Version('2.3'))
+
+        self.update_packages('mpileaks', 'version', ['2.2'])
+        spec = self.concretize('mpileaks')
+        self.assertEqual(spec.version, spack.spec.Version('2.2'))
+
+    def test_preferred_providers(self):
+        """Test preferred providers of virtual packages are applied correctly
+        """
+        self.update_packages('all', 'providers', {'mpi': ['mpich']})
+        spec = self.concretize('mpileaks')
+        self.assertTrue('mpich' in spec)
+
+        self.update_packages('all', 'providers', {'mpi': ['zmpi']})
+        spec = self.concretize('mpileaks')
+        self.assertTrue('zmpi', spec)
diff --git a/lib/spack/spack/test/config.py b/lib/spack/spack/test/config.py
index 252d77e66b..0822e44db8 100644
--- a/lib/spack/spack/test/config.py
+++ b/lib/spack/spack/test/config.py
@@ -32,79 +32,80 @@ from ordereddict_backport import OrderedDict
 from spack.test.mock_packages_test import *
 
 # Some sample compiler config data
-a_comps =  [
+a_comps = [
     {'compiler': {
         'paths': {
-            "cc" : "/gcc473",
+            "cc": "/gcc473",
             "cxx": "/g++473",
             "f77": None,
-            "fc" : None 
-            },
+            "fc": None
+        },
         'modules': None,
         'spec': 'gcc@4.7.3',
         'operating_system': 'CNL10'
-        }},
+    }},
     {'compiler': {
         'paths': {
-            "cc" : "/gcc450",
+            "cc": "/gcc450",
             "cxx": "/g++450",
             "f77": 'gfortran',
-            "fc" : 'gfortran'
-            },
+            "fc": 'gfortran'
+        },
         'modules': None,
         'spec': 'gcc@4.5.0',
         'operating_system': 'CNL10'
-        }},
+    }},
     {'compiler': {
         'paths': {
-            "cc" : "<overwritten>",
+            "cc": "<overwritten>",
             "cxx": "<overwritten>",
             "f77": '<overwritten>',
-            "fc" : '<overwritten>' },
+            "fc": '<overwritten>'},
         'modules': None,
         'spec': 'clang@3.3',
         'operating_system': 'CNL10'
-        }}
+    }}
 ]
 
 b_comps = [
     {'compiler': {
         'paths': {
-            "cc" : "/icc100",
+            "cc": "/icc100",
             "cxx": "/icp100",
             "f77": None,
-            "fc" : None
-            },
+            "fc": None
+        },
         'modules': None,
         'spec': 'icc@10.0',
         'operating_system': 'CNL10'
-        }},
+    }},
     {'compiler': {
         'paths': {
-            "cc" : "/icc111",
+            "cc": "/icc111",
             "cxx": "/icp111",
             "f77": 'ifort',
-            "fc" : 'ifort'
-            },
+            "fc": 'ifort'
+        },
         'modules': None,
         'spec': 'icc@11.1',
         'operating_system': 'CNL10'
-        }},
+    }},
     {'compiler': {
         'paths': {
-            "cc" : "<overwritten>",
+            "cc": "<overwritten>",
             "cxx": "<overwritten>",
             "f77": '<overwritten>',
-            "fc" : '<overwritten>' },
+            "fc": '<overwritten>'},
         'modules': None,
         'spec': 'clang@3.3',
         'operating_system': 'CNL10'
-        }}
+    }}
 ]
 
 # Some Sample repo data
-repos_low = [ "/some/path" ]
-repos_high = [ "/some/other/path" ]
+repos_low = ["/some/path"]
+repos_high = ["/some/other/path"]
+
 
 class ConfigTest(MockPackagesTest):
 
@@ -112,14 +113,15 @@ class ConfigTest(MockPackagesTest):
         super(ConfigTest, self).setUp()
         self.tmp_dir = mkdtemp('.tmp', 'spack-config-test-')
         spack.config.config_scopes = OrderedDict()
-        spack.config.ConfigScope('test_low_priority', os.path.join(self.tmp_dir, 'low'))
-        spack.config.ConfigScope('test_high_priority', os.path.join(self.tmp_dir, 'high'))
+        spack.config.ConfigScope(
+            'test_low_priority', os.path.join(self.tmp_dir, 'low'))
+        spack.config.ConfigScope('test_high_priority',
+                                 os.path.join(self.tmp_dir, 'high'))
 
     def tearDown(self):
         super(ConfigTest, self).tearDown()
         shutil.rmtree(self.tmp_dir, True)
 
-
     def check_config(self, comps, *compiler_names):
         """Check that named compilers in comps match Spack's config."""
         config = spack.config.get_config('compilers')
@@ -146,7 +148,7 @@ class ConfigTest(MockPackagesTest):
         spack.config.update_config('repos', repos_low, 'test_low_priority')
         spack.config.update_config('repos', repos_high, 'test_high_priority')
         config = spack.config.get_config('repos')
-        self.assertEqual(config, repos_high+repos_low)
+        self.assertEqual(config, repos_high + repos_low)
 
     def test_write_key_in_memory(self):
         # Write b_comps "on top of" a_comps.
@@ -157,7 +159,6 @@ class ConfigTest(MockPackagesTest):
         self.check_config(a_comps, 'gcc@4.7.3', 'gcc@4.5.0')
         self.check_config(b_comps, 'icc@10.0', 'icc@11.1', 'clang@3.3')
 
-
     def test_write_key_to_disk(self):
         # Write b_comps "on top of" a_comps.
         spack.config.update_config('compilers', a_comps, 'test_low_priority')
diff --git a/lib/spack/spack/test/database.py b/lib/spack/spack/test/database.py
index e1322f2081..22b1f17890 100644
--- a/lib/spack/spack/test/database.py
+++ b/lib/spack/spack/test/database.py
@@ -31,7 +31,6 @@ import multiprocessing
 
 import spack
 from llnl.util.filesystem import join_path
-from llnl.util.lock import *
 from llnl.util.tty.colify import colify
 from spack.test.mock_database import MockDatabase
 
@@ -72,6 +71,7 @@ def _print_ref_counts():
 
 
 class DatabaseTest(MockDatabase):
+
     def test_005_db_exists(self):
         """Make sure db cache file exists after creating."""
         index_file = join_path(self.install_path, '.spack-db', 'index.yaml')
@@ -88,26 +88,28 @@ class DatabaseTest(MockDatabase):
         # query specs with multiple configurations
         mpileaks_specs = [s for s in all_specs if s.satisfies('mpileaks')]
         callpath_specs = [s for s in all_specs if s.satisfies('callpath')]
-        mpi_specs =      [s for s in all_specs if s.satisfies('mpi')]
+        mpi_specs      = [s for s in all_specs if s.satisfies('mpi')]
 
         self.assertEqual(len(mpileaks_specs), 3)
         self.assertEqual(len(callpath_specs), 3)
         self.assertEqual(len(mpi_specs),      3)
 
         # query specs with single configurations
-        dyninst_specs =  [s for s in all_specs if s.satisfies('dyninst')]
+        dyninst_specs  = [s for s in all_specs if s.satisfies('dyninst')]
         libdwarf_specs = [s for s in all_specs if s.satisfies('libdwarf')]
-        libelf_specs =   [s for s in all_specs if s.satisfies('libelf')]
+        libelf_specs   = [s for s in all_specs if s.satisfies('libelf')]
 
         self.assertEqual(len(dyninst_specs),  1)
         self.assertEqual(len(libdwarf_specs), 1)
         self.assertEqual(len(libelf_specs),   1)
 
         # Query by dependency
-        self.assertEqual(len([s for s in all_specs if s.satisfies('mpileaks ^mpich')]),  1)
-        self.assertEqual(len([s for s in all_specs if s.satisfies('mpileaks ^mpich2')]), 1)
-        self.assertEqual(len([s for s in all_specs if s.satisfies('mpileaks ^zmpi')]),   1)
-
+        self.assertEqual(
+            len([s for s in all_specs if s.satisfies('mpileaks ^mpich')]), 1)
+        self.assertEqual(
+            len([s for s in all_specs if s.satisfies('mpileaks ^mpich2')]), 1)
+        self.assertEqual(
+            len([s for s in all_specs if s.satisfies('mpileaks ^zmpi')]), 1)
 
     def test_015_write_and_read(self):
         # write and read DB
@@ -122,7 +124,6 @@ class DatabaseTest(MockDatabase):
             self.assertEqual(new_rec.path,      rec.path)
             self.assertEqual(new_rec.installed, rec.installed)
 
-
     def _check_db_sanity(self):
         """Utiilty function to check db against install layout."""
         expected = sorted(spack.install_layout.all_specs())
@@ -132,12 +133,10 @@ class DatabaseTest(MockDatabase):
         for e, a in zip(expected, actual):
             self.assertEqual(e, a)
 
-
     def test_020_db_sanity(self):
         """Make sure query() returns what's actually in the db."""
         self._check_db_sanity()
 
-
     def test_030_db_sanity_from_another_process(self):
         def read_and_modify():
             self._check_db_sanity()  # check that other process can read DB
@@ -152,30 +151,28 @@ class DatabaseTest(MockDatabase):
         with self.installed_db.read_transaction():
             self.assertEqual(len(self.installed_db.query('mpileaks ^zmpi')), 0)
 
-
     def test_040_ref_counts(self):
         """Ensure that we got ref counts right when we read the DB."""
         self.installed_db._check_ref_counts()
 
-
     def test_050_basic_query(self):
-        """Ensure that querying the database is consistent with what is installed."""
+        """Ensure querying database is consistent with what is installed."""
         # query everything
         self.assertEqual(len(spack.installed_db.query()), 13)
 
         # query specs with multiple configurations
         mpileaks_specs = self.installed_db.query('mpileaks')
         callpath_specs = self.installed_db.query('callpath')
-        mpi_specs =      self.installed_db.query('mpi')
+        mpi_specs      = self.installed_db.query('mpi')
 
         self.assertEqual(len(mpileaks_specs), 3)
         self.assertEqual(len(callpath_specs), 3)
         self.assertEqual(len(mpi_specs),      3)
 
         # query specs with single configurations
-        dyninst_specs =  self.installed_db.query('dyninst')
+        dyninst_specs  = self.installed_db.query('dyninst')
         libdwarf_specs = self.installed_db.query('libdwarf')
-        libelf_specs =   self.installed_db.query('libelf')
+        libelf_specs   = self.installed_db.query('libelf')
 
         self.assertEqual(len(dyninst_specs),  1)
         self.assertEqual(len(libdwarf_specs), 1)
@@ -186,7 +183,6 @@ class DatabaseTest(MockDatabase):
         self.assertEqual(len(self.installed_db.query('mpileaks ^mpich2')), 1)
         self.assertEqual(len(self.installed_db.query('mpileaks ^zmpi')),   1)
 
-
     def _check_remove_and_add_package(self, spec):
         """Remove a spec from the DB, then add it and make sure everything's
            still ok once it is added.  This checks that it was
@@ -215,15 +211,12 @@ class DatabaseTest(MockDatabase):
         self._check_db_sanity()
         self.installed_db._check_ref_counts()
 
-
     def test_060_remove_and_add_root_package(self):
         self._check_remove_and_add_package('mpileaks ^mpich')
 
-
     def test_070_remove_and_add_dependency_package(self):
         self._check_remove_and_add_package('dyninst')
 
-
     def test_080_root_ref_counts(self):
         rec = self.installed_db.get_record('mpileaks ^mpich')
 
@@ -231,45 +224,89 @@ class DatabaseTest(MockDatabase):
         self.installed_db.remove('mpileaks ^mpich')
 
         # record no longer in DB
-        self.assertEqual(self.installed_db.query('mpileaks ^mpich', installed=any), [])
+        self.assertEqual(
+            self.installed_db.query('mpileaks ^mpich', installed=any), [])
 
         # record's deps have updated ref_counts
-        self.assertEqual(self.installed_db.get_record('callpath ^mpich').ref_count, 0)
+        self.assertEqual(
+            self.installed_db.get_record('callpath ^mpich').ref_count, 0)
         self.assertEqual(self.installed_db.get_record('mpich').ref_count, 1)
 
-        # put the spec back
+        # Put the spec back
         self.installed_db.add(rec.spec, rec.path)
 
         # record is present again
-        self.assertEqual(len(self.installed_db.query('mpileaks ^mpich', installed=any)), 1)
+        self.assertEqual(
+            len(self.installed_db.query('mpileaks ^mpich', installed=any)), 1)
 
         # dependencies have ref counts updated
-        self.assertEqual(self.installed_db.get_record('callpath ^mpich').ref_count, 1)
+        self.assertEqual(
+            self.installed_db.get_record('callpath ^mpich').ref_count, 1)
         self.assertEqual(self.installed_db.get_record('mpich').ref_count, 2)
 
-
     def test_090_non_root_ref_counts(self):
-        mpileaks_mpich_rec = self.installed_db.get_record('mpileaks ^mpich')
-        callpath_mpich_rec = self.installed_db.get_record('callpath ^mpich')
+        self.installed_db.get_record('mpileaks ^mpich')
+        self.installed_db.get_record('callpath ^mpich')
 
         # "force remove" a non-root spec from the DB
         self.installed_db.remove('callpath ^mpich')
 
         # record still in DB but marked uninstalled
-        self.assertEqual(self.installed_db.query('callpath ^mpich', installed=True), [])
-        self.assertEqual(len(self.installed_db.query('callpath ^mpich', installed=any)), 1)
+        self.assertEqual(
+            self.installed_db.query('callpath ^mpich', installed=True), [])
+        self.assertEqual(
+            len(self.installed_db.query('callpath ^mpich', installed=any)), 1)
 
         # record and its deps have same ref_counts
-        self.assertEqual(self.installed_db.get_record('callpath ^mpich', installed=any).ref_count, 1)
+        self.assertEqual(self.installed_db.get_record(
+            'callpath ^mpich', installed=any).ref_count, 1)
         self.assertEqual(self.installed_db.get_record('mpich').ref_count, 2)
 
         # remove only dependent of uninstalled callpath record
         self.installed_db.remove('mpileaks ^mpich')
 
         # record and parent are completely gone.
-        self.assertEqual(self.installed_db.query('mpileaks ^mpich', installed=any), [])
-        self.assertEqual(self.installed_db.query('callpath ^mpich', installed=any), [])
+        self.assertEqual(
+            self.installed_db.query('mpileaks ^mpich', installed=any), [])
+        self.assertEqual(
+            self.installed_db.query('callpath ^mpich', installed=any), [])
 
         # mpich ref count updated properly.
         mpich_rec = self.installed_db.get_record('mpich')
         self.assertEqual(mpich_rec.ref_count, 0)
+
+    def test_100_no_write_with_exception_on_remove(self):
+        def fail_while_writing():
+            with self.installed_db.write_transaction():
+                self._mock_remove('mpileaks ^zmpi')
+                raise Exception()
+
+        with self.installed_db.read_transaction():
+            self.assertEqual(
+                len(self.installed_db.query('mpileaks ^zmpi', installed=any)),
+                1)
+
+        self.assertRaises(Exception, fail_while_writing)
+
+        # reload DB and make sure zmpi is still there.
+        with self.installed_db.read_transaction():
+            self.assertEqual(
+                len(self.installed_db.query('mpileaks ^zmpi', installed=any)),
+                1)
+
+    def test_110_no_write_with_exception_on_install(self):
+        def fail_while_writing():
+            with self.installed_db.write_transaction():
+                self._mock_install('cmake')
+                raise Exception()
+
+        with self.installed_db.read_transaction():
+            self.assertEqual(
+                self.installed_db.query('cmake', installed=any), [])
+
+        self.assertRaises(Exception, fail_while_writing)
+
+        # reload DB and make sure cmake was not written.
+        with self.installed_db.read_transaction():
+            self.assertEqual(
+                self.installed_db.query('cmake', installed=any), [])
diff --git a/lib/spack/spack/test/directory_layout.py b/lib/spack/spack/test/directory_layout.py
index 74669fe8a2..2d0565acae 100644
--- a/lib/spack/spack/test/directory_layout.py
+++ b/lib/spack/spack/test/directory_layout.py
@@ -49,13 +49,11 @@ class DirectoryLayoutTest(MockPackagesTest):
         self.tmpdir = tempfile.mkdtemp()
         self.layout = YamlDirectoryLayout(self.tmpdir)
 
-
     def tearDown(self):
         super(DirectoryLayoutTest, self).tearDown()
         shutil.rmtree(self.tmpdir, ignore_errors=True)
         self.layout = None
 
-
     def test_read_and_write_spec(self):
         """This goes through each package in spack and creates a directory for
            it.  It then ensures that the spec for the directory's
@@ -67,8 +65,8 @@ class DirectoryLayoutTest(MockPackagesTest):
 
         for pkg in packages:
             if pkg.name.startswith('external'):
-                #External package tests cannot be installed
-                continue            
+                # External package tests cannot be installed
+                continue
             spec = pkg.spec
 
             # If a spec fails to concretize, just skip it.  If it is a
@@ -115,7 +113,6 @@ class DirectoryLayoutTest(MockPackagesTest):
             self.assertFalse(os.path.isdir(install_dir))
             self.assertFalse(os.path.exists(install_dir))
 
-
     def test_handle_unknown_package(self):
         """This test ensures that spack can at least do *some*
            operations with packages that are installed but that it
@@ -166,7 +163,6 @@ class DirectoryLayoutTest(MockPackagesTest):
 
         spack.repo.swap(mock_db)
 
-
     def test_find(self):
         """Test that finding specs within an install layout works."""
         packages = list(spack.repo.all_packages())[:max_packages]
@@ -175,13 +171,14 @@ class DirectoryLayoutTest(MockPackagesTest):
         installed_specs = {}
         for pkg in packages:
             if pkg.name.startswith('external'):
-                #External package tests cannot be installed
+                # External package tests cannot be installed
                 continue
             spec = pkg.spec.concretized()
             installed_specs[spec.name] = spec
             self.layout.create_install_directory(spec)
 
-        # Make sure all the installed specs appear in DirectoryLayout.all_specs()
+        # Make sure all the installed specs appear in
+        # DirectoryLayout.all_specs()
         found_specs = dict((s.name, s) for s in self.layout.all_specs())
         for name, spec in found_specs.items():
             self.assertTrue(name in found_specs)
diff --git a/lib/spack/spack/test/environment.py b/lib/spack/spack/test/environment.py
index 2396961888..9b5d75f273 100644
--- a/lib/spack/spack/test/environment.py
+++ b/lib/spack/spack/test/environment.py
@@ -38,7 +38,8 @@ class EnvironmentTest(unittest.TestCase):
         os.environ['UNSET_ME'] = 'foo'
         os.environ['EMPTY_PATH_LIST'] = ''
         os.environ['PATH_LIST'] = '/path/second:/path/third'
-        os.environ['REMOVE_PATH_LIST'] = '/a/b:/duplicate:/a/c:/remove/this:/a/d:/duplicate/:/f/g'  # NOQA: ignore=E501
+        os.environ['REMOVE_PATH_LIST'] = \
+            '/a/b:/duplicate:/a/c:/remove/this:/a/d:/duplicate/:/f/g'
 
     def tearDown(self):
         pass
diff --git a/lib/spack/spack/test/file_cache.py b/lib/spack/spack/test/file_cache.py
new file mode 100644
index 0000000000..cc66beda2e
--- /dev/null
+++ b/lib/spack/spack/test/file_cache.py
@@ -0,0 +1,83 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+"""
+Test Spack's FileCache.
+"""
+import os
+import shutil
+import tempfile
+import unittest
+
+from spack.file_cache import FileCache
+
+
+class FileCacheTest(unittest.TestCase):
+    """Ensure that a file cache can properly write to a file and recover its
+       contents."""
+
+    def setUp(self):
+        self.scratch_dir = tempfile.mkdtemp()
+        self.cache = FileCache(self.scratch_dir)
+
+    def tearDown(self):
+        shutil.rmtree(self.scratch_dir)
+
+    def test_write_and_read_cache_file(self):
+        """Test writing then reading a cached file."""
+        with self.cache.write_transaction('test.yaml') as (old, new):
+            self.assertTrue(old is None)
+            self.assertTrue(new is not None)
+            new.write("foobar\n")
+
+        with self.cache.read_transaction('test.yaml') as stream:
+            text = stream.read()
+            self.assertEqual("foobar\n", text)
+
+    def test_remove(self):
+        """Test removing an entry from the cache."""
+        self.test_write_and_write_cache_file()
+
+        self.cache.remove('test.yaml')
+
+        self.assertFalse(os.path.exists(self.cache.cache_path('test.yaml')))
+        self.assertFalse(os.path.exists(self.cache._lock_path('test.yaml')))
+
+    def test_write_and_write_cache_file(self):
+        """Test two write transactions on a cached file."""
+        with self.cache.write_transaction('test.yaml') as (old, new):
+            self.assertTrue(old is None)
+            self.assertTrue(new is not None)
+            new.write("foobar\n")
+
+        with self.cache.write_transaction('test.yaml') as (old, new):
+            self.assertTrue(old is not None)
+            text = old.read()
+            self.assertEqual("foobar\n", text)
+            self.assertTrue(new is not None)
+            new.write("barbaz\n")
+
+        with self.cache.read_transaction('test.yaml') as stream:
+            text = stream.read()
+            self.assertEqual("barbaz\n", text)
diff --git a/lib/spack/spack/test/git_fetch.py b/lib/spack/spack/test/git_fetch.py
index 4de65760d7..0d1a8fe949 100644
--- a/lib/spack/spack/test/git_fetch.py
+++ b/lib/spack/spack/test/git_fetch.py
@@ -87,33 +87,29 @@ class GitFetchTest(MockPackagesTest):
 
             self.assert_rev(rev)
 
-
     def test_fetch_master(self):
         """Test a default git checkout with no commit or tag specified."""
         self.try_fetch('master', self.repo.r0_file, {
-            'git' : self.repo.path
+            'git': self.repo.path
         })
 
-
     def test_fetch_branch(self):
         """Test fetching a branch."""
         self.try_fetch(self.repo.branch, self.repo.branch_file, {
-            'git'    : self.repo.path,
-            'branch' : self.repo.branch
+            'git': self.repo.path,
+            'branch': self.repo.branch
         })
 
-
     def test_fetch_tag(self):
         """Test fetching a tag."""
         self.try_fetch(self.repo.tag, self.repo.tag_file, {
-            'git' : self.repo.path,
-            'tag' : self.repo.tag
+            'git': self.repo.path,
+            'tag': self.repo.tag
         })
 
-
     def test_fetch_commit(self):
         """Test fetching a particular commit."""
         self.try_fetch(self.repo.r1, self.repo.r1_file, {
-            'git'    : self.repo.path,
-            'commit' : self.repo.r1
+            'git': self.repo.path,
+            'commit': self.repo.r1
         })
diff --git a/lib/spack/spack/test/hg_fetch.py b/lib/spack/spack/test/hg_fetch.py
index 292ffba949..44af6730a1 100644
--- a/lib/spack/spack/test/hg_fetch.py
+++ b/lib/spack/spack/test/hg_fetch.py
@@ -83,17 +83,15 @@ class HgFetchTest(MockPackagesTest):
 
             self.assertEqual(self.repo.get_rev(), rev)
 
-
     def test_fetch_default(self):
         """Test a default hg checkout with no commit or tag specified."""
         self.try_fetch(self.repo.r1, self.repo.r1_file, {
-            'hg' : self.repo.path
+            'hg': self.repo.path
         })
 
-
     def test_fetch_rev0(self):
         """Test fetching a branch."""
         self.try_fetch(self.repo.r0, self.repo.r0_file, {
-            'hg'       : self.repo.path,
-            'revision' : self.repo.r0
+            'hg': self.repo.path,
+            'revision': self.repo.r0
         })
diff --git a/lib/spack/spack/test/install.py b/lib/spack/spack/test/install.py
index 390ec096a9..232d5aeeaf 100644
--- a/lib/spack/spack/test/install.py
+++ b/lib/spack/spack/test/install.py
@@ -55,7 +55,6 @@ class InstallTest(MockPackagesTest):
         spack.install_layout = YamlDirectoryLayout(self.tmpdir)
         spack.installed_db   = Database(self.tmpdir)
 
-
     def tearDown(self):
         super(InstallTest, self).tearDown()
         self.repo.destroy()
@@ -68,14 +67,12 @@ class InstallTest(MockPackagesTest):
         spack.installed_db   = self.orig_db
         shutil.rmtree(self.tmpdir, ignore_errors=True)
 
-
     def fake_fetchify(self, pkg):
         """Fake the URL for a package so it downloads from a file."""
         fetcher = FetchStrategyComposite()
         fetcher.append(URLFetchStrategy(self.repo.url))
         pkg.fetcher = fetcher
 
-
     def test_install_and_uninstall(self):
         # Get a basic concrete spec for the trivial install package.
         spec = Spec('trivial_install_test_package')
@@ -90,11 +87,10 @@ class InstallTest(MockPackagesTest):
         try:
             pkg.do_install()
             pkg.do_uninstall()
-        except Exception, e:
+        except Exception:
             pkg.remove_prefix()
             raise
 
-
     def test_install_environment(self):
         spec = Spec('cmake-client').concretized()
 
@@ -104,6 +100,6 @@ class InstallTest(MockPackagesTest):
         pkg = spec.package
         try:
             pkg.do_install()
-        except Exception, e:
+        except Exception:
             pkg.remove_prefix()
             raise
diff --git a/lib/spack/spack/test/link_tree.py b/lib/spack/spack/test/link_tree.py
index de40991b57..5d0a7430b6 100644
--- a/lib/spack/spack/test/link_tree.py
+++ b/lib/spack/spack/test/link_tree.py
@@ -53,16 +53,13 @@ class LinkTreeTest(unittest.TestCase):
     def tearDown(self):
         self.stage.destroy()
 
-
     def check_file_link(self, filename):
         self.assertTrue(os.path.isfile(filename))
         self.assertTrue(os.path.islink(filename))
 
-
     def check_dir(self, filename):
         self.assertTrue(os.path.isdir(filename))
 
-
     def test_merge_to_new_directory(self):
         with working_dir(self.stage.path):
             self.link_tree.merge('dest')
@@ -79,7 +76,6 @@ class LinkTreeTest(unittest.TestCase):
 
             self.assertFalse(os.path.exists('dest'))
 
-
     def test_merge_to_existing_directory(self):
         with working_dir(self.stage.path):
 
@@ -112,7 +108,6 @@ class LinkTreeTest(unittest.TestCase):
             self.assertFalse(os.path.isfile('dest/c/d/6'))
             self.assertFalse(os.path.isfile('dest/c/d/e/7'))
 
-
     def test_merge_with_empty_directories(self):
         with working_dir(self.stage.path):
             mkdirp('dest/f/g')
@@ -132,7 +127,6 @@ class LinkTreeTest(unittest.TestCase):
             self.assertTrue(os.path.isdir('dest/a/b/h'))
             self.assertTrue(os.path.isdir('dest/f/g'))
 
-
     def test_ignore(self):
         with working_dir(self.stage.path):
             touchp('source/.spec')
diff --git a/lib/spack/spack/test/lock.py b/lib/spack/spack/test/lock.py
index 0e9f6daf4d..fb96539897 100644
--- a/lib/spack/spack/test/lock.py
+++ b/lib/spack/spack/test/lock.py
@@ -46,21 +46,21 @@ class LockTest(unittest.TestCase):
         self.lock_path = join_path(self.tempdir, 'lockfile')
         touch(self.lock_path)
 
-
     def tearDown(self):
-         shutil.rmtree(self.tempdir, ignore_errors=True)
-
+        shutil.rmtree(self.tempdir, ignore_errors=True)
 
     def multiproc_test(self, *functions):
         """Order some processes using simple barrier synchronization."""
         b = Barrier(len(functions), timeout=barrier_timeout)
         procs = [Process(target=f, args=(b,)) for f in functions]
-        for p in procs: p.start()
+
+        for p in procs:
+            p.start()
+
         for p in procs:
             p.join()
             self.assertEqual(p.exitcode, 0)
 
-
     #
     # Process snippets below can be composed into tests.
     #
@@ -68,27 +68,26 @@ class LockTest(unittest.TestCase):
         lock = Lock(self.lock_path)
         lock.acquire_write()  # grab exclusive lock
         barrier.wait()
-        barrier.wait() # hold the lock until exception raises in other procs.
+        barrier.wait()  # hold the lock until exception raises in other procs.
 
     def acquire_read(self, barrier):
         lock = Lock(self.lock_path)
         lock.acquire_read()  # grab shared lock
         barrier.wait()
-        barrier.wait() # hold the lock until exception raises in other procs.
+        barrier.wait()  # hold the lock until exception raises in other procs.
 
     def timeout_write(self, barrier):
         lock = Lock(self.lock_path)
-        barrier.wait() # wait for lock acquire in first process
+        barrier.wait()  # wait for lock acquire in first process
         self.assertRaises(LockError, lock.acquire_write, 0.1)
         barrier.wait()
 
     def timeout_read(self, barrier):
         lock = Lock(self.lock_path)
-        barrier.wait() # wait for lock acquire in first process
+        barrier.wait()  # wait for lock acquire in first process
         self.assertRaises(LockError, lock.acquire_read, 0.1)
         barrier.wait()
 
-
     #
     # Test that exclusive locks on other processes time out when an
     # exclusive lock is held.
@@ -97,11 +96,13 @@ class LockTest(unittest.TestCase):
         self.multiproc_test(self.acquire_write, self.timeout_write)
 
     def test_write_lock_timeout_on_write_2(self):
-        self.multiproc_test(self.acquire_write, self.timeout_write, self.timeout_write)
+        self.multiproc_test(
+            self.acquire_write, self.timeout_write, self.timeout_write)
 
     def test_write_lock_timeout_on_write_3(self):
-        self.multiproc_test(self.acquire_write, self.timeout_write, self.timeout_write, self.timeout_write)
-
+        self.multiproc_test(
+            self.acquire_write, self.timeout_write, self.timeout_write,
+            self.timeout_write)
 
     #
     # Test that shared locks on other processes time out when an
@@ -111,11 +112,13 @@ class LockTest(unittest.TestCase):
         self.multiproc_test(self.acquire_write, self.timeout_read)
 
     def test_read_lock_timeout_on_write_2(self):
-        self.multiproc_test(self.acquire_write, self.timeout_read, self.timeout_read)
+        self.multiproc_test(
+            self.acquire_write, self.timeout_read, self.timeout_read)
 
     def test_read_lock_timeout_on_write_3(self):
-        self.multiproc_test(self.acquire_write, self.timeout_read, self.timeout_read, self.timeout_read)
-
+        self.multiproc_test(
+            self.acquire_write, self.timeout_read, self.timeout_read,
+            self.timeout_read)
 
     #
     # Test that exclusive locks time out when shared locks are held.
@@ -124,27 +127,35 @@ class LockTest(unittest.TestCase):
         self.multiproc_test(self.acquire_read, self.timeout_write)
 
     def test_write_lock_timeout_on_read_2(self):
-        self.multiproc_test(self.acquire_read, self.timeout_write, self.timeout_write)
+        self.multiproc_test(
+            self.acquire_read, self.timeout_write, self.timeout_write)
 
     def test_write_lock_timeout_on_read_3(self):
-        self.multiproc_test(self.acquire_read, self.timeout_write, self.timeout_write, self.timeout_write)
-
+        self.multiproc_test(
+            self.acquire_read, self.timeout_write, self.timeout_write,
+            self.timeout_write)
 
     #
     # Test that exclusive locks time while lots of shared locks are held.
     #
     def test_write_lock_timeout_with_multiple_readers_2_1(self):
-        self.multiproc_test(self.acquire_read, self.acquire_read, self.timeout_write)
+        self.multiproc_test(
+            self.acquire_read, self.acquire_read, self.timeout_write)
 
     def test_write_lock_timeout_with_multiple_readers_2_2(self):
-        self.multiproc_test(self.acquire_read, self.acquire_read, self.timeout_write, self.timeout_write)
+        self.multiproc_test(
+            self.acquire_read, self.acquire_read, self.timeout_write,
+            self.timeout_write)
 
     def test_write_lock_timeout_with_multiple_readers_3_1(self):
-        self.multiproc_test(self.acquire_read, self.acquire_read, self.acquire_read, self.timeout_write)
+        self.multiproc_test(
+            self.acquire_read, self.acquire_read, self.acquire_read,
+            self.timeout_write)
 
     def test_write_lock_timeout_with_multiple_readers_3_2(self):
-        self.multiproc_test(self.acquire_read, self.acquire_read, self.acquire_read, self.timeout_write, self.timeout_write)
-
+        self.multiproc_test(
+            self.acquire_read, self.acquire_read, self.acquire_read,
+            self.timeout_write, self.timeout_write)
 
     #
     # Longer test case that ensures locks are reusable. Ordering is
@@ -155,110 +166,283 @@ class LockTest(unittest.TestCase):
             lock = Lock(self.lock_path)
 
             lock.acquire_write()
-            barrier.wait() # ---------------------------------------- 1
+            barrier.wait()  # ---------------------------------------- 1
             # others test timeout
-            barrier.wait() # ---------------------------------------- 2
+            barrier.wait()  # ---------------------------------------- 2
             lock.release_write()   # release and others acquire read
-            barrier.wait() # ---------------------------------------- 3
+            barrier.wait()  # ---------------------------------------- 3
             self.assertRaises(LockError, lock.acquire_write, 0.1)
             lock.acquire_read()
-            barrier.wait() # ---------------------------------------- 4
+            barrier.wait()  # ---------------------------------------- 4
             lock.release_read()
-            barrier.wait() # ---------------------------------------- 5
+            barrier.wait()  # ---------------------------------------- 5
 
             # p2 upgrades read to write
-            barrier.wait() # ---------------------------------------- 6
+            barrier.wait()  # ---------------------------------------- 6
             self.assertRaises(LockError, lock.acquire_write, 0.1)
             self.assertRaises(LockError, lock.acquire_read, 0.1)
-            barrier.wait() # ---------------------------------------- 7
+            barrier.wait()  # ---------------------------------------- 7
             # p2 releases write and read
-            barrier.wait() # ---------------------------------------- 8
+            barrier.wait()  # ---------------------------------------- 8
 
             # p3 acquires read
-            barrier.wait() # ---------------------------------------- 9
+            barrier.wait()  # ---------------------------------------- 9
             # p3 upgrades read to write
-            barrier.wait() # ---------------------------------------- 10
+            barrier.wait()  # ---------------------------------------- 10
             self.assertRaises(LockError, lock.acquire_write, 0.1)
             self.assertRaises(LockError, lock.acquire_read, 0.1)
-            barrier.wait() # ---------------------------------------- 11
+            barrier.wait()  # ---------------------------------------- 11
             # p3 releases locks
-            barrier.wait() # ---------------------------------------- 12
+            barrier.wait()  # ---------------------------------------- 12
             lock.acquire_read()
-            barrier.wait() # ---------------------------------------- 13
+            barrier.wait()  # ---------------------------------------- 13
             lock.release_read()
 
-
         def p2(barrier):
             lock = Lock(self.lock_path)
 
             # p1 acquires write
-            barrier.wait() # ---------------------------------------- 1
+            barrier.wait()  # ---------------------------------------- 1
             self.assertRaises(LockError, lock.acquire_write, 0.1)
             self.assertRaises(LockError, lock.acquire_read, 0.1)
-            barrier.wait() # ---------------------------------------- 2
+            barrier.wait()  # ---------------------------------------- 2
             lock.acquire_read()
-            barrier.wait() # ---------------------------------------- 3
+            barrier.wait()  # ---------------------------------------- 3
             # p1 tests shared read
-            barrier.wait() # ---------------------------------------- 4
+            barrier.wait()  # ---------------------------------------- 4
             # others release reads
-            barrier.wait() # ---------------------------------------- 5
+            barrier.wait()  # ---------------------------------------- 5
 
-            lock.acquire_write() # upgrade read to write
-            barrier.wait() # ---------------------------------------- 6
+            lock.acquire_write()  # upgrade read to write
+            barrier.wait()  # ---------------------------------------- 6
             # others test timeout
-            barrier.wait() # ---------------------------------------- 7
+            barrier.wait()  # ---------------------------------------- 7
             lock.release_write()  # release read AND write (need both)
             lock.release_read()
-            barrier.wait() # ---------------------------------------- 8
+            barrier.wait()  # ---------------------------------------- 8
 
             # p3 acquires read
-            barrier.wait() # ---------------------------------------- 9
+            barrier.wait()  # ---------------------------------------- 9
             # p3 upgrades read to write
-            barrier.wait() # ---------------------------------------- 10
+            barrier.wait()  # ---------------------------------------- 10
             self.assertRaises(LockError, lock.acquire_write, 0.1)
             self.assertRaises(LockError, lock.acquire_read, 0.1)
-            barrier.wait() # ---------------------------------------- 11
+            barrier.wait()  # ---------------------------------------- 11
             # p3 releases locks
-            barrier.wait() # ---------------------------------------- 12
+            barrier.wait()  # ---------------------------------------- 12
             lock.acquire_read()
-            barrier.wait() # ---------------------------------------- 13
+            barrier.wait()  # ---------------------------------------- 13
             lock.release_read()
 
-
         def p3(barrier):
             lock = Lock(self.lock_path)
 
             # p1 acquires write
-            barrier.wait() # ---------------------------------------- 1
+            barrier.wait()  # ---------------------------------------- 1
             self.assertRaises(LockError, lock.acquire_write, 0.1)
             self.assertRaises(LockError, lock.acquire_read, 0.1)
-            barrier.wait() # ---------------------------------------- 2
+            barrier.wait()  # ---------------------------------------- 2
             lock.acquire_read()
-            barrier.wait() # ---------------------------------------- 3
+            barrier.wait()  # ---------------------------------------- 3
             # p1 tests shared read
-            barrier.wait() # ---------------------------------------- 4
+            barrier.wait()  # ---------------------------------------- 4
             lock.release_read()
-            barrier.wait() # ---------------------------------------- 5
+            barrier.wait()  # ---------------------------------------- 5
 
             # p2 upgrades read to write
-            barrier.wait() # ---------------------------------------- 6
+            barrier.wait()  # ---------------------------------------- 6
             self.assertRaises(LockError, lock.acquire_write, 0.1)
             self.assertRaises(LockError, lock.acquire_read, 0.1)
-            barrier.wait() # ---------------------------------------- 7
+            barrier.wait()  # ---------------------------------------- 7
             # p2 releases write & read
-            barrier.wait() # ---------------------------------------- 8
+            barrier.wait()  # ---------------------------------------- 8
 
             lock.acquire_read()
-            barrier.wait() # ---------------------------------------- 9
+            barrier.wait()  # ---------------------------------------- 9
             lock.acquire_write()
-            barrier.wait() # ---------------------------------------- 10
+            barrier.wait()  # ---------------------------------------- 10
             # others test timeout
-            barrier.wait() # ---------------------------------------- 11
+            barrier.wait()  # ---------------------------------------- 11
             lock.release_read()   # release read AND write in opposite
             lock.release_write()  # order from before on p2
-            barrier.wait() # ---------------------------------------- 12
+            barrier.wait()  # ---------------------------------------- 12
             lock.acquire_read()
-            barrier.wait() # ---------------------------------------- 13
+            barrier.wait()  # ---------------------------------------- 13
             lock.release_read()
 
         self.multiproc_test(p1, p2, p3)
+
+    def test_transaction(self):
+        def enter_fn():
+            vals['entered'] = True
+
+        def exit_fn(t, v, tb):
+            vals['exited'] = True
+            vals['exception'] = (t or v or tb)
+
+        lock = Lock(self.lock_path)
+        vals = {'entered': False, 'exited': False, 'exception': False}
+        with ReadTransaction(lock, enter_fn, exit_fn):
+            pass
+
+        self.assertTrue(vals['entered'])
+        self.assertTrue(vals['exited'])
+        self.assertFalse(vals['exception'])
+
+        vals = {'entered': False, 'exited': False, 'exception': False}
+        with WriteTransaction(lock, enter_fn, exit_fn):
+            pass
+
+        self.assertTrue(vals['entered'])
+        self.assertTrue(vals['exited'])
+        self.assertFalse(vals['exception'])
+
+    def test_transaction_with_exception(self):
+        def enter_fn():
+            vals['entered'] = True
+
+        def exit_fn(t, v, tb):
+            vals['exited'] = True
+            vals['exception'] = (t or v or tb)
+
+        lock = Lock(self.lock_path)
+
+        def do_read_with_exception():
+            with ReadTransaction(lock, enter_fn, exit_fn):
+                raise Exception()
+
+        def do_write_with_exception():
+            with WriteTransaction(lock, enter_fn, exit_fn):
+                raise Exception()
+
+        vals = {'entered': False, 'exited': False, 'exception': False}
+        self.assertRaises(Exception, do_read_with_exception)
+        self.assertTrue(vals['entered'])
+        self.assertTrue(vals['exited'])
+        self.assertTrue(vals['exception'])
+
+        vals = {'entered': False, 'exited': False, 'exception': False}
+        self.assertRaises(Exception, do_write_with_exception)
+        self.assertTrue(vals['entered'])
+        self.assertTrue(vals['exited'])
+        self.assertTrue(vals['exception'])
+
+    def test_transaction_with_context_manager(self):
+        class TestContextManager(object):
+
+            def __enter__(self):
+                vals['entered'] = True
+
+            def __exit__(self, t, v, tb):
+                vals['exited'] = True
+                vals['exception'] = (t or v or tb)
+
+        def exit_fn(t, v, tb):
+            vals['exited_fn'] = True
+            vals['exception_fn'] = (t or v or tb)
+
+        lock = Lock(self.lock_path)
+
+        vals = {'entered': False, 'exited': False, 'exited_fn': False,
+                'exception': False, 'exception_fn': False}
+        with ReadTransaction(lock, TestContextManager, exit_fn):
+            pass
+
+        self.assertTrue(vals['entered'])
+        self.assertTrue(vals['exited'])
+        self.assertFalse(vals['exception'])
+        self.assertTrue(vals['exited_fn'])
+        self.assertFalse(vals['exception_fn'])
+
+        vals = {'entered': False, 'exited': False, 'exited_fn': False,
+                'exception': False, 'exception_fn': False}
+        with ReadTransaction(lock, TestContextManager):
+            pass
+
+        self.assertTrue(vals['entered'])
+        self.assertTrue(vals['exited'])
+        self.assertFalse(vals['exception'])
+        self.assertFalse(vals['exited_fn'])
+        self.assertFalse(vals['exception_fn'])
+
+        vals = {'entered': False, 'exited': False, 'exited_fn': False,
+                'exception': False, 'exception_fn': False}
+        with WriteTransaction(lock, TestContextManager, exit_fn):
+            pass
+
+        self.assertTrue(vals['entered'])
+        self.assertTrue(vals['exited'])
+        self.assertFalse(vals['exception'])
+        self.assertTrue(vals['exited_fn'])
+        self.assertFalse(vals['exception_fn'])
+
+        vals = {'entered': False, 'exited': False, 'exited_fn': False,
+                'exception': False, 'exception_fn': False}
+        with WriteTransaction(lock, TestContextManager):
+            pass
+
+        self.assertTrue(vals['entered'])
+        self.assertTrue(vals['exited'])
+        self.assertFalse(vals['exception'])
+        self.assertFalse(vals['exited_fn'])
+        self.assertFalse(vals['exception_fn'])
+
+    def test_transaction_with_context_manager_and_exception(self):
+        class TestContextManager(object):
+
+            def __enter__(self):
+                vals['entered'] = True
+
+            def __exit__(self, t, v, tb):
+                vals['exited'] = True
+                vals['exception'] = (t or v or tb)
+
+        def exit_fn(t, v, tb):
+            vals['exited_fn'] = True
+            vals['exception_fn'] = (t or v or tb)
+
+        lock = Lock(self.lock_path)
+
+        def do_read_with_exception(exit_fn):
+            with ReadTransaction(lock, TestContextManager, exit_fn):
+                raise Exception()
+
+        def do_write_with_exception(exit_fn):
+            with WriteTransaction(lock, TestContextManager, exit_fn):
+                raise Exception()
+
+        vals = {'entered': False, 'exited': False, 'exited_fn': False,
+                'exception': False, 'exception_fn': False}
+        self.assertRaises(Exception, do_read_with_exception, exit_fn)
+        self.assertTrue(vals['entered'])
+        self.assertTrue(vals['exited'])
+        self.assertTrue(vals['exception'])
+        self.assertTrue(vals['exited_fn'])
+        self.assertTrue(vals['exception_fn'])
+
+        vals = {'entered': False, 'exited': False, 'exited_fn': False,
+                'exception': False, 'exception_fn': False}
+        self.assertRaises(Exception, do_read_with_exception, None)
+        self.assertTrue(vals['entered'])
+        self.assertTrue(vals['exited'])
+        self.assertTrue(vals['exception'])
+        self.assertFalse(vals['exited_fn'])
+        self.assertFalse(vals['exception_fn'])
+
+        vals = {'entered': False, 'exited': False, 'exited_fn': False,
+                'exception': False, 'exception_fn': False}
+        self.assertRaises(Exception, do_write_with_exception, exit_fn)
+        self.assertTrue(vals['entered'])
+        self.assertTrue(vals['exited'])
+        self.assertTrue(vals['exception'])
+        self.assertTrue(vals['exited_fn'])
+        self.assertTrue(vals['exception_fn'])
+
+        vals = {'entered': False, 'exited': False, 'exited_fn': False,
+                'exception': False, 'exception_fn': False}
+        self.assertRaises(Exception, do_write_with_exception, None)
+        self.assertTrue(vals['entered'])
+        self.assertTrue(vals['exited'])
+        self.assertTrue(vals['exception'])
+        self.assertFalse(vals['exited_fn'])
+        self.assertFalse(vals['exception_fn'])
diff --git a/lib/spack/spack/test/make_executable.py b/lib/spack/spack/test/make_executable.py
index b7a45a3f72..87a43a529a 100644
--- a/lib/spack/spack/test/make_executable.py
+++ b/lib/spack/spack/test/make_executable.py
@@ -38,6 +38,7 @@ from spack.util.environment import path_put_first
 
 
 class MakeExecutableTest(unittest.TestCase):
+
     def setUp(self):
         self.tmpdir = tempfile.mkdtemp()
 
@@ -49,34 +50,30 @@ class MakeExecutableTest(unittest.TestCase):
 
         path_put_first('PATH', [self.tmpdir])
 
-
     def tearDown(self):
         shutil.rmtree(self.tmpdir)
 
-
     def test_make_normal(self):
         make = MakeExecutable('make', 8)
         self.assertEqual(make(output=str).strip(), '-j8')
         self.assertEqual(make('install', output=str).strip(), '-j8 install')
 
-
     def test_make_explicit(self):
         make = MakeExecutable('make', 8)
         self.assertEqual(make(parallel=True, output=str).strip(), '-j8')
-        self.assertEqual(make('install', parallel=True, output=str).strip(), '-j8 install')
-
+        self.assertEqual(make('install', parallel=True,
+                              output=str).strip(), '-j8 install')
 
     def test_make_one_job(self):
         make = MakeExecutable('make', 1)
         self.assertEqual(make(output=str).strip(), '')
         self.assertEqual(make('install', output=str).strip(), 'install')
 
-
     def test_make_parallel_false(self):
         make = MakeExecutable('make', 8)
         self.assertEqual(make(parallel=False, output=str).strip(), '')
-        self.assertEqual(make('install', parallel=False, output=str).strip(), 'install')
-
+        self.assertEqual(make('install', parallel=False,
+                              output=str).strip(), 'install')
 
     def test_make_parallel_disabled(self):
         make = MakeExecutable('make', 8)
@@ -100,26 +97,29 @@ class MakeExecutableTest(unittest.TestCase):
 
         del os.environ['SPACK_NO_PARALLEL_MAKE']
 
-
     def test_make_parallel_precedence(self):
         make = MakeExecutable('make', 8)
 
         # These should work
         os.environ['SPACK_NO_PARALLEL_MAKE'] = 'true'
         self.assertEqual(make(parallel=True, output=str).strip(), '')
-        self.assertEqual(make('install', parallel=True, output=str).strip(), 'install')
+        self.assertEqual(make('install', parallel=True,
+                              output=str).strip(), 'install')
 
         os.environ['SPACK_NO_PARALLEL_MAKE'] = '1'
         self.assertEqual(make(parallel=True, output=str).strip(), '')
-        self.assertEqual(make('install', parallel=True, output=str).strip(), 'install')
+        self.assertEqual(make('install', parallel=True,
+                              output=str).strip(), 'install')
 
         # These don't disable (false and random string)
         os.environ['SPACK_NO_PARALLEL_MAKE'] = 'false'
         self.assertEqual(make(parallel=True, output=str).strip(), '-j8')
-        self.assertEqual(make('install', parallel=True, output=str).strip(), '-j8 install')
+        self.assertEqual(make('install', parallel=True,
+                              output=str).strip(), '-j8 install')
 
         os.environ['SPACK_NO_PARALLEL_MAKE'] = 'foobar'
         self.assertEqual(make(parallel=True, output=str).strip(), '-j8')
-        self.assertEqual(make('install', parallel=True, output=str).strip(), '-j8 install')
+        self.assertEqual(make('install', parallel=True,
+                              output=str).strip(), '-j8 install')
 
         del os.environ['SPACK_NO_PARALLEL_MAKE']
diff --git a/lib/spack/spack/test/mirror.py b/lib/spack/spack/test/mirror.py
index b682d4e097..d6d7b30b7c 100644
--- a/lib/spack/spack/test/mirror.py
+++ b/lib/spack/spack/test/mirror.py
@@ -35,6 +35,7 @@ exclude = ['.hg', '.git', '.svn']
 
 
 class MirrorTest(MockPackagesTest):
+
     def setUp(self):
         """Sets up a mock package and a mock repo for each fetch strategy, to
            ensure that the mirror can create archives for each of them.
@@ -42,7 +43,6 @@ class MirrorTest(MockPackagesTest):
         super(MirrorTest, self).setUp()
         self.repos = {}
 
-
     def tearDown(self):
         """Destroy all the stages created by the repos in setup."""
         super(MirrorTest, self).tearDown()
@@ -50,7 +50,6 @@ class MirrorTest(MockPackagesTest):
             repo.destroy()
         self.repos.clear()
 
-
     def set_up_package(self, name, MockRepoClass, url_attr):
         """Set up a mock package to be mirrored.
            Each package needs us to:
@@ -71,16 +70,14 @@ class MirrorTest(MockPackagesTest):
         v = next(iter(pkg.versions))
         pkg.versions[v][url_attr] = repo.url
 
-
     def check_mirror(self):
         with Stage('spack-mirror-test') as stage:
             mirror_root = join_path(stage.path, 'test-mirror')
 
             # register mirror with spack config
-            mirrors = { 'spack-mirror-test' : 'file://' + mirror_root }
+            mirrors = {'spack-mirror-test': 'file://' + mirror_root}
             spack.config.update_config('mirrors', mirrors)
 
-
             os.chdir(stage.path)
             spack.mirror.create(
                 mirror_root, self.repos, no_checksum=True)
@@ -110,16 +107,18 @@ class MirrorTest(MockPackagesTest):
                         original_path = mock_repo.path
                         if 'svn' in name:
                             # have to check out the svn repo to compare.
-                            original_path = join_path(mock_repo.path, 'checked_out')
+                            original_path = join_path(
+                                mock_repo.path, 'checked_out')
                             svn('checkout', mock_repo.url, original_path)
                         dcmp = dircmp(original_path, pkg.stage.source_path)
-                        # make sure there are no new files in the expanded tarball
+                        # make sure there are no new files in the expanded
+                        # tarball
                         self.assertFalse(dcmp.right_only)
                         # and that all original files are present.
-                        self.assertTrue(all(l in exclude for l in dcmp.left_only))
+                        self.assertTrue(
+                            all(l in exclude for l in dcmp.left_only))
                         spack.do_checksum = saved_checksum_setting
 
-
     def test_git_mirror(self):
         self.set_up_package('git-test', MockGitRepo, 'git')
         self.check_mirror()
diff --git a/lib/spack/spack/test/mock_database.py b/lib/spack/spack/test/mock_database.py
index b1194f2451..d5867f06ec 100644
--- a/lib/spack/spack/test/mock_database.py
+++ b/lib/spack/spack/test/mock_database.py
@@ -33,6 +33,7 @@ from spack.test.mock_packages_test import MockPackagesTest
 
 
 class MockDatabase(MockPackagesTest):
+
     def _mock_install(self, spec):
         s = Spec(spec)
         s.concretize()
@@ -95,8 +96,10 @@ class MockDatabase(MockPackagesTest):
             self._mock_install('mpileaks ^zmpi')
 
     def tearDown(self):
-        for spec in spack.installed_db.query():
-            spec.package.do_uninstall(spec)
+        with spack.installed_db.write_transaction():
+            for spec in spack.installed_db.query():
+                spec.package.do_uninstall(spec)
+
         super(MockDatabase, self).tearDown()
         shutil.rmtree(self.install_path)
         spack.install_path = self.spack_install_path
diff --git a/lib/spack/spack/test/mock_packages_test.py b/lib/spack/spack/test/mock_packages_test.py
index 9d96622a6e..82c2712b0e 100644
--- a/lib/spack/spack/test/mock_packages_test.py
+++ b/lib/spack/spack/test/mock_packages_test.py
@@ -155,7 +155,9 @@ packages:
       externalmodule@1.0%gcc@4.5.0: external-module
 """
 
+
 class MockPackagesTest(unittest.TestCase):
+
     def initmock(self):
         # Use the mock packages database for these tests.  This allows
         # us to set up contrived packages that don't interfere with
@@ -172,7 +174,8 @@ class MockPackagesTest(unittest.TestCase):
         self.mock_user_config = os.path.join(self.temp_config, 'user')
         mkdirp(self.mock_site_config)
         mkdirp(self.mock_user_config)
-        for confs in [('compilers.yaml', mock_compiler_config), ('packages.yaml', mock_packages_config)]:
+        for confs in [('compilers.yaml', mock_compiler_config),
+                      ('packages.yaml', mock_packages_config)]:
             conf_yaml = os.path.join(self.mock_site_config, confs[0])
             with open(conf_yaml, 'w') as f:
                 f.write(confs[1])
@@ -209,7 +212,6 @@ class MockPackagesTest(unittest.TestCase):
         pkg.dependencies[spec.name] = {Spec(pkg_name): spec}
         pkg._deptypes[spec.name] = set(deptypes)
 
-
     def cleanmock(self):
         """Restore the real packages path after any test."""
         spack.repo.swap(self.db)
@@ -226,10 +228,8 @@ class MockPackagesTest(unittest.TestCase):
         shutil.rmtree(spack.share_path, ignore_errors=True)
         spack.share_path = self.real_share_path
 
-
     def setUp(self):
         self.initmock()
 
-
     def tearDown(self):
         self.cleanmock()
diff --git a/lib/spack/spack/test/mock_repo.py b/lib/spack/spack/test/mock_repo.py
index 386af282e7..0ae7dbd516 100644
--- a/lib/spack/spack/test/mock_repo.py
+++ b/lib/spack/spack/test/mock_repo.py
@@ -40,6 +40,7 @@ tar      = which('tar',      required=True)
 
 
 class MockRepo(object):
+
     def __init__(self, stage_name, repo_name):
         """This creates a stage where some archive/repo files can be staged
            for testing spack's fetch strategies."""
@@ -50,7 +51,6 @@ class MockRepo(object):
         self.path = join_path(self.stage.path, repo_name)
         mkdirp(self.path)
 
-
     def destroy(self):
         """Destroy resources associated with this mock repo."""
         if self.stage:
@@ -90,6 +90,7 @@ class MockArchive(MockRepo):
 
 
 class MockVCSRepo(MockRepo):
+
     def __init__(self, stage_name, repo_name):
         """This creates a stage and a repo directory within the stage."""
         super(MockVCSRepo, self).__init__(stage_name, repo_name)
@@ -100,6 +101,7 @@ class MockVCSRepo(MockRepo):
 
 
 class MockGitRepo(MockVCSRepo):
+
     def __init__(self):
         super(MockGitRepo, self).__init__('mock-git-stage', 'mock-git-repo')
 
@@ -147,6 +149,7 @@ class MockGitRepo(MockVCSRepo):
 
 
 class MockSvnRepo(MockVCSRepo):
+
     def __init__(self):
         super(MockSvnRepo, self).__init__('mock-svn-stage', 'mock-svn-repo')
 
@@ -176,6 +179,7 @@ class MockSvnRepo(MockVCSRepo):
 
 
 class MockHgRepo(MockVCSRepo):
+
     def __init__(self):
         super(MockHgRepo, self).__init__('mock-hg-stage', 'mock-hg-repo')
         self.url = 'file://' + self.path
diff --git a/lib/spack/spack/test/modules.py b/lib/spack/spack/test/modules.py
index 135cd028e3..5e280d8e43 100644
--- a/lib/spack/spack/test/modules.py
+++ b/lib/spack/spack/test/modules.py
@@ -89,7 +89,10 @@ configuration_alter_environment = {
     'enable': ['tcl'],
     'tcl': {
         'all': {
-            'filter': {'environment_blacklist': ['CMAKE_PREFIX_PATH']}
+            'filter': {'environment_blacklist': ['CMAKE_PREFIX_PATH']},
+            'environment': {
+                'set': {'{name}_ROOT': '{prefix}'}
+            }
         },
         'platform=test target=x86_64': {
             'environment': {
@@ -248,6 +251,8 @@ class TclTests(MockPackagesTest):
         self.assertEqual(
             len([x for x in content if 'setenv FOO "foo"' in x]), 1)
         self.assertEqual(len([x for x in content if 'unsetenv BAR' in x]), 1)
+        self.assertEqual(
+            len([x for x in content if 'setenv MPILEAKS_ROOT' in x]), 1)
 
         spec = spack.spec.Spec('libdwarf %clang platform=test target=x86_32')
         content = self.get_modulefile_content(spec)
@@ -262,6 +267,8 @@ class TclTests(MockPackagesTest):
             len([x for x in content if 'is-loaded foo/bar' in x]), 1)
         self.assertEqual(
             len([x for x in content if 'module load foo/bar' in x]), 1)
+        self.assertEqual(
+            len([x for x in content if 'setenv LIBDWARF_ROOT' in x]), 1)
 
     def test_blacklist(self):
         spack.modules.CONFIGURATION = configuration_blacklist
diff --git a/lib/spack/spack/test/multimethod.py b/lib/spack/spack/test/multimethod.py
index c233ea4fd6..a885374080 100644
--- a/lib/spack/spack/test/multimethod.py
+++ b/lib/spack/spack/test/multimethod.py
@@ -25,15 +25,10 @@
 """
 Test for multi_method dispatch.
 """
-import unittest
-
 import spack
 from spack.multimethod import *
 from spack.version import *
-from spack.spec import Spec
-from spack.multimethod import when
 from spack.test.mock_packages_test import *
-from spack.version import *
 
 
 class MultiMethodTest(MockPackagesTest):
@@ -42,7 +37,6 @@ class MultiMethodTest(MockPackagesTest):
         pkg = spack.repo.get('multimethod@2.0')
         self.assertRaises(NoSuchMethodError, pkg.no_version_2)
 
-
     def test_one_version_match(self):
         pkg = spack.repo.get('multimethod@1.0')
         self.assertEqual(pkg.no_version_2(), 1)
@@ -53,7 +47,6 @@ class MultiMethodTest(MockPackagesTest):
         pkg = spack.repo.get('multimethod@4.0')
         self.assertEqual(pkg.no_version_2(), 4)
 
-
     def test_version_overlap(self):
         pkg = spack.repo.get('multimethod@2.0')
         self.assertEqual(pkg.version_overlap(), 1)
@@ -61,7 +54,6 @@ class MultiMethodTest(MockPackagesTest):
         pkg = spack.repo.get('multimethod@5.0')
         self.assertEqual(pkg.version_overlap(), 2)
 
-
     def test_mpi_version(self):
         pkg = spack.repo.get('multimethod^mpich@3.0.4')
         self.assertEqual(pkg.mpi_version(), 3)
@@ -72,7 +64,6 @@ class MultiMethodTest(MockPackagesTest):
         pkg = spack.repo.get('multimethod^mpich@1.0')
         self.assertEqual(pkg.mpi_version(), 1)
 
-
     def test_undefined_mpi_version(self):
         pkg = spack.repo.get('multimethod^mpich@0.4')
         self.assertEqual(pkg.mpi_version(), 1)
@@ -80,7 +71,6 @@ class MultiMethodTest(MockPackagesTest):
         pkg = spack.repo.get('multimethod^mpich@1.4')
         self.assertEqual(pkg.mpi_version(), 1)
 
-
     def test_default_works(self):
         pkg = spack.repo.get('multimethod%gcc')
         self.assertEqual(pkg.has_a_default(), 'gcc')
@@ -91,21 +81,19 @@ class MultiMethodTest(MockPackagesTest):
         pkg = spack.repo.get('multimethod%pgi')
         self.assertEqual(pkg.has_a_default(), 'default')
 
-
     def test_target_match(self):
         platform = spack.architecture.platform()
         targets = platform.targets.values()
         for target in targets[:-1]:
-            pkg = spack.repo.get('multimethod target='+target.name)
+            pkg = spack.repo.get('multimethod target=' + target.name)
             self.assertEqual(pkg.different_by_target(), target.name)
 
-        pkg = spack.repo.get('multimethod target='+targets[-1].name)
+        pkg = spack.repo.get('multimethod target=' + targets[-1].name)
         if len(targets) == 1:
             self.assertEqual(pkg.different_by_target(), targets[-1].name)
         else:
             self.assertRaises(NoSuchMethodError, pkg.different_by_target)
 
-
     def test_dependency_match(self):
         pkg = spack.repo.get('multimethod^zmpi')
         self.assertEqual(pkg.different_by_dep(), 'zmpi')
@@ -118,7 +106,6 @@ class MultiMethodTest(MockPackagesTest):
         pkg = spack.repo.get('multimethod^foobar')
         self.assertEqual(pkg.different_by_dep(), 'mpich')
 
-
     def test_virtual_dep_match(self):
         pkg = spack.repo.get('multimethod^mpich2')
         self.assertEqual(pkg.different_by_virtual_dep(), 2)
diff --git a/lib/spack/spack/test/namespace_trie.py b/lib/spack/spack/test/namespace_trie.py
index b38ecd6179..7927fc8e60 100644
--- a/lib/spack/spack/test/namespace_trie.py
+++ b/lib/spack/spack/test/namespace_trie.py
@@ -32,7 +32,6 @@ class NamespaceTrieTest(unittest.TestCase):
     def setUp(self):
         self.trie = NamespaceTrie()
 
-
     def test_add_single(self):
         self.trie['foo'] = 'bar'
 
@@ -40,7 +39,6 @@ class NamespaceTrieTest(unittest.TestCase):
         self.assertTrue(self.trie.has_value('foo'))
         self.assertEqual(self.trie['foo'], 'bar')
 
-
     def test_add_multiple(self):
         self.trie['foo.bar'] = 'baz'
 
@@ -54,7 +52,6 @@ class NamespaceTrieTest(unittest.TestCase):
         self.assertFalse(self.trie.is_prefix('foo.bar.baz'))
         self.assertFalse(self.trie.has_value('foo.bar.baz'))
 
-
     def test_add_three(self):
         # add a three-level namespace
         self.trie['foo.bar.baz'] = 'quux'
@@ -89,7 +86,6 @@ class NamespaceTrieTest(unittest.TestCase):
         self.assertFalse(self.trie.is_prefix('foo.bar.baz.quux'))
         self.assertFalse(self.trie.has_value('foo.bar.baz.quux'))
 
-
     def test_add_none_single(self):
         self.trie['foo'] = None
         self.assertTrue(self.trie.is_prefix('foo'))
@@ -99,8 +95,6 @@ class NamespaceTrieTest(unittest.TestCase):
         self.assertFalse(self.trie.is_prefix('foo.bar'))
         self.assertFalse(self.trie.has_value('foo.bar'))
 
-
-
     def test_add_none_multiple(self):
         self.trie['foo.bar'] = None
 
diff --git a/lib/spack/spack/test/operating_system.py b/lib/spack/spack/test/operating_system.py
index ed5f6ff8ad..8723f7244d 100644
--- a/lib/spack/spack/test/operating_system.py
+++ b/lib/spack/spack/test/operating_system.py
@@ -1,18 +1,39 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
 """ Test checks if the operating_system class is created correctly and that
 the functions are using the correct operating_system. Also checks whether
 the operating_system correctly uses the compiler_strategy
 """
-
 import unittest
-import os
-import platform
 from spack.platforms.cray_xc import CrayXc
 from spack.platforms.linux import Linux
 from spack.platforms.darwin import Darwin
 from spack.operating_system.linux_distro import LinuxDistro
-from spack.operating_system.mac_os import MacOs
 from spack.operating_system.cnl import ComputeNodeLinux
 
+
 class TestOperatingSystem(unittest.TestCase):
 
     def setUp(self):
@@ -32,7 +53,7 @@ class TestOperatingSystem(unittest.TestCase):
         self.assertEquals(self.cray_operating_sys.compiler_strategy, "PATH")
 
     def test_cray_back_end_operating_system(self):
-        self.assertIsInstance(self.cray_back_os,ComputeNodeLinux)
+        self.assertIsInstance(self.cray_back_os, ComputeNodeLinux)
 
     def test_cray_back_end_compiler_strategy(self):
         self.assertEquals(self.cray_back_os.compiler_strategy, "MODULES")
@@ -43,7 +64,6 @@ class TestOperatingSystem(unittest.TestCase):
     def test_linux_compiler_strategy(self):
         self.assertEquals(self.linux_operating_sys.compiler_strategy, "PATH")
 
-
     def test_cray_front_end_compiler_list(self):
         """ Operating systems will now be in charge of finding compilers.
             So, depending on which operating system you want to build for
diff --git a/lib/spack/spack/test/optional_deps.py b/lib/spack/spack/test/optional_deps.py
index b5ba0ecf35..a9a2b9abf5 100644
--- a/lib/spack/spack/test/optional_deps.py
+++ b/lib/spack/spack/test/optional_deps.py
@@ -22,10 +22,10 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-
 from spack.spec import Spec
 from spack.test.mock_packages_test import *
 
+
 class ConcretizeTest(MockPackagesTest):
 
     def check_normalize(self, spec_string, expected):
@@ -34,10 +34,10 @@ class ConcretizeTest(MockPackagesTest):
         self.assertEqual(spec, expected)
         self.assertTrue(spec.eq_dag(expected))
 
-
     def test_normalize_simple_conditionals(self):
         self.check_normalize('optional-dep-test', Spec('optional-dep-test'))
-        self.check_normalize('optional-dep-test~a', Spec('optional-dep-test~a'))
+        self.check_normalize('optional-dep-test~a',
+                             Spec('optional-dep-test~a'))
 
         self.check_normalize('optional-dep-test+a',
                              Spec('optional-dep-test+a', Spec('a')))
@@ -45,7 +45,6 @@ class ConcretizeTest(MockPackagesTest):
         self.check_normalize('optional-dep-test a=true',
                              Spec('optional-dep-test a=true', Spec('a')))
 
-
         self.check_normalize('optional-dep-test a=true',
                              Spec('optional-dep-test+a', Spec('a')))
 
@@ -55,25 +54,29 @@ class ConcretizeTest(MockPackagesTest):
         self.check_normalize('optional-dep-test%intel',
                              Spec('optional-dep-test%intel', Spec('c')))
 
-        self.check_normalize('optional-dep-test%intel@64.1',
-                             Spec('optional-dep-test%intel@64.1', Spec('c'), Spec('d')))
+        self.check_normalize(
+            'optional-dep-test%intel@64.1',
+            Spec('optional-dep-test%intel@64.1', Spec('c'), Spec('d')))
 
-        self.check_normalize('optional-dep-test%intel@64.1.2',
-                             Spec('optional-dep-test%intel@64.1.2', Spec('c'), Spec('d')))
+        self.check_normalize(
+            'optional-dep-test%intel@64.1.2',
+            Spec('optional-dep-test%intel@64.1.2', Spec('c'), Spec('d')))
 
         self.check_normalize('optional-dep-test%clang@35',
                              Spec('optional-dep-test%clang@35', Spec('e')))
 
-
     def test_multiple_conditionals(self):
-        self.check_normalize('optional-dep-test+a@1.1',
-                             Spec('optional-dep-test+a@1.1', Spec('a'), Spec('b')))
+        self.check_normalize(
+            'optional-dep-test+a@1.1',
+            Spec('optional-dep-test+a@1.1', Spec('a'), Spec('b')))
 
-        self.check_normalize('optional-dep-test+a%intel',
-                             Spec('optional-dep-test+a%intel', Spec('a'), Spec('c')))
+        self.check_normalize(
+            'optional-dep-test+a%intel',
+            Spec('optional-dep-test+a%intel', Spec('a'), Spec('c')))
 
-        self.check_normalize('optional-dep-test@1.1%intel',
-                             Spec('optional-dep-test@1.1%intel', Spec('b'), Spec('c')))
+        self.check_normalize(
+            'optional-dep-test@1.1%intel',
+            Spec('optional-dep-test@1.1%intel', Spec('b'), Spec('c')))
 
         self.check_normalize('optional-dep-test@1.1%intel@64.1.2+a',
                              Spec('optional-dep-test@1.1%intel@64.1.2+a',
@@ -83,14 +86,12 @@ class ConcretizeTest(MockPackagesTest):
                              Spec('optional-dep-test@1.1%clang@36.5+a',
                                   Spec('b'), Spec('a'), Spec('e')))
 
-
     def test_chained_mpi(self):
         self.check_normalize('optional-dep-test-2+mpi',
                              Spec('optional-dep-test-2+mpi',
                                   Spec('optional-dep-test+mpi',
                                        Spec('mpi'))))
 
-
     def test_default_variant(self):
         spec = Spec('optional-dep-test-3')
         spec.concretize()
@@ -104,7 +105,6 @@ class ConcretizeTest(MockPackagesTest):
         spec.concretize()
         self.assertTrue('b' in spec)
 
-
     def test_transitive_chain(self):
         # Each of these dependencies comes from a conditional
         # dependency on another.  This requires iterating to evaluate
diff --git a/lib/spack/spack/test/package_sanity.py b/lib/spack/spack/test/package_sanity.py
index 9198986f5d..c3c3923855 100644
--- a/lib/spack/spack/test/package_sanity.py
+++ b/lib/spack/spack/test/package_sanity.py
@@ -38,12 +38,10 @@ class PackageSanityTest(unittest.TestCase):
         for name in spack.repo.all_package_names():
             spack.repo.get(name)
 
-
     def test_get_all_packages(self):
         """Get all packages once and make sure that works."""
         self.check_db()
 
-
     def test_get_all_mock_packages(self):
         """Get the mock packages once each too."""
         db = RepoPath(spack.mock_packages_path)
@@ -51,7 +49,6 @@ class PackageSanityTest(unittest.TestCase):
         self.check_db()
         spack.repo.swap(db)
 
-
     def test_url_versions(self):
         """Check URLs for regular packages, if they are explicitly defined."""
         for pkg in spack.repo.all_packages():
diff --git a/lib/spack/spack/test/packages.py b/lib/spack/spack/test/packages.py
index bea42bb33a..fdd079a8f7 100644
--- a/lib/spack/spack/test/packages.py
+++ b/lib/spack/spack/test/packages.py
@@ -22,7 +22,6 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-
 import spack
 from llnl.util.filesystem import join_path
 from spack.repository import Repo
@@ -33,33 +32,26 @@ from spack.util.naming import mod_to_class
 class PackagesTest(MockPackagesTest):
 
     def test_load_package(self):
-        pkg = spack.repo.get('mpich')
-
+        spack.repo.get('mpich')
 
     def test_package_name(self):
         pkg = spack.repo.get('mpich')
         self.assertEqual(pkg.name, 'mpich')
 
-
     def test_package_filename(self):
         repo = Repo(spack.mock_packages_path)
         filename = repo.filename_for_package_name('mpich')
         self.assertEqual(filename,
-                         join_path(spack.mock_packages_path, 'packages', 'mpich', 'package.py'))
-
-
-    def test_package_name(self):
-        pkg = spack.repo.get('mpich')
-        self.assertEqual(pkg.name, 'mpich')
-
+                         join_path(spack.mock_packages_path,
+                                   'packages', 'mpich', 'package.py'))
 
     def test_nonexisting_package_filename(self):
         repo = Repo(spack.mock_packages_path)
         filename = repo.filename_for_package_name('some-nonexisting-package')
         self.assertEqual(
             filename,
-            join_path(spack.mock_packages_path, 'packages', 'some-nonexisting-package', 'package.py'))
-
+            join_path(spack.mock_packages_path,
+                      'packages', 'some-nonexisting-package', 'package.py'))
 
     def test_package_class_names(self):
         self.assertEqual('Mpich',          mod_to_class('mpich'))
@@ -68,37 +60,32 @@ class PackagesTest(MockPackagesTest):
         self.assertEqual('Pmgrcollective', mod_to_class('PmgrCollective'))
         self.assertEqual('_3db',        mod_to_class('3db'))
 
-
     #
     # Below tests target direct imports of spack packages from the
     # spack.pkg namespace
     #
 
     def test_import_package(self):
-        import spack.pkg.builtin.mock.mpich
-
+        import spack.pkg.builtin.mock.mpich             # noqa
 
     def test_import_package_as(self):
-        import spack.pkg.builtin.mock.mpich as mp
-
+        import spack.pkg.builtin.mock.mpich as mp       # noqa
 
     def test_import_class_from_package(self):
-        from spack.pkg.builtin.mock.mpich import Mpich
-
+        from spack.pkg.builtin.mock.mpich import Mpich  # noqa
 
     def test_import_module_from_package(self):
-        from spack.pkg.builtin.mock import mpich
-
+        from spack.pkg.builtin.mock import mpich        # noqa
 
     def test_import_namespace_container_modules(self):
-        import spack.pkg
-        import spack.pkg as p
-        from spack import pkg
+        import spack.pkg                                # noqa
+        import spack.pkg as p                           # noqa
+        from spack import pkg                           # noqa
 
-        import spack.pkg.builtin
-        import spack.pkg.builtin as b
-        from spack.pkg import builtin
+        import spack.pkg.builtin                        # noqa
+        import spack.pkg.builtin as b                   # noqa
+        from spack.pkg import builtin                   # noqa
 
-        import spack.pkg.builtin.mock
-        import spack.pkg.builtin.mock as m
-        from spack.pkg.builtin import mock
+        import spack.pkg.builtin.mock                   # noqa
+        import spack.pkg.builtin.mock as m              # noqa
+        from spack.pkg.builtin import mock              # noqa
diff --git a/lib/spack/spack/test/pattern.py b/lib/spack/spack/test/pattern.py
index 3419d600b8..0c772a0d2d 100644
--- a/lib/spack/spack/test/pattern.py
+++ b/lib/spack/spack/test/pattern.py
@@ -41,6 +41,7 @@ class CompositeTest(unittest.TestCase):
                 raise NotImplemented('subtract not implemented')
 
         class One(Base):
+
             def add(self):
                 Base.counter += 1
 
@@ -48,6 +49,7 @@ class CompositeTest(unittest.TestCase):
                 Base.counter -= 1
 
         class Two(Base):
+
             def add(self):
                 Base.counter += 2
 
diff --git a/lib/spack/spack/test/provider_index.py b/lib/spack/spack/test/provider_index.py
new file mode 100644
index 0000000000..9847dd05a6
--- /dev/null
+++ b/lib/spack/spack/test/provider_index.py
@@ -0,0 +1,93 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+"""Tests for provider index cache files.
+
+Tests assume that mock packages provide this:
+
+  {'blas':   {
+       blas: set([netlib-blas, openblas, openblas-with-lapack])},
+   'lapack': {lapack: set([netlib-lapack, openblas-with-lapack])},
+   'mpi': {mpi@:1: set([mpich@:1]),
+                    mpi@:2.0: set([mpich2]),
+                    mpi@:2.1: set([mpich2@1.1:]),
+                    mpi@:2.2: set([mpich2@1.2:]),
+                    mpi@:3: set([mpich@3:]),
+                    mpi@:10.0: set([zmpi])},
+    'stuff': {stuff: set([externalvirtual])}}
+"""
+from StringIO import StringIO
+
+import spack
+from spack.spec import Spec
+from spack.provider_index import ProviderIndex
+from spack.test.mock_packages_test import *
+
+
+class ProviderIndexTest(MockPackagesTest):
+
+    def test_yaml_round_trip(self):
+        p = ProviderIndex(spack.repo.all_package_names())
+
+        ostream = StringIO()
+        p.to_yaml(ostream)
+
+        istream = StringIO(ostream.getvalue())
+        q = ProviderIndex.from_yaml(istream)
+
+        self.assertEqual(p, q)
+
+    def test_providers_for_simple(self):
+        p = ProviderIndex(spack.repo.all_package_names())
+
+        blas_providers = p.providers_for('blas')
+        self.assertTrue(Spec('netlib-blas') in blas_providers)
+        self.assertTrue(Spec('openblas') in blas_providers)
+        self.assertTrue(Spec('openblas-with-lapack') in blas_providers)
+
+        lapack_providers = p.providers_for('lapack')
+        self.assertTrue(Spec('netlib-lapack') in lapack_providers)
+        self.assertTrue(Spec('openblas-with-lapack') in lapack_providers)
+
+    def test_mpi_providers(self):
+        p = ProviderIndex(spack.repo.all_package_names())
+
+        mpi_2_providers = p.providers_for('mpi@2')
+        self.assertTrue(Spec('mpich2') in mpi_2_providers)
+        self.assertTrue(Spec('mpich@3:') in mpi_2_providers)
+
+        mpi_3_providers = p.providers_for('mpi@3')
+        self.assertTrue(Spec('mpich2') not in mpi_3_providers)
+        self.assertTrue(Spec('mpich@3:') in mpi_3_providers)
+        self.assertTrue(Spec('zmpi') in mpi_3_providers)
+
+    def test_equal(self):
+        p = ProviderIndex(spack.repo.all_package_names())
+        q = ProviderIndex(spack.repo.all_package_names())
+        self.assertEqual(p, q)
+
+    def test_copy(self):
+        p = ProviderIndex(spack.repo.all_package_names())
+        q = p.copy()
+        self.assertEqual(p, q)
diff --git a/lib/spack/spack/test/python_version.py b/lib/spack/spack/test/python_version.py
index 6c09effc56..5af55bdc5f 100644
--- a/lib/spack/spack/test/python_version.py
+++ b/lib/spack/spack/test/python_version.py
@@ -36,7 +36,8 @@ import llnl.util.tty as tty
 import pyqver2
 import spack
 
-spack_max_version = (2,6)
+spack_max_version = (2, 6)
+
 
 class PythonVersionTest(unittest.TestCase):
 
@@ -51,12 +52,10 @@ class PythonVersionTest(unittest.TestCase):
                     if re.match(r'^[^.#].*\.py$', filename):
                         yield os.path.join(root, filename)
 
-
     def package_py_files(self):
         for name in spack.repo.all_package_names():
             yield spack.repo.filename_for_package_name(name)
 
-
     def check_python_versions(self, *files):
         # dict version -> filename -> reasons
         all_issues = {}
@@ -66,7 +65,7 @@ class PythonVersionTest(unittest.TestCase):
                 versions = pyqver2.get_versions(pyfile.read())
                 for ver, reasons in versions.items():
                     if ver > spack_max_version:
-                        if not ver in all_issues:
+                        if ver not in all_issues:
                             all_issues[ver] = {}
                         all_issues[ver][fn] = reasons
 
@@ -87,7 +86,7 @@ class PythonVersionTest(unittest.TestCase):
 
             tty.error("These files require version %d.%d:" % v)
             maxlen = max(len(f) for f, prob in msgs)
-            fmt = "%%-%ds%%s" % (maxlen+3)
+            fmt = "%%-%ds%%s" % (maxlen + 3)
             print fmt % ('File', 'Reason')
             print fmt % ('-' * (maxlen), '-' * 20)
             for msg in msgs:
@@ -95,10 +94,8 @@ class PythonVersionTest(unittest.TestCase):
 
         self.assertTrue(len(all_issues) == 0)
 
-
     def test_core_module_compatibility(self):
         self.check_python_versions(*self.pyfiles(spack.lib_path))
 
-
     def test_package_module_compatibility(self):
         self.check_python_versions(*self.pyfiles(spack.packages_path))
diff --git a/lib/spack/spack/test/sbang.py b/lib/spack/spack/test/sbang.py
index ed54ff90b0..12abce7b35 100644
--- a/lib/spack/spack/test/sbang.py
+++ b/lib/spack/spack/test/sbang.py
@@ -26,6 +26,7 @@
 Test that Spack's shebang filtering works correctly.
 """
 import os
+import stat
 import unittest
 import tempfile
 import shutil
@@ -41,7 +42,9 @@ lua_line_patched = "--!/this/" + ('x' * 200) + "/is/lua\n"
 sbang_line       = '#!/bin/bash %s/bin/sbang\n' % spack.spack_root
 last_line        = "last!\n"
 
+
 class SbangTest(unittest.TestCase):
+
     def setUp(self):
         self.tempdir = tempfile.mkdtemp()
 
@@ -74,10 +77,8 @@ class SbangTest(unittest.TestCase):
             f.write(long_line)
             f.write(last_line)
 
-
     def tearDown(self):
-         shutil.rmtree(self.tempdir, ignore_errors=True)
-
+        shutil.rmtree(self.tempdir, ignore_errors=True)
 
     def test_shebang_handling(self):
         filter_shebangs_in_directory(self.tempdir)
@@ -104,3 +105,14 @@ class SbangTest(unittest.TestCase):
             self.assertEqual(f.readline(), sbang_line)
             self.assertEqual(f.readline(), long_line)
             self.assertEqual(f.readline(), last_line)
+
+    def test_shebang_handles_non_writable_files(self):
+        # make a file non-writable
+        st = os.stat(self.long_shebang)
+        not_writable_mode = st.st_mode & ~stat.S_IWRITE
+        os.chmod(self.long_shebang, not_writable_mode)
+
+        self.test_shebang_handling()
+
+        st = os.stat(self.long_shebang)
+        self.assertEqual(oct(not_writable_mode), oct(st.st_mode))
diff --git a/lib/spack/spack/test/spec_dag.py b/lib/spack/spack/test/spec_dag.py
index 972e79aa20..8f61c7ac76 100644
--- a/lib/spack/spack/test/spec_dag.py
+++ b/lib/spack/spack/test/spec_dag.py
@@ -32,8 +32,6 @@ import spack
 import spack.architecture
 import spack.package
 
-from llnl.util.lang import list_modules
-
 from spack.spec import Spec
 from spack.test.mock_packages_test import *
 
@@ -51,21 +49,19 @@ class SpecDagTest(MockPackagesTest):
         self.assertRaises(spack.spec.UnsatisfiableVersionSpecError,
                           spec.normalize)
 
-
     def test_preorder_node_traversal(self):
         dag = Spec('mpileaks ^zmpi')
         dag.normalize()
 
         names = ['mpileaks', 'callpath', 'dyninst', 'libdwarf', 'libelf',
                  'zmpi', 'fake']
-        pairs = zip([0,1,2,3,4,2,3], names)
+        pairs = zip([0, 1, 2, 3, 4, 2, 3], names)
 
         traversal = dag.traverse()
         self.assertEqual([x.name for x in traversal], names)
 
         traversal = dag.traverse(depth=True)
-        self.assertEqual([(x, y.name) for x,y in traversal], pairs)
-
+        self.assertEqual([(x, y.name) for x, y in traversal], pairs)
 
     def test_preorder_edge_traversal(self):
         dag = Spec('mpileaks ^zmpi')
@@ -73,14 +69,13 @@ class SpecDagTest(MockPackagesTest):
 
         names = ['mpileaks', 'callpath', 'dyninst', 'libdwarf', 'libelf',
                  'libelf', 'zmpi', 'fake', 'zmpi']
-        pairs = zip([0,1,2,3,4,3,2,3,1], names)
+        pairs = zip([0, 1, 2, 3, 4, 3, 2, 3, 1], names)
 
         traversal = dag.traverse(cover='edges')
         self.assertEqual([x.name for x in traversal], names)
 
         traversal = dag.traverse(cover='edges', depth=True)
-        self.assertEqual([(x, y.name) for x,y in traversal], pairs)
-
+        self.assertEqual([(x, y.name) for x, y in traversal], pairs)
 
     def test_preorder_path_traversal(self):
         dag = Spec('mpileaks ^zmpi')
@@ -88,14 +83,13 @@ class SpecDagTest(MockPackagesTest):
 
         names = ['mpileaks', 'callpath', 'dyninst', 'libdwarf', 'libelf',
                  'libelf', 'zmpi', 'fake', 'zmpi', 'fake']
-        pairs = zip([0,1,2,3,4,3,2,3,1,2], names)
+        pairs = zip([0, 1, 2, 3, 4, 3, 2, 3, 1, 2], names)
 
         traversal = dag.traverse(cover='paths')
         self.assertEqual([x.name for x in traversal], names)
 
         traversal = dag.traverse(cover='paths', depth=True)
-        self.assertEqual([(x, y.name) for x,y in traversal], pairs)
-
+        self.assertEqual([(x, y.name) for x, y in traversal], pairs)
 
     def test_postorder_node_traversal(self):
         dag = Spec('mpileaks ^zmpi')
@@ -103,14 +97,13 @@ class SpecDagTest(MockPackagesTest):
 
         names = ['libelf', 'libdwarf', 'dyninst', 'fake', 'zmpi',
                  'callpath', 'mpileaks']
-        pairs = zip([4,3,2,3,2,1,0], names)
+        pairs = zip([4, 3, 2, 3, 2, 1, 0], names)
 
         traversal = dag.traverse(order='post')
         self.assertEqual([x.name for x in traversal], names)
 
         traversal = dag.traverse(depth=True, order='post')
-        self.assertEqual([(x, y.name) for x,y in traversal], pairs)
-
+        self.assertEqual([(x, y.name) for x, y in traversal], pairs)
 
     def test_postorder_edge_traversal(self):
         dag = Spec('mpileaks ^zmpi')
@@ -118,14 +111,13 @@ class SpecDagTest(MockPackagesTest):
 
         names = ['libelf', 'libdwarf', 'libelf', 'dyninst', 'fake', 'zmpi',
                  'callpath', 'zmpi', 'mpileaks']
-        pairs = zip([4,3,3,2,3,2,1,1,0], names)
+        pairs = zip([4, 3, 3, 2, 3, 2, 1, 1, 0], names)
 
         traversal = dag.traverse(cover='edges', order='post')
         self.assertEqual([x.name for x in traversal], names)
 
         traversal = dag.traverse(cover='edges', depth=True, order='post')
-        self.assertEqual([(x, y.name) for x,y in traversal], pairs)
-
+        self.assertEqual([(x, y.name) for x, y in traversal], pairs)
 
     def test_postorder_path_traversal(self):
         dag = Spec('mpileaks ^zmpi')
@@ -133,14 +125,13 @@ class SpecDagTest(MockPackagesTest):
 
         names = ['libelf', 'libdwarf', 'libelf', 'dyninst', 'fake', 'zmpi',
                  'callpath', 'fake', 'zmpi', 'mpileaks']
-        pairs = zip([4,3,3,2,3,2,1,2,1,0], names)
+        pairs = zip([4, 3, 3, 2, 3, 2, 1, 2, 1, 0], names)
 
         traversal = dag.traverse(cover='paths', order='post')
         self.assertEqual([x.name for x in traversal], names)
 
         traversal = dag.traverse(cover='paths', depth=True, order='post')
-        self.assertEqual([(x, y.name) for x,y in traversal], pairs)
-
+        self.assertEqual([(x, y.name) for x, y in traversal], pairs)
 
     def test_conflicting_spec_constraints(self):
         mpileaks = Spec('mpileaks ^mpich ^callpath ^dyninst ^libelf ^libdwarf')
@@ -153,8 +144,7 @@ class SpecDagTest(MockPackagesTest):
             spec._dependencies['mpich'].spec = Spec('mpich@2.0')
 
         self.assertRaises(spack.spec.InconsistentSpecError,
-                lambda: mpileaks.flat_dependencies(copy=False))
-
+                          lambda: mpileaks.flat_dependencies(copy=False))
 
     def test_normalize_twice(self):
         """Make sure normalize can be run twice on the same spec,
@@ -166,7 +156,6 @@ class SpecDagTest(MockPackagesTest):
         spec.normalize()
         self.assertEqual(n1, spec)
 
-
     def test_normalize_a_lot(self):
         spec = Spec('mpileaks')
         spec.normalize()
@@ -174,7 +163,6 @@ class SpecDagTest(MockPackagesTest):
         spec.normalize()
         spec.normalize()
 
-
     def test_normalize_with_virtual_spec(self):
         dag = Spec('mpileaks',
                    Spec('callpath',
@@ -189,80 +177,80 @@ class SpecDagTest(MockPackagesTest):
         # make sure nothing with the same name occurs twice
         counts = {}
         for spec in dag.traverse(key=id):
-            if not spec.name in counts:
+            if spec.name not in counts:
                 counts[spec.name] = 0
             counts[spec.name] += 1
 
         for name in counts:
             self.assertEqual(counts[name], 1, "Count for %s was not 1!" % name)
 
-
     def check_links(self, spec_to_check):
         for spec in spec_to_check.traverse():
             for dependent in spec.dependents():
                 self.assertTrue(
                     spec.name in dependent.dependencies_dict(),
                     "%s not in dependencies of %s" %
-                        (spec.name, dependent.name))
+                    (spec.name, dependent.name))
 
             for dependency in spec.dependencies():
                 self.assertTrue(
                     spec.name in dependency.dependents_dict(),
                     "%s not in dependents of %s" %
-                        (spec.name, dependency.name))
-
+                    (spec.name, dependency.name))
 
     def test_dependents_and_dependencies_are_correct(self):
         spec = Spec('mpileaks',
-                   Spec('callpath',
-                        Spec('dyninst',
-                             Spec('libdwarf',
-                                  Spec('libelf')),
-                             Spec('libelf')),
-                        Spec('mpi')),
-                   Spec('mpi'))
+                    Spec('callpath',
+                         Spec('dyninst',
+                              Spec('libdwarf',
+                                   Spec('libelf')),
+                              Spec('libelf')),
+                         Spec('mpi')),
+                    Spec('mpi'))
 
         self.check_links(spec)
         spec.normalize()
         self.check_links(spec)
 
-
     def test_unsatisfiable_version(self):
         self.set_pkg_dep('mpileaks', 'mpich@1.0')
         spec = Spec('mpileaks ^mpich@2.0 ^callpath ^dyninst ^libelf ^libdwarf')
-        self.assertRaises(spack.spec.UnsatisfiableVersionSpecError, spec.normalize)
-
+        self.assertRaises(spack.spec.UnsatisfiableVersionSpecError,
+                          spec.normalize)
 
     def test_unsatisfiable_compiler(self):
         self.set_pkg_dep('mpileaks', 'mpich%gcc')
-        spec = Spec('mpileaks ^mpich%intel ^callpath ^dyninst ^libelf ^libdwarf')
-        self.assertRaises(spack.spec.UnsatisfiableCompilerSpecError, spec.normalize)
-
+        spec = Spec('mpileaks ^mpich%intel ^callpath ^dyninst ^libelf'
+                    ' ^libdwarf')
+        self.assertRaises(spack.spec.UnsatisfiableCompilerSpecError,
+                          spec.normalize)
 
     def test_unsatisfiable_compiler_version(self):
         self.set_pkg_dep('mpileaks', 'mpich%gcc@4.6')
-        spec = Spec('mpileaks ^mpich%gcc@4.5 ^callpath ^dyninst ^libelf ^libdwarf')
-        self.assertRaises(spack.spec.UnsatisfiableCompilerSpecError, spec.normalize)
-
+        spec = Spec('mpileaks ^mpich%gcc@4.5 ^callpath ^dyninst ^libelf'
+                    ' ^libdwarf')
+        self.assertRaises(spack.spec.UnsatisfiableCompilerSpecError,
+                          spec.normalize)
 
     def test_unsatisfiable_architecture(self):
-        platform = spack.architecture.platform()
-
         self.set_pkg_dep('mpileaks', 'mpich platform=test target=be')
-        spec = Spec('mpileaks ^mpich platform=test target=fe ^callpath ^dyninst ^libelf ^libdwarf')
-        self.assertRaises(spack.spec.UnsatisfiableArchitectureSpecError, spec.normalize)
-
+        spec = Spec('mpileaks ^mpich platform=test target=fe ^callpath'
+                    ' ^dyninst ^libelf ^libdwarf')
+        self.assertRaises(spack.spec.UnsatisfiableArchitectureSpecError,
+                          spec.normalize)
 
     def test_invalid_dep(self):
         spec = Spec('libelf ^mpich')
-        self.assertRaises(spack.spec.InvalidDependencyException, spec.normalize)
+        self.assertRaises(spack.spec.InvalidDependencyException,
+                          spec.normalize)
 
         spec = Spec('libelf ^libdwarf')
-        self.assertRaises(spack.spec.InvalidDependencyException, spec.normalize)
+        self.assertRaises(spack.spec.InvalidDependencyException,
+                          spec.normalize)
 
         spec = Spec('mpich ^dyninst ^libelf')
-        self.assertRaises(spack.spec.InvalidDependencyException, spec.normalize)
-
+        self.assertRaises(spack.spec.InvalidDependencyException,
+                          spec.normalize)
 
     def test_equal(self):
         # Different spec structures to test for equality
@@ -301,10 +289,10 @@ class SpecDagTest(MockPackagesTest):
         self.assertFalse(flip_flat.eq_dag(flip_dag))
         self.assertFalse(dag.eq_dag(flip_dag))
 
-
     def test_normalize_mpileaks(self):
         # Spec parsed in from a string
-        spec = Spec('mpileaks ^mpich ^callpath ^dyninst ^libelf@1.8.11 ^libdwarf')
+        spec = Spec('mpileaks ^mpich ^callpath ^dyninst ^libelf@1.8.11'
+                    ' ^libdwarf')
 
         # What that spec should look like after parsing
         expected_flat = Spec(
@@ -367,7 +355,6 @@ class SpecDagTest(MockPackagesTest):
         self.assertEqual(spec, non_unique_nodes)
         self.assertFalse(spec.eq_dag(non_unique_nodes))
 
-
     def test_normalize_with_virtual_package(self):
         spec = Spec('mpileaks ^mpi ^libelf@1.8.11 ^libdwarf')
         spec.normalize()
@@ -383,7 +370,6 @@ class SpecDagTest(MockPackagesTest):
 
         self.assertEqual(str(spec), str(expected_normalized))
 
-
     def test_contains(self):
         spec = Spec('mpileaks ^mpi ^libelf@1.8.11 ^libdwarf')
         self.assertTrue(Spec('mpi') in spec)
@@ -394,7 +380,6 @@ class SpecDagTest(MockPackagesTest):
         self.assertFalse(Spec('libgoblin') in spec)
         self.assertTrue(Spec('mpileaks') in spec)
 
-
     def test_copy_simple(self):
         orig = Spec('mpileaks')
         copy = orig.copy()
@@ -411,7 +396,6 @@ class SpecDagTest(MockPackagesTest):
         copy_ids = set(id(s) for s in copy.traverse())
         self.assertFalse(orig_ids.intersection(copy_ids))
 
-
     def test_copy_normalized(self):
         orig = Spec('mpileaks')
         orig.normalize()
@@ -429,7 +413,6 @@ class SpecDagTest(MockPackagesTest):
         copy_ids = set(id(s) for s in copy.traverse())
         self.assertFalse(orig_ids.intersection(copy_ids))
 
-
     def test_copy_concretized(self):
         orig = Spec('mpileaks')
         orig.concretize()
@@ -472,24 +455,25 @@ class SpecDagTest(MockPackagesTest):
 
         run3 -b-> build3
     """
+
     def test_deptype_traversal(self):
         dag = Spec('dtuse')
         dag.normalize()
 
-        names = ['dtuse', 'dttop', 'dtlink1', 'dtlink3', 'dtlink4',
-                 'dtrun1', 'dtlink5', 'dtrun3']
+        names = ['dtuse', 'dttop', 'dtbuild1', 'dtbuild2', 'dtlink2',
+                 'dtlink1', 'dtlink3', 'dtlink4']
 
-        traversal = dag.traverse()
+        traversal = dag.traverse(deptype=('build', 'link'))
         self.assertEqual([x.name for x in traversal], names)
 
     def test_deptype_traversal_with_builddeps(self):
         dag = Spec('dttop')
         dag.normalize()
 
-        names = ['dttop', 'dtbuild1', 'dtlink2', 'dtrun2', 'dtlink1',
-                 'dtlink3', 'dtlink4', 'dtrun1', 'dtlink5', 'dtrun3']
+        names = ['dttop', 'dtbuild1', 'dtbuild2', 'dtlink2',
+                 'dtlink1', 'dtlink3', 'dtlink4']
 
-        traversal = dag.traverse()
+        traversal = dag.traverse(deptype=('build', 'link'))
         self.assertEqual([x.name for x in traversal], names)
 
     def test_deptype_traversal_full(self):
@@ -500,15 +484,14 @@ class SpecDagTest(MockPackagesTest):
                  'dtlink1', 'dtlink3', 'dtlink4', 'dtrun1', 'dtlink5',
                  'dtrun3', 'dtbuild3']
 
-        traversal = dag.traverse(deptype_query=spack.alldeps)
+        traversal = dag.traverse(deptype=spack.alldeps)
         self.assertEqual([x.name for x in traversal], names)
 
-    def test_deptype_traversal_pythonpath(self):
+    def test_deptype_traversal_run(self):
         dag = Spec('dttop')
         dag.normalize()
 
-        names = ['dttop', 'dtbuild1', 'dtrun2', 'dtlink1', 'dtrun1',
-                 'dtrun3']
+        names = ['dttop', 'dtrun1', 'dtrun3']
 
-        traversal = dag.traverse(deptype=spack.nolink, deptype_query='run')
+        traversal = dag.traverse(deptype='run')
         self.assertEqual([x.name for x in traversal], names)
diff --git a/lib/spack/spack/test/spec_semantics.py b/lib/spack/spack/test/spec_semantics.py
index b174e5305c..79ffc99298 100644
--- a/lib/spack/spack/test/spec_semantics.py
+++ b/lib/spack/spack/test/spec_semantics.py
@@ -22,18 +22,18 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import unittest
 import spack.architecture
 from spack.spec import *
 from spack.test.mock_packages_test import *
 
+
 class SpecSematicsTest(MockPackagesTest):
     """This tests satisfies(), constrain() and other semantic operations
        on specs."""
 
-    # ================================================================================
+    # ========================================================================
     # Utility functions to set everything up.
-    # ================================================================================
+    # ========================================================================
     def check_satisfies(self, spec, anon_spec, concrete=False):
         left = Spec(spec, concrete=concrete)
         try:
@@ -49,7 +49,6 @@ class SpecSematicsTest(MockPackagesTest):
         # right by left.  Reverse is not always true.
         right.copy().constrain(left)
 
-
     def check_unsatisfiable(self, spec, anon_spec, concrete=False):
         left = Spec(spec, concrete=concrete)
         try:
@@ -62,7 +61,6 @@ class SpecSematicsTest(MockPackagesTest):
 
         self.assertRaises(UnsatisfiableSpecError, right.copy().constrain, left)
 
-
     def check_constrain(self, expected, spec, constraint):
         exp = Spec(expected)
         spec = Spec(spec)
@@ -70,53 +68,48 @@ class SpecSematicsTest(MockPackagesTest):
         spec.constrain(constraint)
         self.assertEqual(exp, spec)
 
-
     def check_constrain_changed(self, spec, constraint):
         spec = Spec(spec)
         self.assertTrue(spec.constrain(constraint))
 
-
     def check_constrain_not_changed(self, spec, constraint):
         spec = Spec(spec)
         self.assertFalse(spec.constrain(constraint))
 
-
     def check_invalid_constraint(self, spec, constraint):
         spec = Spec(spec)
         constraint = Spec(constraint)
         self.assertRaises(UnsatisfiableSpecError, spec.constrain, constraint)
 
-
-    # ================================================================================
+    # ========================================================================
     # Satisfiability
-    # ================================================================================
+    # ========================================================================
     def test_satisfies(self):
         self.check_satisfies('libelf@0.8.13', '@0:1')
         self.check_satisfies('libdwarf^libelf@0.8.13', '^libelf@0:1')
 
-
     def test_satisfies_namespace(self):
         self.check_satisfies('builtin.mpich', 'mpich')
         self.check_satisfies('builtin.mock.mpich', 'mpich')
 
-        # TODO: only works for deps now, but shouldn't we allow this for root spec?
+        # TODO: only works for deps now, but shouldn't we allow for root spec?
         # self.check_satisfies('builtin.mock.mpich', 'mpi')
 
         self.check_satisfies('builtin.mock.mpich', 'builtin.mock.mpich')
 
         self.check_unsatisfiable('builtin.mock.mpich', 'builtin.mpich')
 
-
     def test_satisfies_namespaced_dep(self):
         """Ensure spec from same or unspecified namespace satisfies namespace
            constraint."""
         self.check_satisfies('mpileaks ^builtin.mock.mpich', '^mpich')
 
         self.check_satisfies('mpileaks ^builtin.mock.mpich', '^mpi')
-        self.check_satisfies('mpileaks ^builtin.mock.mpich', '^builtin.mock.mpich')
-
-        self.check_unsatisfiable('mpileaks ^builtin.mock.mpich', '^builtin.mpich')
+        self.check_satisfies(
+            'mpileaks ^builtin.mock.mpich', '^builtin.mock.mpich')
 
+        self.check_unsatisfiable(
+            'mpileaks ^builtin.mock.mpich', '^builtin.mpich')
 
     def test_satisfies_compiler(self):
         self.check_satisfies('foo%gcc', '%gcc')
@@ -124,7 +117,6 @@ class SpecSematicsTest(MockPackagesTest):
         self.check_unsatisfiable('foo%intel', '%gcc')
         self.check_unsatisfiable('foo%intel', '%pgi')
 
-
     def test_satisfies_compiler_version(self):
         self.check_satisfies('foo%gcc', '%gcc@4.7.2')
         self.check_satisfies('foo%intel', '%intel@4.7.2')
@@ -139,7 +131,6 @@ class SpecSematicsTest(MockPackagesTest):
         self.check_satisfies('foo %gcc@4.7.3', '%gcc@4.7')
         self.check_unsatisfiable('foo %gcc@4.7', '%gcc@4.7.3')
 
-
     def test_satisfies_architecture(self):
         self.check_satisfies(
             'foo platform=test target=frontend os=frontend',
@@ -151,7 +142,6 @@ class SpecSematicsTest(MockPackagesTest):
             'foo platform=test target=default_target os=default_os',
             'platform=test target=default_target os=default_os')
 
-
     def test_satisfies_dependencies(self):
         self.check_satisfies('mpileaks^mpich', '^mpich')
         self.check_satisfies('mpileaks^zmpi', '^zmpi')
@@ -159,7 +149,6 @@ class SpecSematicsTest(MockPackagesTest):
         self.check_unsatisfiable('mpileaks^mpich', '^zmpi')
         self.check_unsatisfiable('mpileaks^zmpi', '^mpich')
 
-
     def test_satisfies_dependency_versions(self):
         self.check_satisfies('mpileaks^mpich@2.0', '^mpich@1:3')
         self.check_unsatisfiable('mpileaks^mpich@1.2', '^mpich@2.0')
@@ -173,7 +162,6 @@ class SpecSematicsTest(MockPackagesTest):
         self.check_unsatisfiable(
             'mpileaks^mpich@4.0^callpath@1.7', '^mpich@1:3^callpath@1.4:1.6')
 
-
     def test_satisfies_virtual_dependencies(self):
         self.check_satisfies('mpileaks^mpi', '^mpi')
         self.check_satisfies('mpileaks^mpi', '^mpich')
@@ -181,7 +169,6 @@ class SpecSematicsTest(MockPackagesTest):
         self.check_satisfies('mpileaks^mpi', '^zmpi')
         self.check_unsatisfiable('mpileaks^mpich', '^zmpi')
 
-
     def test_satisfies_virtual_dependency_versions(self):
         self.check_satisfies('mpileaks^mpi@1.5', '^mpi@1.2:1.6')
         self.check_unsatisfiable('mpileaks^mpi@3', '^mpi@1.2:1.6')
@@ -197,26 +184,23 @@ class SpecSematicsTest(MockPackagesTest):
         self.check_unsatisfiable('mpileaks^mpi@3:', '^mpich2')
         self.check_unsatisfiable('mpileaks^mpi@3:', '^mpich@1.0')
 
-
     def test_satisfies_matching_variant(self):
         self.check_satisfies('mpich+foo', 'mpich+foo')
         self.check_satisfies('mpich~foo', 'mpich~foo')
         self.check_satisfies('mpich foo=1', 'mpich foo=1')
 
-        #confirm that synonymous syntax works correctly
+        # confirm that synonymous syntax works correctly
         self.check_satisfies('mpich+foo', 'mpich foo=True')
         self.check_satisfies('mpich foo=true', 'mpich+foo')
         self.check_satisfies('mpich~foo', 'mpich foo=FALSE')
         self.check_satisfies('mpich foo=False', 'mpich~foo')
 
-
     def test_satisfies_unconstrained_variant(self):
         # only asked for mpich, no constraints.  Either will do.
         self.check_satisfies('mpich+foo', 'mpich')
         self.check_satisfies('mpich~foo', 'mpich')
         self.check_satisfies('mpich foo=1', 'mpich')
 
-
     def test_unsatisfiable_variants(self):
         # This case is different depending on whether the specs are concrete.
 
@@ -230,24 +214,21 @@ class SpecSematicsTest(MockPackagesTest):
         self.check_unsatisfiable('mpich', 'mpich~foo', True)
         self.check_unsatisfiable('mpich', 'mpich foo=1', True)
 
-
     def test_unsatisfiable_variant_mismatch(self):
         # No matchi in specs
         self.check_unsatisfiable('mpich~foo', 'mpich+foo')
         self.check_unsatisfiable('mpich+foo', 'mpich~foo')
         self.check_unsatisfiable('mpich foo=1', 'mpich foo=2')
 
-
     def test_satisfies_matching_compiler_flag(self):
         self.check_satisfies('mpich cppflags="-O3"', 'mpich cppflags="-O3"')
-        self.check_satisfies('mpich cppflags="-O3 -Wall"', 'mpich cppflags="-O3 -Wall"')
-
+        self.check_satisfies('mpich cppflags="-O3 -Wall"',
+                             'mpich cppflags="-O3 -Wall"')
 
     def test_satisfies_unconstrained_compiler_flag(self):
         # only asked for mpich, no constraints.  Any will do.
         self.check_satisfies('mpich cppflags="-O3"', 'mpich')
 
-
     def test_unsatisfiable_compiler_flag(self):
         # This case is different depending on whether the specs are concrete.
 
@@ -257,11 +238,10 @@ class SpecSematicsTest(MockPackagesTest):
         # 'mpich' is concrete:
         self.check_unsatisfiable('mpich', 'mpich cppflags="-O3"', True)
 
-
     def test_unsatisfiable_compiler_flag_mismatch(self):
         # No matchi in specs
-        self.check_unsatisfiable('mpich cppflags="-O3"', 'mpich cppflags="-O2"')
-
+        self.check_unsatisfiable(
+            'mpich cppflags="-O3"', 'mpich cppflags="-O2"')
 
     def test_satisfies_virtual(self):
         # Don't use check_satisfies: it checks constrain() too, and
@@ -270,25 +250,30 @@ class SpecSematicsTest(MockPackagesTest):
         self.assertTrue(Spec('mpich2').satisfies(Spec('mpi')))
         self.assertTrue(Spec('zmpi').satisfies(Spec('mpi')))
 
-
     def test_satisfies_virtual_dep_with_virtual_constraint(self):
         """Ensure we can satisfy virtual constraints when there are multiple
            vdep providers in the specs."""
-        self.assertTrue(Spec('netlib-lapack ^openblas').satisfies('netlib-lapack ^openblas'))
-        self.assertFalse(Spec('netlib-lapack ^netlib-blas').satisfies('netlib-lapack ^openblas'))
-
-        self.assertFalse(Spec('netlib-lapack ^openblas').satisfies('netlib-lapack ^netlib-blas'))
-        self.assertTrue(Spec('netlib-lapack ^netlib-blas').satisfies('netlib-lapack ^netlib-blas'))
-
-
-    # ================================================================================
+        self.assertTrue(
+            Spec('netlib-lapack ^openblas').satisfies(
+                'netlib-lapack ^openblas'))
+        self.assertFalse(
+            Spec('netlib-lapack ^netlib-blas').satisfies(
+                'netlib-lapack ^openblas'))
+
+        self.assertFalse(
+            Spec('netlib-lapack ^openblas').satisfies(
+                'netlib-lapack ^netlib-blas'))
+        self.assertTrue(
+            Spec('netlib-lapack ^netlib-blas').satisfies(
+                'netlib-lapack ^netlib-blas'))
+
+    # ========================================================================
     # Indexing specs
-    # ================================================================================
+    # ========================================================================
     def test_self_index(self):
         s = Spec('callpath')
         self.assertTrue(s['callpath'] == s)
 
-
     def test_dep_index(self):
         s = Spec('callpath')
         s.normalize()
@@ -304,7 +289,6 @@ class SpecSematicsTest(MockPackagesTest):
         self.assertTrue(s['libelf'].name   == 'libelf')
         self.assertTrue(s['mpi'].name      == 'mpi')
 
-
     def test_spec_contains_deps(self):
         s = Spec('callpath')
         s.normalize()
@@ -313,7 +297,6 @@ class SpecSematicsTest(MockPackagesTest):
         self.assertTrue('libelf' in s)
         self.assertTrue('mpi' in s)
 
-
     def test_virtual_index(self):
         s = Spec('callpath')
         s.concretize()
@@ -327,7 +310,6 @@ class SpecSematicsTest(MockPackagesTest):
         s_zmpi = Spec('callpath ^zmpi')
         s_zmpi.concretize()
 
-
         self.assertTrue(s['mpi'].name != 'mpi')
         self.assertTrue(s_mpich['mpi'].name == 'mpich')
         self.assertTrue(s_mpich2['mpi'].name == 'mpich2')
@@ -336,29 +318,34 @@ class SpecSematicsTest(MockPackagesTest):
         for spec in [s, s_mpich, s_mpich2, s_zmpi]:
             self.assertTrue('mpi' in spec)
 
-
-    # ================================================================================
+    # ========================================================================
     # Constraints
-    # ================================================================================
+    # ========================================================================
     def test_constrain_variants(self):
         self.check_constrain('libelf@2.1:2.5', 'libelf@0:2.5', 'libelf@2.1:3')
         self.check_constrain('libelf@2.1:2.5%gcc@4.5:4.6',
-                             'libelf@0:2.5%gcc@2:4.6', 'libelf@2.1:3%gcc@4.5:4.7')
+                             'libelf@0:2.5%gcc@2:4.6',
+                             'libelf@2.1:3%gcc@4.5:4.7')
 
         self.check_constrain('libelf+debug+foo', 'libelf+debug', 'libelf+foo')
-        self.check_constrain('libelf+debug+foo', 'libelf+debug', 'libelf+debug+foo')
+        self.check_constrain('libelf+debug+foo',
+                             'libelf+debug', 'libelf+debug+foo')
 
-        self.check_constrain('libelf debug=2 foo=1', 'libelf debug=2', 'libelf foo=1')
-        self.check_constrain('libelf debug=2 foo=1', 'libelf debug=2', 'libelf debug=2 foo=1')
+        self.check_constrain('libelf debug=2 foo=1',
+                             'libelf debug=2', 'libelf foo=1')
+        self.check_constrain('libelf debug=2 foo=1',
+                             'libelf debug=2', 'libelf debug=2 foo=1')
 
         self.check_constrain('libelf+debug~foo', 'libelf+debug', 'libelf~foo')
-        self.check_constrain('libelf+debug~foo', 'libelf+debug', 'libelf+debug~foo')
-
+        self.check_constrain('libelf+debug~foo',
+                             'libelf+debug', 'libelf+debug~foo')
 
     def test_constrain_compiler_flags(self):
-        self.check_constrain('libelf cflags="-O3" cppflags="-Wall"', 'libelf cflags="-O3"', 'libelf cppflags="-Wall"')
-        self.check_constrain('libelf cflags="-O3" cppflags="-Wall"', 'libelf cflags="-O3"', 'libelf cflags="-O3" cppflags="-Wall"')
-
+        self.check_constrain('libelf cflags="-O3" cppflags="-Wall"',
+                             'libelf cflags="-O3"', 'libelf cppflags="-Wall"')
+        self.check_constrain('libelf cflags="-O3" cppflags="-Wall"',
+                             'libelf cflags="-O3"',
+                             'libelf cflags="-O3" cppflags="-Wall"')
 
     def test_constrain_architecture(self):
         self.check_constrain('libelf target=default_target os=default_os',
@@ -369,21 +356,24 @@ class SpecSematicsTest(MockPackagesTest):
                              'libelf target=default_target os=default_os')
 
     def test_constrain_compiler(self):
-        self.check_constrain('libelf %gcc@4.4.7', 'libelf %gcc@4.4.7', 'libelf %gcc@4.4.7')
-        self.check_constrain('libelf %gcc@4.4.7', 'libelf', 'libelf %gcc@4.4.7')
-
+        self.check_constrain('libelf %gcc@4.4.7',
+                             'libelf %gcc@4.4.7', 'libelf %gcc@4.4.7')
+        self.check_constrain('libelf %gcc@4.4.7',
+                             'libelf', 'libelf %gcc@4.4.7')
 
     def test_invalid_constraint(self):
         self.check_invalid_constraint('libelf@0:2.0', 'libelf@2.1:3')
-        self.check_invalid_constraint('libelf@0:2.5%gcc@4.8:4.9', 'libelf@2.1:3%gcc@4.5:4.7')
+        self.check_invalid_constraint(
+            'libelf@0:2.5%gcc@4.8:4.9', 'libelf@2.1:3%gcc@4.5:4.7')
 
         self.check_invalid_constraint('libelf+debug', 'libelf~debug')
         self.check_invalid_constraint('libelf+debug~foo', 'libelf+debug+foo')
         self.check_invalid_constraint('libelf debug=2', 'libelf debug=1')
 
-        self.check_invalid_constraint('libelf cppflags="-O3"', 'libelf cppflags="-O2"')
+        self.check_invalid_constraint(
+            'libelf cppflags="-O3"', 'libelf cppflags="-O2"')
         self.check_invalid_constraint('libelf platform=test target=be os=be',
-                                          'libelf target=fe os=fe')
+                                      'libelf target=fe os=fe')
 
     def test_constrain_changed(self):
         self.check_constrain_changed('libelf', '@1.0')
@@ -396,9 +386,10 @@ class SpecSematicsTest(MockPackagesTest):
         self.check_constrain_changed('libelf', 'cppflags="-O3"')
 
         platform = spack.architecture.platform()
-        self.check_constrain_changed('libelf', 'target='+platform.target('default_target').name)
-        self.check_constrain_changed('libelf', 'os='+platform.operating_system('default_os').name)
-
+        self.check_constrain_changed(
+            'libelf', 'target=' + platform.target('default_target').name)
+        self.check_constrain_changed(
+            'libelf', 'os=' + platform.operating_system('default_os').name)
 
     def test_constrain_not_changed(self):
         self.check_constrain_not_changed('libelf', 'libelf')
@@ -409,12 +400,13 @@ class SpecSematicsTest(MockPackagesTest):
         self.check_constrain_not_changed('libelf+debug', '+debug')
         self.check_constrain_not_changed('libelf~debug', '~debug')
         self.check_constrain_not_changed('libelf debug=2', 'debug=2')
-        self.check_constrain_not_changed('libelf cppflags="-O3"', 'cppflags="-O3"')
+        self.check_constrain_not_changed(
+            'libelf cppflags="-O3"', 'cppflags="-O3"')
 
         platform = spack.architecture.platform()
         default_target = platform.target('default_target').name
-        self.check_constrain_not_changed('libelf target='+default_target, 'target='+default_target)
-
+        self.check_constrain_not_changed(
+            'libelf target=' + default_target, 'target=' + default_target)
 
     def test_constrain_dependency_changed(self):
         self.check_constrain_changed('libelf^foo', 'libelf^foo@1.0')
@@ -426,18 +418,25 @@ class SpecSematicsTest(MockPackagesTest):
 
         platform = spack.architecture.platform()
         default_target = platform.target('default_target').name
-        self.check_constrain_changed('libelf^foo', 'libelf^foo target='+default_target)
-
+        self.check_constrain_changed(
+            'libelf^foo', 'libelf^foo target=' + default_target)
 
     def test_constrain_dependency_not_changed(self):
         self.check_constrain_not_changed('libelf^foo@1.0', 'libelf^foo@1.0')
-        self.check_constrain_not_changed('libelf^foo@1.0:5.0', 'libelf^foo@1.0:5.0')
+        self.check_constrain_not_changed(
+            'libelf^foo@1.0:5.0', 'libelf^foo@1.0:5.0')
         self.check_constrain_not_changed('libelf^foo%gcc', 'libelf^foo%gcc')
-        self.check_constrain_not_changed('libelf^foo%gcc@4.5', 'libelf^foo%gcc@4.5')
-        self.check_constrain_not_changed('libelf^foo+debug', 'libelf^foo+debug')
-        self.check_constrain_not_changed('libelf^foo~debug', 'libelf^foo~debug')
-        self.check_constrain_not_changed('libelf^foo cppflags="-O3"', 'libelf^foo cppflags="-O3"')
+        self.check_constrain_not_changed(
+            'libelf^foo%gcc@4.5', 'libelf^foo%gcc@4.5')
+        self.check_constrain_not_changed(
+            'libelf^foo+debug', 'libelf^foo+debug')
+        self.check_constrain_not_changed(
+            'libelf^foo~debug', 'libelf^foo~debug')
+        self.check_constrain_not_changed(
+            'libelf^foo cppflags="-O3"', 'libelf^foo cppflags="-O3"')
 
         platform = spack.architecture.platform()
         default_target = platform.target('default_target').name
-        self.check_constrain_not_changed('libelf^foo target='+default_target, 'libelf^foo target='+default_target)
+        self.check_constrain_not_changed(
+            'libelf^foo target=' + default_target,
+            'libelf^foo target=' + default_target)
diff --git a/lib/spack/spack/test/spec_syntax.py b/lib/spack/spack/test/spec_syntax.py
index 4a534d7b5c..3079288c77 100644
--- a/lib/spack/spack/test/spec_syntax.py
+++ b/lib/spack/spack/test/spec_syntax.py
@@ -55,17 +55,22 @@ complex_lex = [Token(ID, 'mvapich_foo'),
 
 
 class SpecSyntaxTest(unittest.TestCase):
-    # ================================================================================
+    # ========================================================================
     # Parse checks
-    # ================================================================================
+    # ========================================================================
+
     def check_parse(self, expected, spec=None, remove_arch=True):
         """Assert that the provided spec is able to be parsed.
-           If this is called with one argument, it assumes that the string is
-           canonical (i.e., no spaces and ~ instead of - for variants) and that it
-           will convert back to the string it came from.
 
-           If this is called with two arguments, the first argument is the expected
-           canonical form and the second is a non-canonical input to be parsed.
+           If this is called with one argument, it assumes that the
+           string is canonical (i.e., no spaces and ~ instead of - for
+           variants) and that it will convert back to the string it came
+           from.
+
+           If this is called with two arguments, the first argument is
+           the expected canonical form and the second is a non-canonical
+           input to be parsed.
+
         """
         if spec is None:
             spec = expected
@@ -74,9 +79,8 @@ class SpecSyntaxTest(unittest.TestCase):
         parsed = (" ".join(str(spec) for spec in output))
         self.assertEqual(expected, parsed)
 
-
     def check_lex(self, tokens, spec):
-        """Check that the provided spec parses to the provided list of tokens."""
+        """Check that the provided spec parses to the provided token list."""
         lex_output = SpecLexer().lex(spec)
         for tok, spec_tok in zip(tokens, lex_output):
             if tok.type == ID:
@@ -85,9 +89,9 @@ class SpecSyntaxTest(unittest.TestCase):
                 # Only check the type for non-identifiers.
                 self.assertEqual(tok.type, spec_tok.type)
 
-    # ================================================================================
+    # ========================================================================
     # Parse checks
-    # ===============================================================================
+    # ========================================================================
     def test_package_names(self):
         self.check_parse("mvapich")
         self.check_parse("mvapich_foo")
@@ -104,18 +108,37 @@ class SpecSyntaxTest(unittest.TestCase):
         self.check_parse("openmpi^hwloc@1.2e6:1.4b7-rc3")
 
     def test_full_specs(self):
-        self.check_parse("mvapich_foo^_openmpi@1.2:1.4,1.6%intel@12.1+debug~qt_4^stackwalker@8.1_1e")
-        self.check_parse("mvapich_foo^_openmpi@1.2:1.4,1.6%intel@12.1 debug=2~qt_4^stackwalker@8.1_1e")
-        self.check_parse('mvapich_foo^_openmpi@1.2:1.4,1.6%intel@12.1 cppflags="-O3"+debug~qt_4^stackwalker@8.1_1e')
+        self.check_parse(
+            "mvapich_foo"
+            "^_openmpi@1.2:1.4,1.6%intel@12.1+debug~qt_4"
+            "^stackwalker@8.1_1e")
+        self.check_parse(
+            "mvapich_foo"
+            "^_openmpi@1.2:1.4,1.6%intel@12.1 debug=2~qt_4"
+            "^stackwalker@8.1_1e")
+        self.check_parse(
+            'mvapich_foo'
+            '^_openmpi@1.2:1.4,1.6%intel@12.1 cppflags="-O3"+debug~qt_4'
+            '^stackwalker@8.1_1e')
 
     def test_canonicalize(self):
         self.check_parse(
-            "mvapich_foo^_openmpi@1.2:1.4,1.6%intel@12.1:12.6+debug~qt_4^stackwalker@8.1_1e",
-            "mvapich_foo ^_openmpi@1.6,1.2:1.4%intel@12.1:12.6+debug~qt_4 ^stackwalker@8.1_1e")
+            "mvapich_foo"
+            "^_openmpi@1.2:1.4,1.6%intel@12.1:12.6+debug~qt_4"
+            "^stackwalker@8.1_1e",
+
+            "mvapich_foo "
+            "^_openmpi@1.6,1.2:1.4%intel@12.1:12.6+debug~qt_4 "
+            "^stackwalker@8.1_1e")
 
         self.check_parse(
-            "mvapich_foo^_openmpi@1.2:1.4,1.6%intel@12.1:12.6+debug~qt_4^stackwalker@8.1_1e",
-            "mvapich_foo ^stackwalker@8.1_1e ^_openmpi@1.6,1.2:1.4%intel@12.1:12.6~qt_4+debug")
+            "mvapich_foo"
+            "^_openmpi@1.2:1.4,1.6%intel@12.1:12.6+debug~qt_4"
+            "^stackwalker@8.1_1e",
+
+            "mvapich_foo "
+            "^stackwalker@8.1_1e "
+            "^_openmpi@1.6,1.2:1.4%intel@12.1:12.6~qt_4+debug")
 
         self.check_parse(
             "x^y@1,2:3,4%intel@1,2,3,4+a~b+c~d+e~f",
@@ -130,58 +153,81 @@ class SpecSyntaxTest(unittest.TestCase):
         self.assertRaises(SpecParseError, self.check_parse, "x::")
 
     def test_duplicate_variant(self):
-        self.assertRaises(DuplicateVariantError, self.check_parse, "x@1.2+debug+debug")
-        self.assertRaises(DuplicateVariantError, self.check_parse, "x ^y@1.2+debug debug=true")
-        self.assertRaises(DuplicateVariantError, self.check_parse, "x ^y@1.2 debug=false debug=true")
-        self.assertRaises(DuplicateVariantError, self.check_parse, "x ^y@1.2 debug=false~debug")
-
+        self.assertRaises(DuplicateVariantError,
+                          self.check_parse, "x@1.2+debug+debug")
+        self.assertRaises(DuplicateVariantError,
+                          self.check_parse, "x ^y@1.2+debug debug=true")
+        self.assertRaises(DuplicateVariantError, self.check_parse,
+                          "x ^y@1.2 debug=false debug=true")
+        self.assertRaises(DuplicateVariantError,
+                          self.check_parse, "x ^y@1.2 debug=false~debug")
 
     def test_duplicate_depdendence(self):
-        self.assertRaises(DuplicateDependencyError, self.check_parse, "x ^y ^y")
+        self.assertRaises(DuplicateDependencyError,
+                          self.check_parse, "x ^y ^y")
 
     def test_duplicate_compiler(self):
-        self.assertRaises(DuplicateCompilerSpecError, self.check_parse, "x%intel%intel")
-        self.assertRaises(DuplicateCompilerSpecError, self.check_parse, "x%intel%gcc")
-        self.assertRaises(DuplicateCompilerSpecError, self.check_parse, "x%gcc%intel")
-        self.assertRaises(DuplicateCompilerSpecError, self.check_parse, "x ^y%intel%intel")
-        self.assertRaises(DuplicateCompilerSpecError, self.check_parse, "x ^y%intel%gcc")
-        self.assertRaises(DuplicateCompilerSpecError, self.check_parse, "x ^y%gcc%intel")
-
-
-    # ================================================================================
+        self.assertRaises(DuplicateCompilerSpecError,
+                          self.check_parse, "x%intel%intel")
+        self.assertRaises(DuplicateCompilerSpecError,
+                          self.check_parse, "x%intel%gcc")
+        self.assertRaises(DuplicateCompilerSpecError,
+                          self.check_parse, "x%gcc%intel")
+        self.assertRaises(DuplicateCompilerSpecError,
+                          self.check_parse, "x ^y%intel%intel")
+        self.assertRaises(DuplicateCompilerSpecError,
+                          self.check_parse, "x ^y%intel%gcc")
+        self.assertRaises(DuplicateCompilerSpecError,
+                          self.check_parse, "x ^y%gcc%intel")
+
+    # ========================================================================
     # Lex checks
-    # ================================================================================
+    # ========================================================================
     def test_ambiguous(self):
         # This first one is ambiguous because - can be in an identifier AND
         # indicate disabling an option.
         self.assertRaises(
             AssertionError, self.check_lex, complex_lex,
-            "mvapich_foo^_openmpi@1.2:1.4,1.6%intel@12.1:12.6+debug-qt_4^stackwalker@8.1_1e")
+            "mvapich_foo"
+            "^_openmpi@1.2:1.4,1.6%intel@12.1:12.6+debug-qt_4"
+            "^stackwalker@8.1_1e")
 
-    # The following lexes are non-ambiguous (add a space before -qt_4) and should all
-    # result in the tokens in complex_lex
+    # The following lexes are non-ambiguous (add a space before -qt_4)
+    # and should all result in the tokens in complex_lex
     def test_minimal_spaces(self):
         self.check_lex(
             complex_lex,
-            "mvapich_foo^_openmpi@1.2:1.4,1.6%intel@12.1:12.6+debug -qt_4^stackwalker@8.1_1e")
+            "mvapich_foo"
+            "^_openmpi@1.2:1.4,1.6%intel@12.1:12.6+debug -qt_4"
+            "^stackwalker@8.1_1e")
         self.check_lex(
             complex_lex,
-            "mvapich_foo^_openmpi@1.2:1.4,1.6%intel@12.1:12.6+debug~qt_4^stackwalker@8.1_1e")
+            "mvapich_foo"
+            "^_openmpi@1.2:1.4,1.6%intel@12.1:12.6+debug~qt_4"
+            "^stackwalker@8.1_1e")
 
     def test_spaces_between_dependences(self):
         self.check_lex(
             complex_lex,
-            "mvapich_foo ^_openmpi@1.2:1.4,1.6%intel@12.1:12.6+debug -qt_4 ^stackwalker @ 8.1_1e")
+            "mvapich_foo "
+            "^_openmpi@1.2:1.4,1.6%intel@12.1:12.6+debug -qt_4 "
+            "^stackwalker @ 8.1_1e")
         self.check_lex(
             complex_lex,
-            "mvapich_foo ^_openmpi@1.2:1.4,1.6%intel@12.1:12.6+debug~qt_4 ^stackwalker @ 8.1_1e")
+            "mvapich_foo "
+            "^_openmpi@1.2:1.4,1.6%intel@12.1:12.6+debug~qt_4 "
+            "^stackwalker @ 8.1_1e")
 
     def test_spaces_between_options(self):
         self.check_lex(
             complex_lex,
-            "mvapich_foo ^_openmpi @1.2:1.4,1.6 %intel @12.1:12.6 +debug -qt_4 ^stackwalker @8.1_1e")
+            "mvapich_foo "
+            "^_openmpi @1.2:1.4,1.6 %intel @12.1:12.6 +debug -qt_4 "
+            "^stackwalker @8.1_1e")
 
     def test_way_too_many_spaces(self):
         self.check_lex(
             complex_lex,
-            "mvapich_foo ^ _openmpi @ 1.2 : 1.4 , 1.6 % intel @ 12.1 : 12.6 + debug - qt_4 ^ stackwalker @ 8.1_1e")
+            "mvapich_foo "
+            "^ _openmpi @1.2 : 1.4 , 1.6 % intel @ 12.1 : 12.6 + debug - qt_4 "
+            "^ stackwalker @ 8.1_1e")
diff --git a/lib/spack/spack/test/spec_yaml.py b/lib/spack/spack/test/spec_yaml.py
index 0230fc203a..964aea9422 100644
--- a/lib/spack/spack/test/spec_yaml.py
+++ b/lib/spack/spack/test/spec_yaml.py
@@ -30,41 +30,36 @@ YAML format preserves DAG informatoin in the spec.
 from spack.spec import Spec
 from spack.test.mock_packages_test import *
 
-class SpecDagTest(MockPackagesTest):
+
+class SpecYamlTest(MockPackagesTest):
 
     def check_yaml_round_trip(self, spec):
         yaml_text = spec.to_yaml()
         spec_from_yaml = Spec.from_yaml(yaml_text)
         self.assertTrue(spec.eq_dag(spec_from_yaml))
 
-
     def test_simple_spec(self):
         spec = Spec('mpileaks')
         self.check_yaml_round_trip(spec)
 
-
     def test_normal_spec(self):
         spec = Spec('mpileaks+debug~opt')
         spec.normalize()
         self.check_yaml_round_trip(spec)
 
-
     def test_ambiguous_version_spec(self):
         spec = Spec('mpileaks@1.0:5.0,6.1,7.3+debug~opt')
         spec.normalize()
         self.check_yaml_round_trip(spec)
 
-
     def test_concrete_spec(self):
         spec = Spec('mpileaks+debug~opt')
         spec.concretize()
         self.check_yaml_round_trip(spec)
 
-
     def test_yaml_subdag(self):
         spec = Spec('mpileaks^mpich+debug')
         spec.concretize()
-
         yaml_spec = Spec.from_yaml(spec.to_yaml())
 
         for dep in ('callpath', 'mpich', 'dyninst', 'libdwarf', 'libelf'):
diff --git a/lib/spack/spack/test/stage.py b/lib/spack/spack/test/stage.py
index d3e3bf1383..ec661bfe50 100644
--- a/lib/spack/spack/test/stage.py
+++ b/lib/spack/spack/test/stage.py
@@ -62,6 +62,7 @@ def use_tmp(use_tmp):
 
 
 class StageTest(unittest.TestCase):
+
     def setUp(self):
         """This sets up a mock archive to fetch, and a mock temp space for use
            by the Stage class.  It doesn't actually create the Stage -- that
@@ -89,7 +90,6 @@ class StageTest(unittest.TestCase):
         # be removed.
         self.working_dir = os.getcwd()
 
-
     def tearDown(self):
         """Blows away the test environment directory."""
         shutil.rmtree(test_files_dir)
@@ -100,7 +100,6 @@ class StageTest(unittest.TestCase):
         # restore spack's original tmp environment
         spack.tmp_dirs = self.old_tmp_dirs
 
-
     def get_stage_path(self, stage, stage_name):
         """Figure out where a stage should be living.  This depends on
            whether it's named.
@@ -114,7 +113,6 @@ class StageTest(unittest.TestCase):
             self.assertTrue(stage.path.startswith(spack.stage_path))
             return stage.path
 
-
     def check_setup(self, stage, stage_name):
         """Figure out whether a stage was set up correctly."""
         stage_path = self.get_stage_path(stage, stage_name)
@@ -139,14 +137,12 @@ class StageTest(unittest.TestCase):
             # Make sure the stage path is NOT a link for a non-tmp stage
             self.assertFalse(os.path.islink(stage_path))
 
-
     def check_fetch(self, stage, stage_name):
         stage_path = self.get_stage_path(stage, stage_name)
         self.assertTrue(archive_name in os.listdir(stage_path))
         self.assertEqual(join_path(stage_path, archive_name),
                          stage.fetcher.archive_file)
 
-
     def check_expand_archive(self, stage, stage_name):
         stage_path = self.get_stage_path(stage, stage_name)
         self.assertTrue(archive_name in os.listdir(stage_path))
@@ -162,19 +158,16 @@ class StageTest(unittest.TestCase):
         with open(readme) as file:
             self.assertEqual(readme_text, file.read())
 
-
     def check_chdir(self, stage, stage_name):
         stage_path = self.get_stage_path(stage, stage_name)
         self.assertEqual(os.path.realpath(stage_path), os.getcwd())
 
-
     def check_chdir_to_source(self, stage, stage_name):
         stage_path = self.get_stage_path(stage, stage_name)
         self.assertEqual(
             join_path(os.path.realpath(stage_path), archive_dir),
             os.getcwd())
 
-
     def check_destroy(self, stage, stage_name):
         """Figure out whether a stage was destroyed correctly."""
         stage_path = self.get_stage_path(stage, stage_name)
@@ -187,35 +180,30 @@ class StageTest(unittest.TestCase):
             target = os.path.realpath(stage_path)
             self.assertFalse(os.path.exists(target))
 
-
     def test_setup_and_destroy_name_with_tmp(self):
         with use_tmp(True):
             with Stage(archive_url, name=stage_name) as stage:
                 self.check_setup(stage, stage_name)
             self.check_destroy(stage, stage_name)
 
-
     def test_setup_and_destroy_name_without_tmp(self):
         with use_tmp(False):
             with Stage(archive_url, name=stage_name) as stage:
                 self.check_setup(stage, stage_name)
             self.check_destroy(stage, stage_name)
 
-
     def test_setup_and_destroy_no_name_with_tmp(self):
         with use_tmp(True):
             with Stage(archive_url) as stage:
                 self.check_setup(stage, None)
             self.check_destroy(stage, None)
 
-
     def test_setup_and_destroy_no_name_without_tmp(self):
         with use_tmp(False):
             with Stage(archive_url) as stage:
                 self.check_setup(stage, None)
             self.check_destroy(stage, None)
 
-
     def test_chdir(self):
         with Stage(archive_url, name=stage_name) as stage:
             stage.chdir()
@@ -223,7 +211,6 @@ class StageTest(unittest.TestCase):
             self.check_chdir(stage, stage_name)
         self.check_destroy(stage, stage_name)
 
-
     def test_fetch(self):
         with Stage(archive_url, name=stage_name) as stage:
             stage.fetch()
@@ -232,7 +219,6 @@ class StageTest(unittest.TestCase):
             self.check_fetch(stage, stage_name)
         self.check_destroy(stage, stage_name)
 
-
     def test_expand_archive(self):
         with Stage(archive_url, name=stage_name) as stage:
             stage.fetch()
@@ -242,8 +228,7 @@ class StageTest(unittest.TestCase):
             self.check_expand_archive(stage, stage_name)
         self.check_destroy(stage, stage_name)
 
-
-    def test_expand_archive(self):
+    def test_expand_archive_with_chdir(self):
         with Stage(archive_url, name=stage_name) as stage:
             stage.fetch()
             self.check_setup(stage, stage_name)
@@ -254,7 +239,6 @@ class StageTest(unittest.TestCase):
             self.check_chdir_to_source(stage, stage_name)
         self.check_destroy(stage, stage_name)
 
-
     def test_restage(self):
         with Stage(archive_url, name=stage_name) as stage:
             stage.fetch()
@@ -278,20 +262,17 @@ class StageTest(unittest.TestCase):
             self.assertFalse('foobar' in os.listdir(stage.source_path))
         self.check_destroy(stage, stage_name)
 
-
     def test_no_keep_without_exceptions(self):
         with Stage(archive_url, name=stage_name, keep=False) as stage:
             pass
         self.check_destroy(stage, stage_name)
 
-
     def test_keep_without_exceptions(self):
         with Stage(archive_url, name=stage_name, keep=True) as stage:
             pass
         path = self.get_stage_path(stage, stage_name)
         self.assertTrue(os.path.isdir(path))
 
-
     def test_no_keep_with_exceptions(self):
         try:
             with Stage(archive_url, name=stage_name, keep=False) as stage:
@@ -300,8 +281,7 @@ class StageTest(unittest.TestCase):
             path = self.get_stage_path(stage, stage_name)
             self.assertTrue(os.path.isdir(path))
         except:
-            pass # ignore here.
-
+            pass  # ignore here.
 
     def test_keep_exceptions(self):
         try:
@@ -311,4 +291,4 @@ class StageTest(unittest.TestCase):
             path = self.get_stage_path(stage, stage_name)
             self.assertTrue(os.path.isdir(path))
         except:
-            pass # ignore here.
+            pass  # ignore here.
diff --git a/lib/spack/spack/test/svn_fetch.py b/lib/spack/spack/test/svn_fetch.py
index 0a745a090b..9ef7593ed1 100644
--- a/lib/spack/spack/test/svn_fetch.py
+++ b/lib/spack/spack/test/svn_fetch.py
@@ -94,17 +94,15 @@ class SvnFetchTest(MockPackagesTest):
 
             self.assert_rev(rev)
 
-
     def test_fetch_default(self):
         """Test a default checkout and make sure it's on rev 1"""
         self.try_fetch(self.repo.r1, self.repo.r1_file, {
-            'svn' : self.repo.url
+            'svn': self.repo.url
         })
 
-
     def test_fetch_r1(self):
         """Test fetching an older revision (0)."""
         self.try_fetch(self.repo.r0, self.repo.r0_file, {
-            'svn'      : self.repo.url,
-            'revision' : self.repo.r0
+            'svn': self.repo.url,
+            'revision': self.repo.r0
         })
diff --git a/lib/spack/spack/test/tally_plugin.py b/lib/spack/spack/test/tally_plugin.py
index 96af1c9b21..808694d186 100644
--- a/lib/spack/spack/test/tally_plugin.py
+++ b/lib/spack/spack/test/tally_plugin.py
@@ -26,6 +26,7 @@ import os
 
 from nose.plugins import Plugin
 
+
 class Tally(Plugin):
     name = 'tally'
 
diff --git a/lib/spack/spack/test/url_extrapolate.py b/lib/spack/spack/test/url_extrapolate.py
index ffd4230f71..ca14dab958 100644
--- a/lib/spack/spack/test/url_extrapolate.py
+++ b/lib/spack/spack/test/url_extrapolate.py
@@ -34,20 +34,21 @@ class UrlExtrapolateTest(unittest.TestCase):
     def check_url(self, base, version, new_url):
         self.assertEqual(url.substitute_version(base, version), new_url)
 
-
     def test_libelf_version(self):
         base = "http://www.mr511.de/software/libelf-0.8.13.tar.gz"
         self.check_url(base, '0.8.13', base)
-        self.check_url(base, '0.8.12', "http://www.mr511.de/software/libelf-0.8.12.tar.gz")
-        self.check_url(base, '0.3.1',  "http://www.mr511.de/software/libelf-0.3.1.tar.gz")
-        self.check_url(base, '1.3.1b', "http://www.mr511.de/software/libelf-1.3.1b.tar.gz")
-
+        self.check_url(
+            base, '0.8.12', "http://www.mr511.de/software/libelf-0.8.12.tar.gz")
+        self.check_url(
+            base, '0.3.1',  "http://www.mr511.de/software/libelf-0.3.1.tar.gz")
+        self.check_url(
+            base, '1.3.1b', "http://www.mr511.de/software/libelf-1.3.1b.tar.gz")
 
     def test_libdwarf_version(self):
         base = "http://www.prevanders.net/libdwarf-20130729.tar.gz"
         self.check_url(base, '20130729', base)
-        self.check_url(base, '8.12', "http://www.prevanders.net/libdwarf-8.12.tar.gz")
-
+        self.check_url(
+            base, '8.12', "http://www.prevanders.net/libdwarf-8.12.tar.gz")
 
     def test_dyninst_version(self):
         # Dyninst has a version twice in the URL.
@@ -58,7 +59,6 @@ class UrlExtrapolateTest(unittest.TestCase):
         self.check_url(base, '8.3.1',
                        "http://www.dyninst.org/sites/default/files/downloads/dyninst/8.3.1/DyninstAPI-8.3.1.tgz")
 
-
     def test_partial_version_prefix(self):
         # Test now with a partial prefix earlier in the URL -- this is
         # hard to figure out so Spack only substitutes the last
@@ -72,7 +72,6 @@ class UrlExtrapolateTest(unittest.TestCase):
         self.check_url(base, '8.3.1',
                        "http://www.dyninst.org/sites/default/files/downloads/dyninst/8.1/DyninstAPI-8.3.1.tgz")
 
-
     def test_scalasca_partial_version(self):
         # Note that this probably doesn't actually work, but sites are
         # inconsistent about their directory structure, so it's not
@@ -84,19 +83,16 @@ class UrlExtrapolateTest(unittest.TestCase):
         self.check_url('http://apps.fz-juelich.de/scalasca/releases/cube/4.3/dist/cube-4.3-TP1.tar.gz', '8.3.1',
                        'http://apps.fz-juelich.de/scalasca/releases/cube/4.3/dist/cube-8.3.1.tar.gz')
 
-
     def test_mpileaks_version(self):
         self.check_url('https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz', '2.1.3',
                        'https://github.com/hpc/mpileaks/releases/download/v2.1.3/mpileaks-2.1.3.tar.gz')
 
-
     def test_gcc(self):
         self.check_url('http://open-source-box.org/gcc/gcc-4.9.2/gcc-4.9.2.tar.bz2', '4.7',
                        'http://open-source-box.org/gcc/gcc-4.7/gcc-4.7.tar.bz2')
         self.check_url('http://open-source-box.org/gcc/gcc-4.4.7/gcc-4.4.7.tar.bz2', '4.4.7',
                        'http://open-source-box.org/gcc/gcc-4.4.7/gcc-4.4.7.tar.bz2')
 
-
     def test_github_raw(self):
         self.check_url('https://github.com/losalamos/CLAMR/blob/packages/PowerParser_v2.0.7.tgz?raw=true', '2.0.7',
                        'https://github.com/losalamos/CLAMR/blob/packages/PowerParser_v2.0.7.tgz?raw=true')
diff --git a/lib/spack/spack/test/url_parse.py b/lib/spack/spack/test/url_parse.py
index 648996aaaa..6c944a3e7a 100644
--- a/lib/spack/spack/test/url_parse.py
+++ b/lib/spack/spack/test/url_parse.py
@@ -32,11 +32,11 @@ import spack.url as url
 
 
 class UrlParseTest(unittest.TestCase):
+
     def assert_not_detected(self, string):
         self.assertRaises(
             url.UndetectableVersionError, url.parse_name_and_version, string)
 
-
     def check(self, name, v, string, **kwargs):
         # Make sure correct name and version are extracted.
         parsed_name, parsed_v = url.parse_name_and_version(string)
@@ -52,7 +52,6 @@ class UrlParseTest(unittest.TestCase):
         # build one with a specific version.
         self.assertEqual(string, url.substitute_version(string, v))
 
-
     def test_wwwoffle_version(self):
         self.check(
             'wwwoffle', '2.9h',
@@ -72,7 +71,7 @@ class UrlParseTest(unittest.TestCase):
 
     def test_version_all_dots(self):
         self.check(
-            'foo.bar.la', '1.14','http://example.com/foo.bar.la.1.14.zip')
+            'foo.bar.la', '1.14', 'http://example.com/foo.bar.la.1.14.zip')
 
     def test_version_underscore_separator(self):
         self.check(
@@ -286,7 +285,7 @@ class UrlParseTest(unittest.TestCase):
             'mvapich2', '1.9',
             'http://mvapich.cse.ohio-state.edu/download/mvapich2/mv2/mvapich2-1.9.tgz')
 
-    def test_mvapich2_19_version(self):
+    def test_mvapich2_20_version(self):
         self.check(
             'mvapich2', '2.0',
             'http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.0.tar.gz')
diff --git a/lib/spack/spack/test/url_substitution.py b/lib/spack/spack/test/url_substitution.py
index 9cc04834b6..ea6374e3d2 100644
--- a/lib/spack/spack/test/url_substitution.py
+++ b/lib/spack/spack/test/url_substitution.py
@@ -26,37 +26,31 @@
 This test does sanity checks on substituting new versions into URLs
 """
 import unittest
-
 import spack.url as url
 
 
+base = "https://comp.llnl.gov/linear_solvers/download/hypre-2.9.0b.tar.gz"
+stem = "https://comp.llnl.gov/linear_solvers/download/hypre-"
+
+
 class PackageSanityTest(unittest.TestCase):
-    def test_hypre_url_substitution(self):
-        base = "https://computation-rnd.llnl.gov/linear_solvers/download/hypre-2.9.0b.tar.gz"
 
+    def test_hypre_url_substitution(self):
         self.assertEqual(url.substitute_version(base, '2.9.0b'), base)
         self.assertEqual(
-            url.substitute_version(base, '2.8.0b'),
-            "https://computation-rnd.llnl.gov/linear_solvers/download/hypre-2.8.0b.tar.gz")
+            url.substitute_version(base, '2.8.0b'), stem + "2.8.0b.tar.gz")
         self.assertEqual(
-            url.substitute_version(base, '2.7.0b'),
-            "https://computation-rnd.llnl.gov/linear_solvers/download/hypre-2.7.0b.tar.gz")
+            url.substitute_version(base, '2.7.0b'), stem + "2.7.0b.tar.gz")
         self.assertEqual(
-            url.substitute_version(base, '2.6.0b'),
-            "https://computation-rnd.llnl.gov/linear_solvers/download/hypre-2.6.0b.tar.gz")
+            url.substitute_version(base, '2.6.0b'), stem + "2.6.0b.tar.gz")
         self.assertEqual(
-            url.substitute_version(base, '1.14.0b'),
-            "https://computation-rnd.llnl.gov/linear_solvers/download/hypre-1.14.0b.tar.gz")
+            url.substitute_version(base, '1.14.0b'), stem + "1.14.0b.tar.gz")
         self.assertEqual(
-            url.substitute_version(base, '1.13.0b'),
-            "https://computation-rnd.llnl.gov/linear_solvers/download/hypre-1.13.0b.tar.gz")
+            url.substitute_version(base, '1.13.0b'), stem + "1.13.0b.tar.gz")
         self.assertEqual(
-            url.substitute_version(base, '2.0.0'),
-            "https://computation-rnd.llnl.gov/linear_solvers/download/hypre-2.0.0.tar.gz")
+            url.substitute_version(base, '2.0.0'), stem + "2.0.0.tar.gz")
         self.assertEqual(
-            url.substitute_version(base, '1.6.0'),
-            "https://computation-rnd.llnl.gov/linear_solvers/download/hypre-1.6.0.tar.gz")
-
+            url.substitute_version(base, '1.6.0'), stem + "1.6.0.tar.gz")
 
     def test_otf2_url_substitution(self):
         base = "http://www.vi-hps.org/upload/packages/otf2/otf2-1.4.tar.gz"
diff --git a/lib/spack/spack/test/yaml.py b/lib/spack/spack/test/yaml.py
index f1b83e7b71..dedbd15d10 100644
--- a/lib/spack/spack/test/yaml.py
+++ b/lib/spack/spack/test/yaml.py
@@ -45,26 +45,25 @@ config_file:
 """
 
 test_data = {
-    'config_file' : syaml.syaml_dict([
+    'config_file': syaml.syaml_dict([
         ('x86_64', syaml.syaml_dict([
             ('foo', '/path/to/foo'),
             ('bar', '/path/to/bar'),
-            ('baz', '/path/to/baz' )])),
-        ('some_list', [ 'item 1', 'item 2', 'item 3' ]),
-        ('another_list', [ 1, 2, 3 ]),
+            ('baz', '/path/to/baz')])),
+        ('some_list', ['item 1', 'item 2', 'item 3']),
+        ('another_list', [1, 2, 3]),
         ('some_key', 'some_string')
     ])}
 
+
 class YamlTest(unittest.TestCase):
 
     def setUp(self):
         self.data = syaml.load(test_file)
 
-
     def test_parse(self):
         self.assertEqual(test_data, self.data)
 
-
     def test_dict_order(self):
         self.assertEqual(
             ['x86_64', 'some_list', 'another_list', 'some_key'],
@@ -74,7 +73,6 @@ class YamlTest(unittest.TestCase):
             ['foo', 'bar', 'baz'],
             self.data['config_file']['x86_64'].keys())
 
-
     def test_line_numbers(self):
         def check(obj, start_line, end_line):
             self.assertEqual(obj._start_mark.line, start_line)
diff --git a/lib/spack/spack/url.py b/lib/spack/spack/url.py
index f678a2dca9..02c9c04380 100644
--- a/lib/spack/spack/url.py
+++ b/lib/spack/spack/url.py
@@ -56,12 +56,12 @@ import spack.error
 import spack.util.compression as comp
 from spack.version import Version
 
+
 #
 # Note: We call the input to most of these functions a "path" but the functions
 # work on paths and URLs.  There's not a good word for both of these, but
 # "path" seemed like the most generic term.
 #
-
 def find_list_url(url):
     """Finds a good list URL for the supplied URL.  This depends on
        the site.  By default, just assumes that a good list URL is the
@@ -71,8 +71,8 @@ def find_list_url(url):
 
     url_types = [
         # e.g. https://github.com/llnl/callpath/archive/v1.0.1.tar.gz
-        (r'^(https://github.com/[^/]+/[^/]+)/archive/', lambda m: m.group(1) + '/releases')
-        ]
+        (r'^(https://github.com/[^/]+/[^/]+)/archive/',
+         lambda m: m.group(1) + '/releases')]
 
     for pattern, fun in url_types:
         match = re.search(pattern, url)
@@ -89,8 +89,10 @@ def strip_query_and_fragment(path):
 
         query, frag = components[3:5]
         suffix = ''
-        if query: suffix += '?' + query
-        if frag:  suffix += '#' + frag
+        if query:
+            suffix += '?' + query
+        if frag:
+            suffix += '#' + frag
 
         return (urlunsplit(stripped), suffix)
 
@@ -152,8 +154,10 @@ def downloaded_file_extension(path):
     """
     match = re.search(r'github.com/.+/(zip|tar)ball/', path)
     if match:
-        if   match.group(1) == 'zip': return 'zip'
-        elif match.group(1) == 'tar': return 'tar.gz'
+        if match.group(1) == 'zip':
+            return 'zip'
+        elif match.group(1) == 'tar':
+            return 'tar.gz'
 
     prefix, ext, suffix = split_url_extension(path)
     if not ext:
@@ -193,7 +197,8 @@ def parse_version_offset(path):
         (r'[-_](R\d+[AB]\d*(-\d+)?)', path),
 
         # e.g., https://github.com/hpc/libcircle/releases/download/0.2.1-rc.1/libcircle-0.2.1-rc.1.tar.gz
-        # e.g., https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz
+        # e.g.,
+        # https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz
         (r'github.com/[^/]+/[^/]+/releases/download/v?([^/]+)/.*$', path),
 
         # e.g. boost_1_39_0
@@ -201,7 +206,7 @@ def parse_version_offset(path):
 
         # e.g. foobar-4.5.1-1
         # e.g. ruby-1.9.1-p243
-        (r'-((\d+\.)*\d\.\d+-(p|rc|RC)?\d+)(?:[-._](?:bin|dist|stable|src|sources))?$', stem),
+        (r'-((\d+\.)*\d\.\d+-(p|rc|RC)?\d+)(?:[-._](?:bin|dist|stable|src|sources))?$', stem),  # noqa
 
         # e.g. lame-398-1
         (r'-((\d)+-\d)', stem),
@@ -275,7 +280,8 @@ def parse_name_offset(path, v=None):
 
     name_types = [
         (r'/sourceforge/([^/]+)/', path),
-        (r'github.com/[^/]+/[^/]+/releases/download/%s/(.*)-%s$' % (v, v), path),
+        (r'github.com/[^/]+/[^/]+/releases/download/%s/(.*)-%s$' %
+         (v, v), path),
         (r'/([^/]+)/(tarball|zipball)/', path),
         (r'/([^/]+)[_.-](bin|dist|stable|src|sources)[_.-]%s' % v, path),
         (r'github.com/[^/]+/([^/]+)/archive', path),
@@ -283,7 +289,8 @@ def parse_name_offset(path, v=None):
         (r'([^/]+)[_.-]v?%s' % v, stem),   # prefer the stem
         (r'([^/]+)%s' % v, stem),
 
-        (r'/([^/]+)[_.-]v?%s' % v, path),   # accept the path if name is not in stem.
+        # accept the path if name is not in stem.
+        (r'/([^/]+)[_.-]v?%s' % v, path),
         (r'/([^/]+)%s' % v, path),
 
         (r'^([^/]+)[_.-]v?%s' % v, path),
@@ -326,7 +333,7 @@ def insensitize(string):
     return re.sub(r'([a-zA-Z])', to_ins, string)
 
 
-def cumsum(elts, init=0, fn=lambda x:x):
+def cumsum(elts, init=0, fn=lambda x: x):
     """Return cumulative sum of result of fn on each element in elts."""
     sums = []
     s = init
@@ -337,21 +344,20 @@ def cumsum(elts, init=0, fn=lambda x:x):
 
 
 def substitution_offsets(path):
-    """This returns offsets for substituting versions and names in the provided path.
-       It is a helper for substitute_version().
+    """This returns offsets for substituting versions and names in the
+       provided path.  It is a helper for substitute_version().
     """
     # Get name and version offsets
     try:
         ver,  vs, vl = parse_version_offset(path)
         name, ns, nl = parse_name_offset(path, ver)
-    except UndetectableNameError, e:
+    except UndetectableNameError:
         return (None, -1, -1, (), ver, vs, vl, (vs,))
-    except UndetectableVersionError, e:
+    except UndetectableVersionError:
         return (None, -1, -1, (), None, -1, -1, ())
 
     # protect extensions like bz2 from getting inadvertently
     # considered versions.
-    ext = comp.extension(path)
     path = comp.strip_extension(path)
 
     # Construct a case-insensitive regular expression for the package name.
@@ -449,7 +455,7 @@ def color_url(path, **kwargs):
           Cyan: The version found by parse_version_offset().
           Red:  The name found by parse_name_offset().
 
-          Green:   Instances of version string substituted by substitute_version().
+          Green:   Instances of version string from substitute_version().
           Magenta: Instances of the name (protected from substitution).
 
        Optional args:
@@ -469,31 +475,46 @@ def color_url(path, **kwargs):
     nerr = verr = 0
     out = StringIO()
     for i in range(len(path)):
-        if   i == vs:    out.write('@c'); verr += 1
-        elif i == ns:    out.write('@r'); nerr += 1
+        if i == vs:
+            out.write('@c')
+            verr += 1
+        elif i == ns:
+            out.write('@r')
+            nerr += 1
         elif subs:
-            if i in voffs: out.write('@g')
-            elif i in noffs: out.write('@m')
+            if i in voffs:
+                out.write('@g')
+            elif i in noffs:
+                out.write('@m')
 
         out.write(path[i])
 
-        if   i == vs + vl - 1:  out.write('@.'); verr += 1
-        elif i == ns + nl - 1:  out.write('@.'); nerr += 1
+        if i == vs + vl - 1:
+            out.write('@.')
+            verr += 1
+        elif i == ns + nl - 1:
+            out.write('@.')
+            nerr += 1
         elif subs:
             if i in vends or i in nends:
                 out.write('@.')
 
     if errors:
-        if nerr == 0: out.write(" @r{[no name]}")
-        if verr == 0: out.write(" @r{[no version]}")
-        if nerr == 1: out.write(" @r{[incomplete name]}")
-        if verr == 1: out.write(" @r{[incomplete version]}")
+        if nerr == 0:
+            out.write(" @r{[no name]}")
+        if verr == 0:
+            out.write(" @r{[no version]}")
+        if nerr == 1:
+            out.write(" @r{[incomplete name]}")
+        if verr == 1:
+            out.write(" @r{[incomplete version]}")
 
     return colorize(out.getvalue())
 
 
 class UrlParseError(spack.error.SpackError):
     """Raised when the URL module can't parse something correctly."""
+
     def __init__(self, msg, path):
         super(UrlParseError, self).__init__(msg)
         self.path = path
@@ -501,6 +522,7 @@ class UrlParseError(spack.error.SpackError):
 
 class UndetectableVersionError(UrlParseError):
     """Raised when we can't parse a version from a string."""
+
     def __init__(self, path):
         super(UndetectableVersionError, self).__init__(
             "Couldn't detect version in: " + path, path)
@@ -508,6 +530,7 @@ class UndetectableVersionError(UrlParseError):
 
 class UndetectableNameError(UrlParseError):
     """Raised when we can't parse a package name from a string."""
+
     def __init__(self, path):
         super(UndetectableNameError, self).__init__(
             "Couldn't parse package name in: " + path, path)
diff --git a/lib/spack/spack/util/compression.py b/lib/spack/spack/util/compression.py
index dc1188eb0f..64554ab2f7 100644
--- a/lib/spack/spack/util/compression.py
+++ b/lib/spack/spack/util/compression.py
@@ -32,7 +32,9 @@ PRE_EXTS = ["tar"]
 EXTS     = ["gz", "bz2", "xz", "Z", "zip", "tgz"]
 
 # Add PRE_EXTS and EXTS last so that .tar.gz is matched *before* .tar or .gz
-ALLOWED_ARCHIVE_TYPES = [".".join(l) for l in product(PRE_EXTS, EXTS)] + PRE_EXTS + EXTS
+ALLOWED_ARCHIVE_TYPES = [".".join(l) for l in product(
+    PRE_EXTS, EXTS)] + PRE_EXTS + EXTS
+
 
 def allowed_archive(path):
     return any(path.endswith(t) for t in ALLOWED_ARCHIVE_TYPES)
diff --git a/lib/spack/spack/util/crypto.py b/lib/spack/spack/util/crypto.py
index 1ae9793518..22777fdb68 100644
--- a/lib/spack/spack/util/crypto.py
+++ b/lib/spack/spack/util/crypto.py
@@ -31,7 +31,7 @@ _acceptable_hashes = [
     hashlib.sha224,
     hashlib.sha256,
     hashlib.sha384,
-    hashlib.sha512 ]
+    hashlib.sha512]
 
 """Index for looking up hasher for a digest."""
 _size_to_hash = dict((h().digest_size, h) for h in _acceptable_hashes)
@@ -52,7 +52,6 @@ def checksum(hashlib_algo, filename, **kwargs):
     return hasher.hexdigest()
 
 
-
 class Checker(object):
     """A checker checks files against one particular hex digest.
        It will automatically determine what hashing algorithm
@@ -74,25 +73,25 @@ class Checker(object):
        adjusting the block_size optional arg.  By default it's
        a 1MB (2**20 bytes) buffer.
     """
+
     def __init__(self, hexdigest, **kwargs):
         self.block_size = kwargs.get('block_size', 2**20)
         self.hexdigest = hexdigest
         self.sum       = None
 
         bytes = len(hexdigest) / 2
-        if not bytes in _size_to_hash:
+        if bytes not in _size_to_hash:
             raise ValueError(
-                'Spack knows no hash algorithm for this digest: %s' % hexdigest)
+                'Spack knows no hash algorithm for this digest: %s'
+                % hexdigest)
 
         self.hash_fun = _size_to_hash[bytes]
 
-
     @property
     def hash_name(self):
         """Get the name of the hash function this Checker is using."""
         return self.hash_fun().name
 
-
     def check(self, filename):
         """Read the file with the specified name and check its checksum
            against self.hexdigest.  Return True if they match, False
diff --git a/lib/spack/spack/util/debug.py b/lib/spack/spack/util/debug.py
index e8a0595416..cf485a611d 100644
--- a/lib/spack/spack/util/debug.py
+++ b/lib/spack/spack/util/debug.py
@@ -33,10 +33,11 @@ import code
 import traceback
 import signal
 
+
 def debug_handler(sig, frame):
     """Interrupt running process, and provide a python prompt for
     interactive debugging."""
-    d = {'_frame':frame}         # Allow access to frame object.
+    d = {'_frame': frame}         # Allow access to frame object.
     d.update(frame.f_globals)    # Unless shadowed by global
     d.update(frame.f_locals)
 
@@ -48,5 +49,5 @@ def debug_handler(sig, frame):
 
 
 def register_interrupt_handler():
-    """Register a handler to print a stack trace and enter an interpreter on Ctrl-C"""
+    """Print traceback and enter an interpreter on Ctrl-C"""
     signal.signal(signal.SIGINT, debug_handler)
diff --git a/lib/spack/spack/util/executable.py b/lib/spack/spack/util/executable.py
index 14b56e8d6c..5c27b92df5 100644
--- a/lib/spack/spack/util/executable.py
+++ b/lib/spack/spack/util/executable.py
@@ -165,7 +165,6 @@ class Executable(object):
                 raise ProcessError("Command exited with status %d:" %
                                    proc.returncode, cmd_line)
 
-
             if output is str or error is str:
                 result = ''
                 if output is str:
@@ -227,6 +226,7 @@ def which(name, **kwargs):
 
 
 class ProcessError(spack.error.SpackError):
+
     def __init__(self, msg, long_message=None):
         # These are used for detailed debugging information for
         # package builds.  They're built up gradually as the exception
diff --git a/lib/spack/spack/util/multiproc.py b/lib/spack/spack/util/multiproc.py
index 038cd90121..6a25c45713 100644
--- a/lib/spack/spack/util/multiproc.py
+++ b/lib/spack/spack/util/multiproc.py
@@ -32,18 +32,21 @@ from itertools import izip
 
 __all__ = ['spawn', 'parmap', 'Barrier']
 
+
 def spawn(f):
-    def fun(pipe,x):
+    def fun(pipe, x):
         pipe.send(f(x))
         pipe.close()
     return fun
 
-def parmap(f,X):
-    pipe=[Pipe() for x in X]
-    proc=[Process(target=spawn(f),args=(c,x)) for x,(p,c) in izip(X,pipe)]
+
+def parmap(f, X):
+    pipe = [Pipe() for x in X]
+    proc = [Process(target=spawn(f), args=(c, x))
+            for x, (p, c) in izip(X, pipe)]
     [p.start() for p in proc]
     [p.join() for p in proc]
-    return [p.recv() for (p,c) in pipe]
+    return [p.recv() for (p, c) in pipe]
 
 
 class Barrier:
@@ -53,6 +56,7 @@ class Barrier:
 
     See http://greenteapress.com/semaphores/downey08semaphores.pdf, p. 41.
     """
+
     def __init__(self, n, timeout=None):
         self.n = n
         self.to = timeout
@@ -61,7 +65,6 @@ class Barrier:
         self.turnstile1 = Semaphore(0)
         self.turnstile2 = Semaphore(1)
 
-
     def wait(self):
         if not self.mutex.acquire(timeout=self.to):
             raise BarrierTimeoutError()
@@ -90,4 +93,5 @@ class Barrier:
         self.turnstile2.release()
 
 
-class BarrierTimeoutError: pass
+class BarrierTimeoutError:
+    pass
diff --git a/lib/spack/spack/util/naming.py b/lib/spack/spack/util/naming.py
index 2d9762942d..9a5cdee411 100644
--- a/lib/spack/spack/util/naming.py
+++ b/lib/spack/spack/util/naming.py
@@ -31,9 +31,15 @@ from StringIO import StringIO
 
 import spack
 
-__all__ = ['mod_to_class', 'spack_module_to_python_module', 'valid_module_name',
-           'valid_fully_qualified_module_name', 'validate_fully_qualified_module_name',
-           'validate_module_name', 'possible_spack_module_names', 'NamespaceTrie']
+__all__ = [
+    'mod_to_class',
+    'spack_module_to_python_module',
+    'valid_module_name',
+    'valid_fully_qualified_module_name',
+    'validate_fully_qualified_module_name',
+    'validate_module_name',
+    'possible_spack_module_names',
+    'NamespaceTrie']
 
 # Valid module names can contain '-' but can't start with it.
 _valid_module_re = r'^\w[\w-]*$'
@@ -67,8 +73,8 @@ def mod_to_class(mod_name):
     class_name = string.capwords(class_name, '-')
     class_name = class_name.replace('-', '')
 
-    # If a class starts with a number, prefix it with Number_ to make it a valid
-    # Python class name.
+    # If a class starts with a number, prefix it with Number_ to make it
+    # a valid Python class name.
     if re.match(r'^[0-9]', class_name):
         class_name = "_%s" % class_name
 
@@ -126,6 +132,7 @@ def validate_fully_qualified_module_name(mod_name):
 
 class InvalidModuleNameError(spack.error.SpackError):
     """Raised when we encounter a bad module name."""
+
     def __init__(self, name):
         super(InvalidModuleNameError, self).__init__(
             "Invalid module name: " + name)
@@ -134,6 +141,7 @@ class InvalidModuleNameError(spack.error.SpackError):
 
 class InvalidFullyQualifiedModuleNameError(spack.error.SpackError):
     """Raised when we encounter a bad full package name."""
+
     def __init__(self, name):
         super(InvalidFullyQualifiedModuleNameError, self).__init__(
             "Invalid fully qualified package name: " + name)
@@ -141,17 +149,17 @@ class InvalidFullyQualifiedModuleNameError(spack.error.SpackError):
 
 
 class NamespaceTrie(object):
+
     class Element(object):
+
         def __init__(self, value):
             self.value = value
 
-
     def __init__(self, separator='.'):
         self._subspaces = {}
         self._value = None
         self._sep = separator
 
-
     def __setitem__(self, namespace, value):
         first, sep, rest = namespace.partition(self._sep)
 
@@ -164,7 +172,6 @@ class NamespaceTrie(object):
 
         self._subspaces[first][rest] = value
 
-
     def _get_helper(self, namespace, full_name):
         first, sep, rest = namespace.partition(self._sep)
         if not first:
@@ -176,13 +183,12 @@ class NamespaceTrie(object):
         else:
             return self._subspaces[first]._get_helper(rest, full_name)
 
-
     def __getitem__(self, namespace):
         return self._get_helper(namespace, namespace)
 
-
     def is_prefix(self, namespace):
-        """True if the namespace has a value, or if it's the prefix of one that does."""
+        """True if the namespace has a value, or if it's the prefix of one that
+           does."""
         first, sep, rest = namespace.partition(self._sep)
         if not first:
             return True
@@ -191,7 +197,6 @@ class NamespaceTrie(object):
         else:
             return self._subspaces[first].is_prefix(rest)
 
-
     def is_leaf(self, namespace):
         """True if this namespace has no children in the trie."""
         first, sep, rest = namespace.partition(self._sep)
@@ -202,7 +207,6 @@ class NamespaceTrie(object):
         else:
             return self._subspaces[first].is_leaf(rest)
 
-
     def has_value(self, namespace):
         """True if there is a value set for the given namespace."""
         first, sep, rest = namespace.partition(self._sep)
@@ -213,20 +217,17 @@ class NamespaceTrie(object):
         else:
             return self._subspaces[first].has_value(rest)
 
-
     def __contains__(self, namespace):
         """Returns whether a value has been set for the namespace."""
         return self.has_value(namespace)
 
-
     def _str_helper(self, stream, level=0):
         indent = (level * '    ')
         for name in sorted(self._subspaces):
             stream.write(indent + name + '\n')
             if self._value:
                 stream.write(indent + '  ' + repr(self._value.value))
-            stream.write(self._subspaces[name]._str_helper(stream, level+1))
-
+            stream.write(self._subspaces[name]._str_helper(stream, level + 1))
 
     def __str__(self):
         stream = StringIO()
diff --git a/lib/spack/spack/util/pattern.py b/lib/spack/spack/util/pattern.py
index bc5e9d2ffe..c36445193c 100644
--- a/lib/spack/spack/util/pattern.py
+++ b/lib/spack/spack/util/pattern.py
@@ -53,7 +53,9 @@ def composite(interface=None, method_list=None, container=list):
     # Check if at least one of the 'interface' or the 'method_list' arguments
     # are defined
     if interface is None and method_list is None:
-        raise TypeError("Either 'interface' or 'method_list' must be defined on a call to composite")  # NOQA : ignore=E501
+        raise TypeError(
+            "Either 'interface' or 'method_list' must be defined on a call "
+            "to composite")
 
     def cls_decorator(cls):
         # Retrieve the base class of the composite. Inspect its methods and
@@ -102,7 +104,8 @@ def composite(interface=None, method_list=None, container=list):
             # python@2.7: interface_methods = {name: method for name, method in
             # inspect.getmembers(interface, predicate=no_special_no_private)}
             interface_methods = {}
-            for name, method in inspect.getmembers(interface, predicate=no_special_no_private):  # NOQA: ignore=E501
+            for name, method in inspect.getmembers(
+                    interface, predicate=no_special_no_private):
                 interface_methods[name] = method
             ##########
             # python@2.7: interface_methods_dict = {name: IterateOver(name,
@@ -118,7 +121,8 @@ def composite(interface=None, method_list=None, container=list):
         # python@2.7: cls_method = {name: method for name, method in
         # inspect.getmembers(cls, predicate=inspect.ismethod)}
         cls_method = {}
-        for name, method in inspect.getmembers(cls, predicate=inspect.ismethod):  # NOQA: ignore=E501
+        for name, method in inspect.getmembers(
+                cls, predicate=inspect.ismethod):
             cls_method[name] = method
         ##########
         dictionary_for_type_call.update(cls_method)
diff --git a/lib/spack/spack/util/prefix.py b/lib/spack/spack/util/prefix.py
index e1a0f2958b..985d862269 100644
--- a/lib/spack/spack/util/prefix.py
+++ b/lib/spack/spack/util/prefix.py
@@ -27,6 +27,7 @@ This file contains utilities to help with installing packages.
 """
 from llnl.util.filesystem import join_path
 
+
 class Prefix(str):
     """This class represents an installation prefix, but provides useful
        attributes for referring to directories inside the prefix.
diff --git a/lib/spack/spack/util/spack_yaml.py b/lib/spack/spack/util/spack_yaml.py
index 909f9a57a8..7bcdf2d61f 100644
--- a/lib/spack/spack/util/spack_yaml.py
+++ b/lib/spack/spack/util/spack_yaml.py
@@ -34,7 +34,6 @@
 import yaml
 from yaml.nodes import *
 from yaml.constructor import ConstructorError
-from yaml.representer import SafeRepresenter
 from ordereddict_backport import OrderedDict
 
 # Only export load and dump
@@ -42,15 +41,23 @@ __all__ = ['load', 'dump']
 
 # Make new classes so we can add custom attributes.
 # Also, use OrderedDict instead of just dict.
+
+
 class syaml_dict(OrderedDict):
+
     def __repr__(self):
-        mappings = ('%r: %r' % (k,v) for k,v in self.items())
+        mappings = ('%r: %r' % (k, v) for k, v in self.items())
         return '{%s}' % ', '.join(mappings)
+
+
 class syaml_list(list):
     __repr__ = list.__repr__
+
+
 class syaml_str(str):
     __repr__ = str.__repr__
 
+
 def mark(obj, node):
     """Add start and end markers to an object."""
     obj._start_mark = node.start_mark
@@ -73,6 +80,7 @@ class OrderedLineLoader(yaml.Loader):
     # The standard YAML constructors return empty instances and fill
     # in with mappings later.  We preserve this behavior.
     #
+
     def construct_yaml_str(self, node):
         value = self.construct_scalar(node)
         try:
@@ -83,14 +91,12 @@ class OrderedLineLoader(yaml.Loader):
         mark(value, node)
         return value
 
-
     def construct_yaml_seq(self, node):
         data = syaml_list()
         mark(data, node)
         yield data
         data.extend(self.construct_sequence(node))
 
-
     def construct_yaml_map(self, node):
         data = syaml_dict()
         mark(data, node)
@@ -104,22 +110,23 @@ class OrderedLineLoader(yaml.Loader):
     #
     def construct_sequence(self, node, deep=False):
         if not isinstance(node, SequenceNode):
-            raise ConstructorError(None, None,
-                    "expected a sequence node, but found %s" % node.id,
-                    node.start_mark)
-        value =  syaml_list(self.construct_object(child, deep=deep)
-                             for child in node.value)
+            raise ConstructorError(
+                None, None,
+                "expected a sequence node, but found %s" % node.id,
+                node.start_mark)
+        value = syaml_list(self.construct_object(child, deep=deep)
+                           for child in node.value)
         mark(value, node)
         return value
 
-
     def construct_mapping(self, node, deep=False):
         """Store mappings as OrderedDicts instead of as regular python
            dictionaries to preserve file ordering."""
         if not isinstance(node, MappingNode):
-            raise ConstructorError(None, None,
-                    "expected a mapping node, but found %s" % node.id,
-                    node.start_mark)
+            raise ConstructorError(
+                None, None,
+                "expected a mapping node, but found %s" % node.id,
+                node.start_mark)
 
         mapping = syaml_dict()
         for key_node, value_node in node.value:
@@ -127,22 +134,26 @@ class OrderedLineLoader(yaml.Loader):
             try:
                 hash(key)
             except TypeError, exc:
-                raise ConstructorError("while constructing a mapping", node.start_mark,
-                        "found unacceptable key (%s)" % exc, key_node.start_mark)
+                raise ConstructorError(
+                    "while constructing a mapping", node.start_mark,
+                    "found unacceptable key (%s)" % exc, key_node.start_mark)
             value = self.construct_object(value_node, deep=deep)
             if key in mapping:
-                raise ConstructorError("while constructing a mapping", node.start_mark,
-                                       "found already in-use key (%s)" % key, key_node.start_mark)
+                raise ConstructorError(
+                    "while constructing a mapping", node.start_mark,
+                    "found already in-use key (%s)" % key, key_node.start_mark)
             mapping[key] = value
 
         mark(mapping, node)
         return mapping
 
 # register above new constructors
-OrderedLineLoader.add_constructor(u'tag:yaml.org,2002:map', OrderedLineLoader.construct_yaml_map)
-OrderedLineLoader.add_constructor(u'tag:yaml.org,2002:seq', OrderedLineLoader.construct_yaml_seq)
-OrderedLineLoader.add_constructor(u'tag:yaml.org,2002:str', OrderedLineLoader.construct_yaml_str)
-
+OrderedLineLoader.add_constructor(
+    u'tag:yaml.org,2002:map', OrderedLineLoader.construct_yaml_map)
+OrderedLineLoader.add_constructor(
+    u'tag:yaml.org,2002:seq', OrderedLineLoader.construct_yaml_seq)
+OrderedLineLoader.add_constructor(
+    u'tag:yaml.org,2002:str', OrderedLineLoader.construct_yaml_str)
 
 
 class OrderedLineDumper(yaml.Dumper):
@@ -154,6 +165,7 @@ class OrderedLineDumper(yaml.Dumper):
       regular Python equivalents, instead of ugly YAML pyobjects.
 
     """
+
     def represent_mapping(self, tag, mapping, flow_style=None):
         value = []
         node = MappingNode(tag, value, flow_style=flow_style)
@@ -173,7 +185,8 @@ class OrderedLineDumper(yaml.Dumper):
             node_value = self.represent_data(item_value)
             if not (isinstance(node_key, ScalarNode) and not node_key.style):
                 best_style = False
-            if not (isinstance(node_value, ScalarNode) and not node_value.style):
+            if not (isinstance(node_value, ScalarNode) and
+                    not node_value.style):
                 best_style = False
             value.append((node_key, node_value))
         if flow_style is None:
diff --git a/lib/spack/spack/util/string.py b/lib/spack/spack/util/string.py
index ce017b8126..dae7afbf46 100644
--- a/lib/spack/spack/util/string.py
+++ b/lib/spack/spack/util/string.py
@@ -23,6 +23,7 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 
+
 def comma_list(sequence, article=''):
     if type(sequence) != list:
         sequence = list(sequence)
@@ -32,7 +33,7 @@ def comma_list(sequence, article=''):
     elif len(sequence) == 1:
         return sequence[0]
     else:
-        out =  ', '.join(str(s) for s in sequence[:-1])
+        out = ', '.join(str(s) for s in sequence[:-1])
         if len(sequence) != 2:
             out += ','   # oxford comma
         out += ' '
@@ -41,6 +42,7 @@ def comma_list(sequence, article=''):
         out += str(sequence[-1])
         return out
 
+
 def comma_or(sequence):
     return comma_list(sequence, 'or')
 
diff --git a/lib/spack/spack/util/web.py b/lib/spack/spack/util/web.py
index 47abc507e0..25f1e605d6 100644
--- a/lib/spack/spack/util/web.py
+++ b/lib/spack/spack/util/web.py
@@ -25,8 +25,7 @@
 import re
 import os
 import sys
-import subprocess
-import urllib2, cookielib
+import urllib2
 import urlparse
 from multiprocessing import Pool
 from HTMLParser import HTMLParser, HTMLParseError
@@ -44,6 +43,7 @@ TIMEOUT = 10
 class LinkParser(HTMLParser):
     """This parser just takes an HTML page and strips out the hrefs on the
        links.  Good enough for a really simple spider. """
+
     def __init__(self):
         HTMLParser.__init__(self)
         self.links = []
@@ -84,7 +84,7 @@ def _spider(args):
         req.get_method = lambda: "HEAD"
         resp = urllib2.urlopen(req, timeout=TIMEOUT)
 
-        if not "Content-type" in resp.headers:
+        if "Content-type" not in resp.headers:
             tty.debug("ignoring page " + url)
             return pages, links
 
@@ -125,11 +125,11 @@ def _spider(args):
             if abs_link in visited:
                 continue
 
-        # If we're not at max depth, follow links.
-        if depth < max_depth:
-            subcalls.append((abs_link, visited, root, None,
-                             depth+1, max_depth, raise_on_error))
-            visited.add(abs_link)
+            # If we're not at max depth, follow links.
+            if depth < max_depth:
+                subcalls.append((abs_link, visited, root, None,
+                                 depth + 1, max_depth, raise_on_error))
+                visited.add(abs_link)
 
         if subcalls:
             try:
@@ -142,22 +142,22 @@ def _spider(args):
                 pool.terminate()
                 pool.join()
 
-    except urllib2.URLError, e:
+    except urllib2.URLError as e:
         tty.debug(e)
         if raise_on_error:
             raise spack.error.NoNetworkConnectionError(str(e), url)
 
-    except HTMLParseError, e:
+    except HTMLParseError as e:
         # This error indicates that Python's HTML parser sucks.
         msg = "Got an error parsing HTML."
 
         # Pre-2.7.3 Pythons in particular have rather prickly HTML parsing.
-        if sys.version_info[:3] < (2,7,3):
+        if sys.version_info[:3] < (2, 7, 3):
             msg += " Use Python 2.7.3 or newer for better HTML parsing."
 
         tty.warn(msg, url, "HTMLParseError: " + str(e))
 
-    except Exception, e:
+    except Exception as e:
         # Other types of errors are completely ignored, except in debug mode.
         tty.debug("Error in _spider: %s" % e)
 
@@ -173,7 +173,8 @@ def spider(root_url, **kwargs):
        performance over a sequential fetch.
     """
     max_depth = kwargs.setdefault('depth', 1)
-    pages, links = _spider((root_url, set(), root_url, None, 1, max_depth, False))
+    pages, links = _spider((root_url, set(), root_url, None,
+                            1, max_depth, False))
     return pages, links
 
 
@@ -235,7 +236,7 @@ def find_versions_of_archive(*archive_urls, **kwargs):
             try:
                 ver = spack.url.parse_version(url)
                 versions[ver] = url
-            except spack.url.UndetectableVersionError as e:
+            except spack.url.UndetectableVersionError:
                 continue
 
     return versions
diff --git a/lib/spack/spack/variant.py b/lib/spack/spack/variant.py
index ad875f5ef5..b2c1a73489 100644
--- a/lib/spack/spack/variant.py
+++ b/lib/spack/spack/variant.py
@@ -29,8 +29,10 @@ currently variants are just flags.
 
 """
 
+
 class Variant(object):
     """Represents a variant on a build.  Can be either on or off."""
+
     def __init__(self, default, description):
         self.default     = default
         self.description = str(description)
diff --git a/lib/spack/spack/version.py b/lib/spack/spack/version.py
index 6f6c83b3d8..e1311eb0d9 100644
--- a/lib/spack/spack/version.py
+++ b/lib/spack/spack/version.py
@@ -50,6 +50,8 @@ from functools import wraps
 
 from functools_backport import total_ordering
 
+__all__ = ['Version', 'VersionRange', 'VersionList', 'ver']
+
 # Valid version characters
 VALID_VERSION = r'[A-Za-z0-9_.-]'
 
@@ -346,8 +348,8 @@ class VersionRange(object):
 
         s, o = self, other
         if s.start != o.start:
-            return s.start is None or (o.start is not None and s.start < o.start)  # NOQA: ignore=E501
-
+            return s.start is None or (
+                o.start is not None and s.start < o.start)
         return (s.end != o.end and
                 o.end is None or (s.end is not None and s.end < o.end))
 
diff --git a/lib/spack/spack/yaml_version_check.py b/lib/spack/spack/yaml_version_check.py
index c2d084d6c3..2c5b511d7f 100644
--- a/lib/spack/spack/yaml_version_check.py
+++ b/lib/spack/spack/yaml_version_check.py
@@ -34,6 +34,7 @@ import spack.config
 def check_yaml_versions():
     check_compiler_yaml_version()
 
+
 def check_compiler_yaml_version():
     config_scopes = spack.config.config_scopes
     for scope in config_scopes.values():
@@ -46,7 +47,8 @@ def check_compiler_yaml_version():
         if data:
             compilers = data['compilers']
             if len(compilers) > 0:
-                if (not isinstance(compilers, list)) or 'operating_system' not in compilers[0]['compiler']:
+                if (not isinstance(compilers, list) or
+                    'operating_system' not in compilers[0]['compiler']):
                     new_file = os.path.join(scope.path, '_old_compilers.yaml')
                     tty.warn('%s in out of date compilers format. '
                              'Moved to %s. Spack automatically generate '
diff --git a/share/spack/csh/convert-pyext.sh b/share/spack/csh/convert-pyext.sh
new file mode 100644
index 0000000000..a48bcdbcca
--- /dev/null
+++ b/share/spack/csh/convert-pyext.sh
@@ -0,0 +1,5 @@
+#!/bin/bash --noprofile
+PYEXT_REGEX=".*/.*/package.py"
+
+find var/spack/repos/builtin/packages/ -type f -regextype sed -regex ${PYEXT_REGEX} -exec \
+    sed -i 's/python('\''setup.py'\'', /setup_py(/' {} \;
diff --git a/share/spack/qa/run-flake8 b/share/spack/qa/run-flake8
index 595df417ec..c59bfc9490 100755
--- a/share/spack/qa/run-flake8
+++ b/share/spack/qa/run-flake8
@@ -22,9 +22,13 @@ changed=$(git diff --name-only --find-renames develop... | grep '.py$')
 
 # Add approved style exemptions to the changed packages.
 for file in $changed; do
-    if [[ $file = *package.py ]]; then
-        cp "$file" "$file~"
+    # Make a backup to restore later
+    cp "$file" "$file.sbak~"
 
+    #
+    # Exemptions for package.py files
+    #
+    if [[ $file = *package.py ]]; then
         # Exempt lines with urls and descriptions from overlong line errors.
         perl -i -pe 's/^(\s*homepage\s*=.*)$/\1  # NOQA: ignore=E501/' $file
         perl -i -pe 's/^(\s*url\s*=.*)$/\1  # NOQA: ignore=E501/' $file
@@ -36,6 +40,11 @@ for file in $changed; do
         # Exempt '@when' decorated functions from redefinition errors.
         perl -i -pe 's/^(\s*\@when\(.*\).*)$/\1  # NOQA: ignore=F811/' $file
     fi
+
+    #
+    # Exemptions for all files
+    #
+    perl -i -pe 's/^(.*(https?|file)\:.*)$/\1  # NOQA: ignore=E501/' $file
 done
 
 return_code=0
@@ -58,8 +67,8 @@ fi
 
 # Restore original package files after modifying them.
 for file in $changed; do
-    if [[ $file = *package.py ]]; then
-        mv "${file}~" "${file}"
+    if [[ -e "${file}.sbak~" ]]; then
+        mv "${file}.sbak~" "${file}"
     fi
 done
 
diff --git a/share/spack/qa/run-unit-tests b/share/spack/qa/run-unit-tests
new file mode 100755
index 0000000000..33fb1bfae2
--- /dev/null
+++ b/share/spack/qa/run-unit-tests
@@ -0,0 +1,20 @@
+#!/usr/bin/env bash
+#
+# This script runs Spack unit tests.
+#
+# It should be executed from the top-level directory of the repo,
+# e.g.:
+#
+#    share/spack/qa/run-unit-tests
+#
+# To run it, you'll need to have the Python coverage installed locally.
+#
+
+# Regular spack setup and tests
+. ./share/spack/setup-env.sh
+spack compilers
+spack config get compilers
+spack install -v libdwarf
+
+# Run unit tests with code coverage
+coverage run bin/spack test
diff --git a/share/spack/setup-env.sh b/share/spack/setup-env.sh
index c6183f990d..2eb1dfecb3 100755
--- a/share/spack/setup-env.sh
+++ b/share/spack/setup-env.sh
@@ -117,19 +117,19 @@ function spack {
             # If spack module command comes back with an error, do nothing.
             case $_sp_subcommand in
                 "use")
-                    if _sp_full_spec=$(command spack $_sp_flags module find $_sp_subcommand_args --module-type dotkit $_sp_spec); then
+                    if _sp_full_spec=$(command spack $_sp_flags module loads --input-only $_sp_subcommand_args --module-type dotkit $_sp_spec); then
                         use $_sp_module_args $_sp_full_spec
                     fi ;;
                 "unuse")
-                    if _sp_full_spec=$(command spack $_sp_flags module find $_sp_subcommand_args --module-type dotkit $_sp_spec); then
+                    if _sp_full_spec=$(command spack $_sp_flags module loads --input-only $_sp_subcommand_args --module-type dotkit $_sp_spec); then
                         unuse $_sp_module_args $_sp_full_spec
                     fi ;;
                 "load")
-                    if _sp_full_spec=$(command spack $_sp_flags module find $_sp_subcommand_args --module-type tcl $_sp_spec); then
+                    if _sp_full_spec=$(command spack $_sp_flags module loads --input-only $_sp_subcommand_args --module-type tcl $_sp_spec); then
                         module load $_sp_module_args $_sp_full_spec
                     fi ;;
                 "unload")
-                    if _sp_full_spec=$(command spack $_sp_flags module find $_sp_subcommand_args --module-type tcl $_sp_spec); then
+                    if _sp_full_spec=$(command spack $_sp_flags module loads --input-only $_sp_subcommand_args --module-type tcl $_sp_spec); then
                         module unload $_sp_module_args $_sp_full_spec
                     fi ;;
             esac
diff --git a/var/spack/repos/builtin.mock/packages/a/package.py b/var/spack/repos/builtin.mock/packages/a/package.py
index 40b92240fc..0d75ee1256 100644
--- a/var/spack/repos/builtin.mock/packages/a/package.py
+++ b/var/spack/repos/builtin.mock/packages/a/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class A(Package):
     """Simple package with no dependencies"""
 
diff --git a/var/spack/repos/builtin.mock/packages/b/package.py b/var/spack/repos/builtin.mock/packages/b/package.py
index c447a56b48..5729f24e79 100644
--- a/var/spack/repos/builtin.mock/packages/b/package.py
+++ b/var/spack/repos/builtin.mock/packages/b/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class B(Package):
     """Simple package with no dependencies"""
 
diff --git a/var/spack/repos/builtin.mock/packages/c/package.py b/var/spack/repos/builtin.mock/packages/c/package.py
index 5b6079c4e3..80777a05bb 100644
--- a/var/spack/repos/builtin.mock/packages/c/package.py
+++ b/var/spack/repos/builtin.mock/packages/c/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class C(Package):
     """Simple package with no dependencies"""
 
diff --git a/var/spack/repos/builtin.mock/packages/callpath/package.py b/var/spack/repos/builtin.mock/packages/callpath/package.py
index c297a123b8..56b969df98 100644
--- a/var/spack/repos/builtin.mock/packages/callpath/package.py
+++ b/var/spack/repos/builtin.mock/packages/callpath/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Callpath(Package):
     homepage = "https://github.com/tgamblin/callpath"
     url      = "http://github.com/tgamblin/callpath-1.0.tar.gz"
diff --git a/var/spack/repos/builtin.mock/packages/cmake-client/package.py b/var/spack/repos/builtin.mock/packages/cmake-client/package.py
index c58430317a..0c78f0bf68 100644
--- a/var/spack/repos/builtin.mock/packages/cmake-client/package.py
+++ b/var/spack/repos/builtin.mock/packages/cmake-client/package.py
@@ -25,6 +25,7 @@
 from spack import *
 import os
 
+
 def check(condition, msg):
     """Raise an install error if condition is False."""
     if not condition:
@@ -40,15 +41,14 @@ class CmakeClient(Package):
 
     depends_on('cmake', type='build')
 
-
     def setup_environment(self, spack_env, run_env):
         spack_cc    # Ensure spack module-scope variable is avaiabl
         check(from_cmake == "from_cmake",
               "setup_environment couldn't read global set by cmake.")
 
         check(self.spec['cmake'].link_arg == "test link arg",
-              "link arg on dependency spec not readable from setup_environment.")
-
+              "link arg on dependency spec not readable from "
+              "setup_environment.")
 
     def setup_dependent_environment(self, spack_env, run_env, dspec):
         spack_cc    # Ensure spack module-scope variable is avaiable
@@ -56,8 +56,8 @@ class CmakeClient(Package):
               "setup_dependent_environment couldn't read global set by cmake.")
 
         check(self.spec['cmake'].link_arg == "test link arg",
-              "link arg on dependency spec not readable from setup_dependent_environment.")
-
+              "link arg on dependency spec not readable from "
+              "setup_dependent_environment.")
 
     def setup_dependent_package(self, module, dspec):
         spack_cc    # Ensure spack module-scope variable is avaiable
@@ -65,9 +65,8 @@ class CmakeClient(Package):
               "setup_dependent_package couldn't read global set by cmake.")
 
         check(self.spec['cmake'].link_arg == "test link arg",
-              "link arg on dependency spec not readable from setup_dependent_package.")
-
-
+              "link arg on dependency spec not readable from "
+              "setup_dependent_package.")
 
     def install(self, spec, prefix):
         # check that cmake is in the global scope.
diff --git a/var/spack/repos/builtin.mock/packages/cmake/package.py b/var/spack/repos/builtin.mock/packages/cmake/package.py
index 0356cf8afb..c8b6464e69 100644
--- a/var/spack/repos/builtin.mock/packages/cmake/package.py
+++ b/var/spack/repos/builtin.mock/packages/cmake/package.py
@@ -25,6 +25,7 @@
 from spack import *
 import os
 
+
 def check(condition, msg):
     """Raise an install error if condition is False."""
     if not condition:
@@ -39,7 +40,6 @@ class Cmake(Package):
     version('3.4.3',    '4cb3ff35b2472aae70f542116d616e63',
             url='https://cmake.org/files/v3.4/cmake-3.4.3.tar.gz')
 
-
     def setup_environment(self, spack_env, run_env):
         spack_cc    # Ensure spack module-scope variable is avaiable
         spack_env.set('for_install', 'for_install')
@@ -48,7 +48,6 @@ class Cmake(Package):
         spack_cc    # Ensure spack module-scope variable is avaiable
         spack_env.set('from_cmake', 'from_cmake')
 
-
     def setup_dependent_package(self, module, dspec):
         spack_cc    # Ensure spack module-scope variable is avaiable
 
@@ -57,7 +56,6 @@ class Cmake(Package):
 
         self.spec.link_arg = "test link arg"
 
-
     def install(self, spec, prefix):
         mkdirp(prefix.bin)
 
diff --git a/var/spack/repos/builtin.mock/packages/direct_mpich/package.py b/var/spack/repos/builtin.mock/packages/direct_mpich/package.py
index 663908d56c..f38589ad4d 100644
--- a/var/spack/repos/builtin.mock/packages/direct_mpich/package.py
+++ b/var/spack/repos/builtin.mock/packages/direct_mpich/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class DirectMpich(Package):
     homepage = "http://www.example.com"
     url      = "http://www.example.com/direct_mpich-1.0.tar.gz"
diff --git a/var/spack/repos/builtin.mock/packages/dyninst/package.py b/var/spack/repos/builtin.mock/packages/dyninst/package.py
index ad486011e2..daf1b82ec6 100644
--- a/var/spack/repos/builtin.mock/packages/dyninst/package.py
+++ b/var/spack/repos/builtin.mock/packages/dyninst/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Dyninst(Package):
     homepage = "https://paradyn.org"
     url      = "http://www.paradyn.org/release8.1/DyninstAPI-8.1.1.tgz"
diff --git a/var/spack/repos/builtin.mock/packages/e/package.py b/var/spack/repos/builtin.mock/packages/e/package.py
index b951a3eaa6..c764007563 100644
--- a/var/spack/repos/builtin.mock/packages/e/package.py
+++ b/var/spack/repos/builtin.mock/packages/e/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class E(Package):
     """Simple package with no dependencies"""
 
diff --git a/var/spack/repos/builtin.mock/packages/externalmodule/package.py b/var/spack/repos/builtin.mock/packages/externalmodule/package.py
index f7b0da3fd9..f7c9b056a4 100644
--- a/var/spack/repos/builtin.mock/packages/externalmodule/package.py
+++ b/var/spack/repos/builtin.mock/packages/externalmodule/package.py
@@ -25,6 +25,7 @@
 ##############################################################################
 from spack import *
 
+
 class Externalmodule(Package):
     homepage = "http://somewhere.com"
     url      = "http://somewhere.com/module-1.0.tar.gz"
diff --git a/var/spack/repos/builtin.mock/packages/externalprereq/package.py b/var/spack/repos/builtin.mock/packages/externalprereq/package.py
index bd3c4348bf..226742f2cb 100644
--- a/var/spack/repos/builtin.mock/packages/externalprereq/package.py
+++ b/var/spack/repos/builtin.mock/packages/externalprereq/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Externalprereq(Package):
     homepage = "http://somewhere.com"
     url      = "http://somewhere.com/prereq-1.0.tar.gz"
diff --git a/var/spack/repos/builtin.mock/packages/externaltest/package.py b/var/spack/repos/builtin.mock/packages/externaltest/package.py
index 2318887aec..252c42556e 100644
--- a/var/spack/repos/builtin.mock/packages/externaltest/package.py
+++ b/var/spack/repos/builtin.mock/packages/externaltest/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Externaltest(Package):
     homepage = "http://somewhere.com"
     url      = "http://somewhere.com/test-1.0.tar.gz"
diff --git a/var/spack/repos/builtin.mock/packages/externaltool/package.py b/var/spack/repos/builtin.mock/packages/externaltool/package.py
index 9ff2396f36..d2daddd350 100644
--- a/var/spack/repos/builtin.mock/packages/externaltool/package.py
+++ b/var/spack/repos/builtin.mock/packages/externaltool/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Externaltool(Package):
     homepage = "http://somewhere.com"
     url      = "http://somewhere.com/tool-1.0.tar.gz"
diff --git a/var/spack/repos/builtin.mock/packages/externalvirtual/package.py b/var/spack/repos/builtin.mock/packages/externalvirtual/package.py
index e19ef332f0..1f3553014b 100644
--- a/var/spack/repos/builtin.mock/packages/externalvirtual/package.py
+++ b/var/spack/repos/builtin.mock/packages/externalvirtual/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Externalvirtual(Package):
     homepage = "http://somewhere.com"
     url      = "http://somewhere.com/stuff-1.0.tar.gz"
diff --git a/var/spack/repos/builtin.mock/packages/fake/package.py b/var/spack/repos/builtin.mock/packages/fake/package.py
index 15aabf1101..b83eec7470 100644
--- a/var/spack/repos/builtin.mock/packages/fake/package.py
+++ b/var/spack/repos/builtin.mock/packages/fake/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Fake(Package):
     homepage = "http://www.fake-spack-example.org"
     url      = "http://www.fake-spack-example.org/downloads/fake-1.0.tar.gz"
diff --git a/var/spack/repos/builtin.mock/packages/git-test/package.py b/var/spack/repos/builtin.mock/packages/git-test/package.py
index aeea41146f..730e71ac6b 100644
--- a/var/spack/repos/builtin.mock/packages/git-test/package.py
+++ b/var/spack/repos/builtin.mock/packages/git-test/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class GitTest(Package):
     """Mock package that uses git for fetching."""
     homepage = "http://www.git-fetch-example.com"
diff --git a/var/spack/repos/builtin.mock/packages/hg-test/package.py b/var/spack/repos/builtin.mock/packages/hg-test/package.py
index 64719eb53c..70a9b7f2c7 100644
--- a/var/spack/repos/builtin.mock/packages/hg-test/package.py
+++ b/var/spack/repos/builtin.mock/packages/hg-test/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class HgTest(Package):
     """Test package that does fetching with mercurial."""
     homepage = "http://www.hg-fetch-example.com"
diff --git a/var/spack/repos/builtin.mock/packages/hypre/package.py b/var/spack/repos/builtin.mock/packages/hypre/package.py
index 3aedea9bf2..b9e31b09dc 100644
--- a/var/spack/repos/builtin.mock/packages/hypre/package.py
+++ b/var/spack/repos/builtin.mock/packages/hypre/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Hypre(Package):
     """Hypre is included here as an example of a package that depends on
        both LAPACK and BLAS."""
diff --git a/var/spack/repos/builtin.mock/packages/indirect_mpich/package.py b/var/spack/repos/builtin.mock/packages/indirect_mpich/package.py
index 6ed779889b..bbbf196129 100644
--- a/var/spack/repos/builtin.mock/packages/indirect_mpich/package.py
+++ b/var/spack/repos/builtin.mock/packages/indirect_mpich/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class IndirectMpich(Package):
     """Test case for a package that depends on MPI and one of its
        dependencies requires a *particular version* of MPI.
diff --git a/var/spack/repos/builtin.mock/packages/libdwarf/package.py b/var/spack/repos/builtin.mock/packages/libdwarf/package.py
index b53e295e23..0fcbe4a62e 100644
--- a/var/spack/repos/builtin.mock/packages/libdwarf/package.py
+++ b/var/spack/repos/builtin.mock/packages/libdwarf/package.py
@@ -23,11 +23,11 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
-import os
 
 # Only build certain parts of dwarf because the other ones break.
 dwarf_dirs = ['libdwarf', 'dwarfdump2']
 
+
 class Libdwarf(Package):
     homepage = "http://www.prevanders.net/dwarf.html"
     url      = "http://www.prevanders.net/libdwarf-20130729.tar.gz"
diff --git a/var/spack/repos/builtin.mock/packages/libelf/package.py b/var/spack/repos/builtin.mock/packages/libelf/package.py
index f52d8cefe1..90d00ad339 100644
--- a/var/spack/repos/builtin.mock/packages/libelf/package.py
+++ b/var/spack/repos/builtin.mock/packages/libelf/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Libelf(Package):
     homepage = "http://www.mr511.de/software/english.html"
     url      = "http://www.mr511.de/software/libelf-0.8.13.tar.gz"
diff --git a/var/spack/repos/builtin.mock/packages/mpich/package.py b/var/spack/repos/builtin.mock/packages/mpich/package.py
index f278f26b8b..936127398c 100644
--- a/var/spack/repos/builtin.mock/packages/mpich/package.py
+++ b/var/spack/repos/builtin.mock/packages/mpich/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Mpich(Package):
     homepage   = "http://www.mpich.org"
     url        = "http://www.mpich.org/static/downloads/3.0.4/mpich-3.0.4.tar.gz"
diff --git a/var/spack/repos/builtin.mock/packages/mpich2/package.py b/var/spack/repos/builtin.mock/packages/mpich2/package.py
index e6b68d2490..c92b4ba43a 100644
--- a/var/spack/repos/builtin.mock/packages/mpich2/package.py
+++ b/var/spack/repos/builtin.mock/packages/mpich2/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Mpich2(Package):
     homepage   = "http://www.mpich.org"
     url        = "http://www.mpich.org/static/downloads/1.5/mpich2-1.5.tar.gz"
diff --git a/var/spack/repos/builtin.mock/packages/mpileaks/package.py b/var/spack/repos/builtin.mock/packages/mpileaks/package.py
index bc26f539ba..10fbf3845e 100644
--- a/var/spack/repos/builtin.mock/packages/mpileaks/package.py
+++ b/var/spack/repos/builtin.mock/packages/mpileaks/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Mpileaks(Package):
     homepage = "http://www.llnl.gov"
     url      = "http://www.llnl.gov/mpileaks-1.0.tar.gz"
@@ -35,6 +36,8 @@ class Mpileaks(Package):
 
     variant('debug', default=False, description='Debug variant')
     variant('opt',   default=False, description='Optimized variant')
+    variant('shared', default=True, description='Build shared library')
+    variant('static', default=True, description='Build static library')
 
     depends_on("mpi")
     depends_on("callpath")
diff --git a/var/spack/repos/builtin.mock/packages/multimethod/package.py b/var/spack/repos/builtin.mock/packages/multimethod/package.py
index ca991632dd..fa3f815135 100644
--- a/var/spack/repos/builtin.mock/packages/multimethod/package.py
+++ b/var/spack/repos/builtin.mock/packages/multimethod/package.py
@@ -22,12 +22,10 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import imp
-from llnl.util.filesystem import join_path
-from spack.util.naming import mod_to_class
 from spack import *
 import spack.architecture
 
+
 class Multimethod(Package):
     """This package is designed for use with Spack's multimethod test.
        It has a bunch of test cases for the @when decorator that the
@@ -52,7 +50,6 @@ class Multimethod(Package):
     def no_version_2(self):
         return 4
 
-
     #
     # These functions overlap, so there is ambiguity, but we'll take
     # the first one.
@@ -65,7 +62,6 @@ class Multimethod(Package):
     def version_overlap(self):
         return 2
 
-
     #
     # More complicated case with cascading versions.
     #
@@ -84,7 +80,6 @@ class Multimethod(Package):
     def mpi_version(self):
         return 1
 
-
     #
     # Use these to test whether the default method is called when no
     # match is found.  This also tests whether we can switch methods
@@ -101,8 +96,6 @@ class Multimethod(Package):
     def has_a_default(self):
         return 'intel'
 
-
-
     #
     # Make sure we can switch methods on different target
     #
@@ -112,15 +105,16 @@ class Multimethod(Package):
         targets = targets[:-1]
 
     for target in targets:
-        @when('target='+target.name)
+        @when('target=' + target.name)
         def different_by_target(self):
-            if isinstance(self.spec.architecture.target,basestring):
+            if isinstance(self.spec.architecture.target, basestring):
                 return self.spec.architecture.target
             else:
                 return self.spec.architecture.target.name
     #
     # Make sure we can switch methods on different dependencies
     #
+
     @when('^mpich')
     def different_by_dep(self):
         return 'mpich'
@@ -129,7 +123,6 @@ class Multimethod(Package):
     def different_by_dep(self):
         return 'zmpi'
 
-
     #
     # Make sure we can switch on virtual dependencies
     #
diff --git a/var/spack/repos/builtin.mock/packages/netlib-blas/package.py b/var/spack/repos/builtin.mock/packages/netlib-blas/package.py
index 9d567f2e9b..0a5b1d0e6a 100644
--- a/var/spack/repos/builtin.mock/packages/netlib-blas/package.py
+++ b/var/spack/repos/builtin.mock/packages/netlib-blas/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class NetlibBlas(Package):
     homepage = "http://www.netlib.org/lapack/"
     url      = "http://www.netlib.org/lapack/lapack-3.5.0.tgz"
diff --git a/var/spack/repos/builtin.mock/packages/netlib-lapack/package.py b/var/spack/repos/builtin.mock/packages/netlib-lapack/package.py
index 46d6ae43dc..755d3001a4 100644
--- a/var/spack/repos/builtin.mock/packages/netlib-lapack/package.py
+++ b/var/spack/repos/builtin.mock/packages/netlib-lapack/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class NetlibLapack(Package):
     homepage = "http://www.netlib.org/lapack/"
     url      = "http://www.netlib.org/lapack/lapack-3.5.0.tgz"
diff --git a/var/spack/repos/builtin.mock/packages/openblas-with-lapack/package.py b/var/spack/repos/builtin.mock/packages/openblas-with-lapack/package.py
index b36237c1e2..0f14fbaa61 100644
--- a/var/spack/repos/builtin.mock/packages/openblas-with-lapack/package.py
+++ b/var/spack/repos/builtin.mock/packages/openblas-with-lapack/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class OpenblasWithLapack(Package):
     """Dummy version of OpenBLAS that also provides LAPACK, for testing."""
     homepage = "http://www.openblas.net"
diff --git a/var/spack/repos/builtin.mock/packages/openblas/package.py b/var/spack/repos/builtin.mock/packages/openblas/package.py
index 5b39447e83..f6cdeeea49 100644
--- a/var/spack/repos/builtin.mock/packages/openblas/package.py
+++ b/var/spack/repos/builtin.mock/packages/openblas/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Openblas(Package):
     """OpenBLAS: An optimized BLAS library"""
     homepage = "http://www.openblas.net"
diff --git a/var/spack/repos/builtin.mock/packages/optional-dep-test-2/package.py b/var/spack/repos/builtin.mock/packages/optional-dep-test-2/package.py
index f97959c763..337f54e24e 100644
--- a/var/spack/repos/builtin.mock/packages/optional-dep-test-2/package.py
+++ b/var/spack/repos/builtin.mock/packages/optional-dep-test-2/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class OptionalDepTest2(Package):
     """Depends on the optional-dep-test package"""
 
diff --git a/var/spack/repos/builtin.mock/packages/optional-dep-test-3/package.py b/var/spack/repos/builtin.mock/packages/optional-dep-test-3/package.py
index d8fe33c3da..2904b3782d 100644
--- a/var/spack/repos/builtin.mock/packages/optional-dep-test-3/package.py
+++ b/var/spack/repos/builtin.mock/packages/optional-dep-test-3/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class OptionalDepTest3(Package):
     """Depends on the optional-dep-test package"""
 
diff --git a/var/spack/repos/builtin.mock/packages/optional-dep-test/package.py b/var/spack/repos/builtin.mock/packages/optional-dep-test/package.py
index 80c1da55f8..2c07e61769 100644
--- a/var/spack/repos/builtin.mock/packages/optional-dep-test/package.py
+++ b/var/spack/repos/builtin.mock/packages/optional-dep-test/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class OptionalDepTest(Package):
     """Description"""
 
diff --git a/var/spack/repos/builtin.mock/packages/python/package.py b/var/spack/repos/builtin.mock/packages/python/package.py
index dc21b475e5..a5290161ad 100644
--- a/var/spack/repos/builtin.mock/packages/python/package.py
+++ b/var/spack/repos/builtin.mock/packages/python/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Python(Package):
     """Dummy Python package to demonstrate preferred versions."""
     homepage = "http://www.python.org"
@@ -40,4 +41,3 @@ class Python(Package):
 
     def install(self, spec, prefix):
         pass
-
diff --git a/var/spack/repos/builtin.mock/packages/svn-test/package.py b/var/spack/repos/builtin.mock/packages/svn-test/package.py
index 2f197593e0..01d0929c28 100644
--- a/var/spack/repos/builtin.mock/packages/svn-test/package.py
+++ b/var/spack/repos/builtin.mock/packages/svn-test/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class SvnTest(Package):
     """Mock package that uses svn for fetching."""
     url      = "http://www.example.com/svn-test-1.0.tar.gz"
diff --git a/var/spack/repos/builtin.mock/packages/trivial_install_test_package/package.py b/var/spack/repos/builtin.mock/packages/trivial_install_test_package/package.py
index 7c65909ad2..2129d9788b 100644
--- a/var/spack/repos/builtin.mock/packages/trivial_install_test_package/package.py
+++ b/var/spack/repos/builtin.mock/packages/trivial_install_test_package/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class TrivialInstallTestPackage(Package):
     """This package is a stub with a trivial install method.  It allows us
        to test the install and uninstall logic of spack."""
diff --git a/var/spack/repos/builtin.mock/packages/zmpi/package.py b/var/spack/repos/builtin.mock/packages/zmpi/package.py
index fcd3afe93b..b6a5b33011 100644
--- a/var/spack/repos/builtin.mock/packages/zmpi/package.py
+++ b/var/spack/repos/builtin.mock/packages/zmpi/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Zmpi(Package):
     """This is a fake MPI package used to demonstrate virtual package providers
        with dependencies."""
diff --git a/var/spack/repos/builtin/packages/LuaJIT/package.py b/var/spack/repos/builtin/packages/LuaJIT/package.py
index db6f7d3cad..244c63c8fb 100644
--- a/var/spack/repos/builtin/packages/LuaJIT/package.py
+++ b/var/spack/repos/builtin/packages/LuaJIT/package.py
@@ -25,6 +25,7 @@
 import os
 from spack import *
 
+
 class Luajit(Package):
     """Flast flexible JITed lua"""
     homepage = "http://www.luajit.org"
diff --git a/var/spack/repos/builtin/packages/R/package.py b/var/spack/repos/builtin/packages/R/package.py
index 11c5909efa..e880a3aa66 100644
--- a/var/spack/repos/builtin/packages/R/package.py
+++ b/var/spack/repos/builtin/packages/R/package.py
@@ -22,10 +22,9 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import os
-
 from spack import *
 from spack.util.environment import *
+import shutil
 
 
 class R(Package):
@@ -74,6 +73,10 @@ class R(Package):
     depends_on('pcre')
     depends_on('jdk')
 
+    @property
+    def etcdir(self):
+        return join_path(prefix, 'rlib', 'R', 'etc')
+
     def install(self, spec, prefix):
         rlibdir = join_path(prefix, 'rlib')
         configure_args = ['--prefix=%s' % prefix,
@@ -88,6 +91,12 @@ class R(Package):
         make()
         make('install')
 
+        # Make a copy of Makeconf because it will be needed to properly build R
+        # dependencies in Spack.
+        src_makeconf = join_path(self.etcdir, 'Makeconf')
+        dst_makeconf = join_path(self.etcdir, 'Makeconf.spack')
+        shutil.copy(src_makeconf, dst_makeconf)
+
         self.filter_compilers(spec, prefix)
 
     def filter_compilers(self, spec, prefix):
@@ -98,18 +107,16 @@ class R(Package):
         cc and c++. We want them to be bound to whatever compiler
         they were built with."""
 
-        etcdir = join_path(prefix, 'rlib', 'R', 'etc')
-
         kwargs = {'ignore_absent': True, 'backup': False, 'string': True}
 
-        filter_file(env['CC'],  self.compiler.cc,
-                    join_path(etcdir, 'Makeconf'), **kwargs)
+        filter_file(env['CC'], self.compiler.cc,
+                    join_path(self.etcdir, 'Makeconf'), **kwargs)
         filter_file(env['CXX'], self.compiler.cxx,
-                    join_path(etcdir, 'Makeconf'), **kwargs)
+                    join_path(self.etcdir, 'Makeconf'), **kwargs)
         filter_file(env['F77'], self.compiler.f77,
-                    join_path(etcdir, 'Makeconf'), **kwargs)
+                    join_path(self.etcdir, 'Makeconf'), **kwargs)
         filter_file(env['FC'], self.compiler.fc,
-                    join_path(etcdir, 'Makeconf'), **kwargs)
+                    join_path(self.etcdir, 'Makeconf'), **kwargs)
 
     # ========================================================================
     # Set up environment to make install easy for R extensions.
@@ -117,7 +124,7 @@ class R(Package):
 
     @property
     def r_lib_dir(self):
-        return os.path.join('rlib', 'R', 'library')
+        return join_path('rlib', 'R', 'library')
 
     def setup_dependent_environment(self, spack_env, run_env, extension_spec):
         # Set R_LIBS to include the library dir for the
@@ -125,27 +132,42 @@ class R(Package):
         r_libs_path = []
         for d in extension_spec.traverse(deptype=nolink, deptype_query='run'):
             if d.package.extends(self.spec):
-                r_libs_path.append(os.path.join(d.prefix, self.r_lib_dir))
+                r_libs_path.append(join_path(d.prefix, self.r_lib_dir))
 
         r_libs_path = ':'.join(r_libs_path)
         spack_env.set('R_LIBS', r_libs_path)
+        spack_env.set('R_MAKEVARS_SITE',
+                      join_path(self.etcdir, 'Makeconf.spack'))
+
+        # Use the number of make_jobs set in spack. The make program will
+        # determine how many jobs can actually be started.
+        spack_env.set('MAKEFLAGS', '-j{0}'.format(make_jobs))
 
         # For run time environment set only the path for extension_spec and
         # prepend it to R_LIBS
         if extension_spec.package.extends(self.spec):
-            run_env.prepend_path('R_LIBS', os.path.join(
+            run_env.prepend_path('R_LIBS', join_path(
                 extension_spec.prefix, self.r_lib_dir))
 
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('LIBRARY_PATH',
+                             join_path(self.prefix, 'rlib', 'R', 'lib'))
+        run_env.prepend_path('LD_LIBRARY_PATH',
+                             join_path(self.prefix, 'rlib', 'R', 'lib'))
+        run_env.prepend_path('CPATH',
+                             join_path(self.prefix, 'rlib', 'R', 'include'))
+
     def setup_dependent_package(self, module, ext_spec):
         """Called before R modules' install() methods. In most cases,
         extensions will only need to have one line:
-            R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' %
-            self.stage.source_path)"""
+            R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+              self.stage.source_path)"""
+
         # R extension builds can have a global R executable function
         module.R = Executable(join_path(self.spec.prefix.bin, 'R'))
 
         # Add variable for library directry
-        module.r_lib_dir = os.path.join(ext_spec.prefix, self.r_lib_dir)
+        module.r_lib_dir = join_path(ext_spec.prefix, self.r_lib_dir)
 
         # Make the site packages directory for extensions, if it does not exist
         # already.
diff --git a/var/spack/repos/builtin/packages/SAMRAI/package.py b/var/spack/repos/builtin/packages/SAMRAI/package.py
index 73c51ced23..e0648290d6 100644
--- a/var/spack/repos/builtin/packages/SAMRAI/package.py
+++ b/var/spack/repos/builtin/packages/SAMRAI/package.py
@@ -24,12 +24,14 @@
 ##############################################################################
 from spack import *
 
+
 class Samrai(Package):
     """SAMRAI (Structured Adaptive Mesh Refinement Application Infrastructure)
-       is an object-oriented C++ software library enables exploration of numerical,
-       algorithmic, parallel computing, and software issues associated with applying
-       structured adaptive mesh refinement (SAMR) technology in large-scale parallel
-       application development.
+       is an object-oriented C++ software library enables exploration of
+       numerical, algorithmic, parallel computing, and software issues
+       associated with applying structured adaptive mesh refinement
+       (SAMR) technology in large-scale parallel application development.
+
     """
     homepage = "https://computation.llnl.gov/project/SAMRAI/"
     url      = "https://computation.llnl.gov/project/SAMRAI/download/SAMRAI-v3.9.1.tar.gz"
diff --git a/var/spack/repos/builtin/packages/ack/package.py b/var/spack/repos/builtin/packages/ack/package.py
new file mode 100644
index 0000000000..70249aebac
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ack/package.py
@@ -0,0 +1,51 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Ack(Package):
+    """ack 2.14 is a tool like grep, optimized for programmers.
+
+       Designed for programmers with large heterogeneous trees of
+       source code, ack is written purely in portable Perl 5 and takes
+       advantage of the power of Perl's regular expressions."""
+
+    homepage = "http://beyondgrep.com/"
+    url      = "http://beyondgrep.com/ack-2.14-single-file"
+
+    version('2.14', 'e74150a1609d28a70b450ef9cc2ed56b', expand=False)
+
+    depends_on('perl')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        ack = 'ack-{0}-single-file'.format(self.version)
+
+        # rewrite the script's #! line to call the perl dependency
+        shbang = '#!' + join_path(spec['perl'].prefix.bin, 'perl')
+        filter_file(r'^#!/usr/bin/env perl', shbang, ack)
+
+        install(ack, join_path(prefix.bin, "ack"))
+        set_executable(join_path(prefix.bin, "ack"))
diff --git a/var/spack/repos/builtin/packages/activeharmony/package.py b/var/spack/repos/builtin/packages/activeharmony/package.py
index 9d15bd71d9..6a4e67a1ca 100644
--- a/var/spack/repos/builtin/packages/activeharmony/package.py
+++ b/var/spack/repos/builtin/packages/activeharmony/package.py
@@ -24,8 +24,10 @@
 ##############################################################################
 from spack import *
 
+
 class Activeharmony(Package):
-    """Active Harmony: a framework for auto-tuning (the automated search for values to improve the performance of a target application)."""
+    """Active Harmony: a framework for auto-tuning (the automated search for
+       values to improve the performance of a target application)."""
     homepage = "http://www.dyninst.org/harmony"
     url      = "http://www.dyninst.org/sites/default/files/downloads/harmony/ah-4.5.tar.gz"
 
@@ -34,6 +36,3 @@ class Activeharmony(Package):
     def install(self, spec, prefix):
         make("CFLAGS=-O3")
         make("install", 'PREFIX=%s' % prefix)
-
-from spack import *
-
diff --git a/var/spack/repos/builtin/packages/adept-utils/package.py b/var/spack/repos/builtin/packages/adept-utils/package.py
index 592681bb82..1a6998fd96 100644
--- a/var/spack/repos/builtin/packages/adept-utils/package.py
+++ b/var/spack/repos/builtin/packages/adept-utils/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class AdeptUtils(Package):
     """Utility libraries for LLNL performance tools."""
 
diff --git a/var/spack/repos/builtin/packages/adol-c/package.py b/var/spack/repos/builtin/packages/adol-c/package.py
index a6052ad7bd..c5d53de230 100644
--- a/var/spack/repos/builtin/packages/adol-c/package.py
+++ b/var/spack/repos/builtin/packages/adol-c/package.py
@@ -23,21 +23,24 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
-import sys
+
 
 class AdolC(Package):
-    """A package for the automatic differentiation of first and higher derivatives of vector functions in C and C++ programs by operator overloading."""
+    """A package for the automatic differentiation of first and higher
+    derivatives of vector functions in C and C++ programs by operator
+    overloading."""
     homepage = "https://projects.coin-or.org/ADOL-C"
     url      = "http://www.coin-or.org/download/source/ADOL-C/ADOL-C-2.6.1.tgz"
 
     version('head',  svn='https://projects.coin-or.org/svn/ADOL-C/trunk/')
     version('2.6.1', '1032b28427d6e399af4610e78c0f087b')
-    
+
     variant('doc',      default=True,  description='Install documentation')
     variant('openmp',   default=False, description='Enable OpenMP support')
     variant('sparse',   default=False, description='Enable sparse drivers')
-    variant('tests',    default=True,  description='Build all included examples as a test case')
-    
+    variant('tests',    default=True,
+            description='Build all included examples as a test case')
+
     patch('openmp_exam.patch')
 
     def install(self, spec, prefix):
@@ -49,10 +52,14 @@ class AdolC(Package):
         if '+openmp' in spec:
             if spec.satisfies('%gcc'):
                 make_args.extend([
-                    '--with-openmp-flag=-fopenmp' # FIXME: Is this required? -I <path to omp.h> -L <LLVM OpenMP library path>
+                    # FIXME: Is this required? -I <path to omp.h> -L <LLVM
+                    # OpenMP library path>
+                    '--with-openmp-flag=-fopenmp'
                 ])
             else:
-                raise InstallError("OpenMP flags for compilers other than GCC are not implemented.")
+                raise InstallError(
+                    "OpenMP flags for compilers other than GCC "
+                    "are not implemented.")
 
         if '+sparse' in spec:
             make_args.extend([
@@ -63,7 +70,7 @@ class AdolC(Package):
         # whether Adol-C works as expected
         if '+tests' in spec:
             make_args.extend([
-                '--enable-docexa', # Documeted examples
+                '--enable-docexa',  # Documeted examples
                 '--enable-addexa'  # Additional examples
             ])
             if '+openmp' in spec:
@@ -74,31 +81,36 @@ class AdolC(Package):
         configure(*make_args)
         make()
         make("install")
-        
+
         # Copy the config.h file, as some packages might require it
         source_directory = self.stage.source_path
-        config_h = join_path(source_directory,'ADOL-C','src','config.h')
-        install(config_h, join_path(prefix.include,'adolc'))
-        
+        config_h = join_path(source_directory, 'ADOL-C', 'src', 'config.h')
+        install(config_h, join_path(prefix.include, 'adolc'))
+
         # Install documentation to {prefix}/share
         if '+doc' in spec:
-            install_tree(join_path('ADOL-C','doc'),
-                         join_path(prefix.share,'doc'))
-        
+            install_tree(join_path('ADOL-C', 'doc'),
+                         join_path(prefix.share, 'doc'))
+
         # Install examples to {prefix}/share
         if '+tests' in spec:
-            install_tree(join_path('ADOL-C','examples'),
-                         join_path(prefix.share,'examples'))
-        
+            install_tree(join_path('ADOL-C', 'examples'),
+                         join_path(prefix.share, 'examples'))
+
             # Run some examples that don't require user input
             # TODO: Check that bundled examples produce the correct results
-            with working_dir(join_path(source_directory,'ADOL-C','examples')):
+            with working_dir(join_path(
+                    source_directory, 'ADOL-C', 'examples')):
                 Executable('./tapeless_scalar')()
                 Executable('./tapeless_vector')()
-              
-            with working_dir(join_path(source_directory,'ADOL-C','examples','additional_examples')):
+
+            with working_dir(join_path(
+                    source_directory,
+                    'ADOL-C', 'examples', 'additional_examples')):
                 Executable('./checkpointing/checkpointing')()
-                
+
             if '+openmp' in spec:
-                with working_dir(join_path(source_directory,'ADOL-C','examples','additional_examples')):
+                with working_dir(join_path(
+                        source_directory,
+                        'ADOL-C', 'examples', 'additional_examples')):
                     Executable('./checkpointing/checkpointing')()
diff --git a/var/spack/repos/builtin/packages/antlr/package.py b/var/spack/repos/builtin/packages/antlr/package.py
index eb67facaf3..891061c62f 100644
--- a/var/spack/repos/builtin/packages/antlr/package.py
+++ b/var/spack/repos/builtin/packages/antlr/package.py
@@ -24,8 +24,9 @@
 ##############################################################################
 from spack import *
 
+
 class Antlr(Package):
-    
+
     homepage = "http://www.antlr.org"
     url      = "https://github.com/antlr/antlr/tarball/v2.7.7"
 
@@ -41,22 +42,23 @@ class Antlr(Package):
     # CharScanner.hpp must include this line: #include <cstring> or else
     # ncap2 will not compile (this tarball is already patched).
     version('2.7.7', '914865e853fe8e1e61a9f23d045cb4ab',
-        # Patched version as described above
-        url='http://dust.ess.uci.edu/tmp/antlr-2.7.7.tar.gz')
-        # Unpatched version
-        # url='http://dust.ess.uci.edu/nco/antlr-2.7.7.tar.gz')
+            # Patched version as described above
+            url='http://dust.ess.uci.edu/tmp/antlr-2.7.7.tar.gz')
+    # Unpatched version
+    # url='http://dust.ess.uci.edu/nco/antlr-2.7.7.tar.gz')
 
     variant('cxx', default=False, description='Enable ANTLR for C++')
     variant('java', default=False, description='Enable ANTLR for Java')
     variant('python', default=False, description='Enable ANTLR for Python')
     variant('csharp', default=False, description='Enable ANTLR for Csharp')
 
-
     def install(self, spec, prefix):
         # Check for future enabling of variants
         for v in ('+java', '+python', '+csharp'):
             if v in spec:
-                raise Error('Illegal variant %s; for now, Spack only knows how to build antlr or antlr+cxx')
+                raise Error(
+                    ('Illegal variant %s; ' % v) + 'for now, '
+                    'Spack only knows how to build antlr or antlr+cxx')
 
         config_args = [
             '--prefix=%s' % prefix,
diff --git a/var/spack/repos/builtin/packages/apex/package.py b/var/spack/repos/builtin/packages/apex/package.py
index 59fbe50c93..832e10a1ec 100644
--- a/var/spack/repos/builtin/packages/apex/package.py
+++ b/var/spack/repos/builtin/packages/apex/package.py
@@ -25,6 +25,7 @@
 from spack import *
 from spack.util.environment import *
 
+
 class Apex(Package):
     homepage = "http://github.com/khuck/xpress-apex"
     url      = "http://github.com/khuck/xpress-apex/archive/v0.1.tar.gz"
@@ -39,17 +40,17 @@ class Apex(Package):
 
     def install(self, spec, prefix):
 
-        path=get_path("PATH")
+        path = get_path("PATH")
         path.remove(spec["binutils"].prefix.bin)
         path_set("PATH", path)
         with working_dir("build", create=True):
             cmake('-DBOOST_ROOT=%s' % spec['boost'].prefix,
-                '-DUSE_BFD=TRUE', 
-                '-DBFD_ROOT=%s' % spec['binutils'].prefix,
-                '-DUSE_ACTIVEHARMONY=TRUE', 
-                '-DACTIVEHARMONY_ROOT=%s' % spec['activeharmony'].prefix,
-                '-DUSE_OMPT=TRUE', 
-                '-DOMPT_ROOT=%s' % spec['ompt-openmp'].prefix,
-                '..', *std_cmake_args)
+                  '-DUSE_BFD=TRUE',
+                  '-DBFD_ROOT=%s' % spec['binutils'].prefix,
+                  '-DUSE_ACTIVEHARMONY=TRUE',
+                  '-DACTIVEHARMONY_ROOT=%s' % spec['activeharmony'].prefix,
+                  '-DUSE_OMPT=TRUE',
+                  '-DOMPT_ROOT=%s' % spec['ompt-openmp'].prefix,
+                  '..', *std_cmake_args)
             make()
             make("install")
diff --git a/var/spack/repos/builtin/packages/apr-util/package.py b/var/spack/repos/builtin/packages/apr-util/package.py
index 05dc670aed..8e01d3bbdd 100644
--- a/var/spack/repos/builtin/packages/apr-util/package.py
+++ b/var/spack/repos/builtin/packages/apr-util/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class AprUtil(Package):
     """Apache Portable Runtime Utility"""
     homepage  = 'https://apr.apache.org/'
diff --git a/var/spack/repos/builtin/packages/apr/package.py b/var/spack/repos/builtin/packages/apr/package.py
index 398e1c323d..0cd51f52e3 100644
--- a/var/spack/repos/builtin/packages/apr/package.py
+++ b/var/spack/repos/builtin/packages/apr/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Apr(Package):
     """Apache portable runtime."""
     homepage  = 'https://apr.apache.org/'
diff --git a/var/spack/repos/builtin/packages/armadillo/package.py b/var/spack/repos/builtin/packages/armadillo/package.py
index b3e5994e30..4356f60aca 100644
--- a/var/spack/repos/builtin/packages/armadillo/package.py
+++ b/var/spack/repos/builtin/packages/armadillo/package.py
@@ -33,11 +33,13 @@ class Armadillo(Package):
     homepage = "http://arma.sourceforge.net/"
     url = "http://sourceforge.net/projects/arma/files/armadillo-7.200.1.tar.xz"
 
+    version('7.200.2', 'b21585372d67a8876117fd515d8cf0a2')
     version('7.200.1', 'ed86d6df0058979e107502e1fe3e469e')
 
     variant('hdf5', default=False, description='Include HDF5 support')
 
-    depends_on('arpack')
+    depends_on('cmake@2.8:', type='build')
+    depends_on('arpack-ng')  # old arpack causes undefined symbols
     depends_on('blas')
     depends_on('lapack')
     depends_on('superlu@5.2:')
@@ -46,8 +48,8 @@ class Armadillo(Package):
     def install(self, spec, prefix):
         cmake_args = [
             # ARPACK support
-            '-DARPACK_LIBRARY={0}/libarpack.a'.format(
-                spec['arpack'].prefix.lib),
+            '-DARPACK_LIBRARY={0}/libarpack.{1}'.format(
+                spec['arpack-ng'].prefix.lib, dso_suffix),
             # BLAS support
             '-DBLAS_LIBRARY={0}'.format(spec['blas'].blas_shared_lib),
             # LAPACK support
diff --git a/var/spack/repos/builtin/packages/arpack-ng/package.py b/var/spack/repos/builtin/packages/arpack-ng/package.py
index d5dc703c06..728c2345f2 100644
--- a/var/spack/repos/builtin/packages/arpack-ng/package.py
+++ b/var/spack/repos/builtin/packages/arpack-ng/package.py
@@ -59,7 +59,8 @@ class ArpackNg(Package):
     version('3.4.0', 'ae9ca13f2143a7ea280cb0e2fd4bfae4')
     version('3.3.0', 'ed3648a23f0a868a43ef44c97a21bad5')
 
-    variant('shared', default=True, description='Enables the build of shared libraries')
+    variant('shared', default=True,
+            description='Enables the build of shared libraries')
     variant('mpi', default=False, description='Activates MPI support')
 
     # The function pdlamch10 does not set the return variable.
@@ -86,10 +87,19 @@ class ArpackNg(Package):
         options.extend(std_cmake_args)
         options.append('-DCMAKE_INSTALL_NAME_DIR:PATH=%s/lib' % prefix)
 
-        # TODO:
-        # Arpack calls directly find_package(BLAS REQUIRED) and
-        # find_package(LAPACK REQUIRED). Make sure correct Blas/Lapack are
-        # picked up.
+        # Make sure we use Spack's blas/lapack:
+        options.extend([
+            '-DLAPACK_FOUND=true',
+            '-DLAPACK_INCLUDE_DIRS=%s' % spec['lapack'].prefix.include,
+            '-DLAPACK_LIBRARIES=%s' % (
+                spec['lapack'].lapack_shared_lib if '+shared' in spec else
+                spec['lapack'].lapack_static_lib),
+            '-DBLAS_FOUND=true',
+            '-DBLAS_INCLUDE_DIRS=%s' % spec['blas'].prefix.include,
+            '-DBLAS_LIBRARIES=%s' % (
+                spec['blas'].blas_shared_lib if '+shared' in spec else
+                spec['blas'].blas_static_lib)
+        ])
 
         if '+mpi' in spec:
             options.append('-DMPI=ON')
@@ -101,9 +111,8 @@ class ArpackNg(Package):
 
         cmake('.', *options)
         make()
-        # TODO: make test does not work
-        # make('test')
-
+        if self.run_tests:
+            make('test')
         make('install')
 
     @when('@3.3.0')
@@ -120,10 +129,23 @@ class ArpackNg(Package):
                 'F77=%s' % spec['mpi'].mpif77
             ])
 
-        if '~shared' in spec:
-            options.append('--enable-shared=no')
+        if '+shared' in spec:
+            options.extend([
+                '--with-blas=%s' % to_link_flags(
+                    spec['blas'].blas_shared_lib),
+                '--with-lapack=%s' % to_link_flags(
+                    spec['lapack'].lapack_shared_lib)
+            ])
+        else:
+            options.extend([
+                '--with-blas=%s' % spec['blas'].blas_static_lib,
+                '--with-lapack=%s' % spec['lapack'].lapack_static_lib,
+                '--enable-shared=no'
+            ])
 
         bootstrap()
         configure(*options)
         make()
+        if self.run_tests:
+            make('check')
         make('install')
diff --git a/var/spack/repos/builtin/packages/asciidoc/package.py b/var/spack/repos/builtin/packages/asciidoc/package.py
index a846e0ba65..be8db684f5 100644
--- a/var/spack/repos/builtin/packages/asciidoc/package.py
+++ b/var/spack/repos/builtin/packages/asciidoc/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Asciidoc(Package):
     """ A presentable text document format for writing articles, UNIX man
     pages and other small to medium sized documents."""
diff --git a/var/spack/repos/builtin/packages/atk/package.py b/var/spack/repos/builtin/packages/atk/package.py
index 1d26145fd1..d5b6933ec3 100644
--- a/var/spack/repos/builtin/packages/atk/package.py
+++ b/var/spack/repos/builtin/packages/atk/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Atk(Package):
     """ATK provides the set of accessibility interfaces that are
        implemented by other toolkits and applications. Using the ATK
@@ -32,9 +33,16 @@ class Atk(Package):
     homepage = "https://developer.gnome.org/atk/"
     url      = "http://ftp.gnome.org/pub/gnome/sources/atk/2.14/atk-2.14.0.tar.xz"
 
+    version('2.20.0', '5187b0972f4d3905f285540b31395e20')
     version('2.14.0', 'ecb7ca8469a5650581b1227d78051b8b')
 
-    depends_on("glib")
+    depends_on('glib')
+    depends_on('pkg-config', type='build')
+
+    def url_for_version(self, version):
+        """Handle atk's version-based custom URLs."""
+        url = 'http://ftp.gnome.org/pub/gnome/sources/atk'
+        return 'url+/%s/atk-%s.tar.xz' % (version.up_to(2), version)
 
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
diff --git a/var/spack/repos/builtin/packages/atlas/package.py b/var/spack/repos/builtin/packages/atlas/package.py
index c43d92c34f..f9d5da6166 100644
--- a/var/spack/repos/builtin/packages/atlas/package.py
+++ b/var/spack/repos/builtin/packages/atlas/package.py
@@ -23,20 +23,24 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
+from spack.package_test import *
 from spack.util.executable import Executable
 import os.path
 
+
 class Atlas(Package):
-    """
-    Automatically Tuned Linear Algebra Software, generic shared ATLAS is an approach for the automatic generation and
-    optimization of numerical software. Currently ATLAS supplies optimized versions for the complete set of linear
-    algebra kernels known as the Basic Linear Algebra Subroutines (BLAS), and a subset of the linear algebra routines
-    in the LAPACK library.
+    """Automatically Tuned Linear Algebra Software, generic shared ATLAS is an
+    approach for the automatic generation and optimization of numerical
+    software. Currently ATLAS supplies optimized versions for the complete set
+    of linear algebra kernels known as the Basic Linear Algebra Subroutines
+    (BLAS), and a subset of the linear algebra routines in the LAPACK library.
     """
     homepage = "http://math-atlas.sourceforge.net/"
 
     version('3.10.2', 'a4e21f343dec8f22e7415e339f09f6da',
-            url='http://downloads.sourceforge.net/project/math-atlas/Stable/3.10.2/atlas3.10.2.tar.bz2', preferred=True)
+            url='https://sourceforge.net/projects/math-atlas/files/Stable/3.10.2/atlas3.10.2.tar.bz2', preferred=True)
+    # not all packages (e.g. Trilinos@12.6.3) stopped using deprecated in 3.6.0
+    # Lapack routines. Stick with 3.5.0 until this is fixed.
     resource(name='lapack',
              url='http://www.netlib.org/lapack/lapack-3.5.0.tgz',
              md5='b1d3e3e425b2e44a06760ff173104bdf',
@@ -44,7 +48,7 @@ class Atlas(Package):
              when='@3:')
 
     version('3.11.34', '0b6c5389c095c4c8785fd0f724ec6825',
-            url='http://sourceforge.net/projects/math-atlas/files/Developer%20%28unstable%29/3.11.34/atlas3.11.34.tar.bz2/download')
+            url='http://sourceforge.net/projects/math-atlas/files/Developer%20%28unstable%29/3.11.34/atlas3.11.34.tar.bz2')
 
     variant('shared', default=True, description='Builds shared library')
 
@@ -66,9 +70,24 @@ class Atlas(Package):
 
         options = []
         if '+shared' in spec:
-            options.append('--shared')
+            options.extend([
+                '--shared'
+            ])
+            # TODO: for non GNU add '-Fa', 'alg', '-fPIC' ?
+
+        # configure for 64-bit build
+        options.extend([
+            '-b', '64'
+        ])
 
-        # Lapack resource
+        # set compilers:
+        options.extend([
+            '-C', 'ic', spack_cc,
+            '-C', 'if', spack_f77
+        ])
+
+        # Lapack resource to provide full lapack build. Note that
+        # ATLAS only provides a few LAPACK routines natively.
         lapack_stage = self.stage[1]
         lapack_tarfile = os.path.basename(lapack_stage.fetcher.url)
         lapack_tarfile_path = join_path(lapack_stage.path, lapack_tarfile)
@@ -81,4 +100,35 @@ class Atlas(Package):
             make('check')
             make('ptcheck')
             make('time')
+            if '+shared' in spec:
+                with working_dir('lib'):
+                    make('shared_all')
+
             make("install")
+            self.install_test()
+
+    def setup_dependent_package(self, module, dspec):
+        # libsatlas.[so,dylib,dll ] contains all serial APIs (serial lapack,
+        # serial BLAS), and all ATLAS symbols needed to support them. Whereas
+        # libtatlas.[so,dylib,dll ] is parallel (multithreaded) version.
+        name = 'libsatlas.%s' % dso_suffix
+        libdir = find_library_path(name,
+                                   self.prefix.lib64,
+                                   self.prefix.lib)
+
+        if '+shared' in self.spec:
+            self.spec.blas_shared_lib   = join_path(libdir, name)
+            self.spec.lapack_shared_lib = self.spec.blas_shared_lib
+
+    def install_test(self):
+        source_file = join_path(os.path.dirname(self.module.__file__),
+                                'test_cblas_dgemm.c')
+        blessed_file = join_path(os.path.dirname(self.module.__file__),
+                                 'test_cblas_dgemm.output')
+
+        include_flags = ["-I%s" % join_path(self.spec.prefix, "include")]
+        link_flags = ["-L%s" % join_path(self.spec.prefix, "lib"),
+                      "-lsatlas"]
+
+        output = compile_c_and_execute(source_file, include_flags, link_flags)
+        compare_output_file(output, blessed_file)
diff --git a/var/spack/repos/builtin/packages/atlas/test_cblas_dgemm.c b/var/spack/repos/builtin/packages/atlas/test_cblas_dgemm.c
new file mode 100644
index 0000000000..2cb90fb883
--- /dev/null
+++ b/var/spack/repos/builtin/packages/atlas/test_cblas_dgemm.c
@@ -0,0 +1,49 @@
+#include <cblas.h>
+#include <stdio.h>
+
+double m[] = {
+  3, 1, 3,
+  1, 5, 9,
+  2, 6, 5
+};
+
+double x[] = {
+  -1, 3, -3
+};
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+     void dgesv_(int *n, int *nrhs,  double *a,  int  *lda,
+           int *ipivot, double *b, int *ldb, int *info);
+
+#ifdef __cplusplus
+}
+#endif
+
+int main(void) {
+  int i;
+  // blas:
+  double A[6] = {1.0, 2.0, 1.0, -3.0, 4.0, -1.0};
+  double B[6] = {1.0, 2.0, 1.0, -3.0, 4.0, -1.0};
+  double C[9] = {.5, .5, .5, .5, .5, .5, .5, .5, .5};
+  cblas_dgemm(CblasColMajor, CblasNoTrans, CblasTrans,
+              3, 3, 2, 1, A, 3, B, 3, 2, C, 3);
+  for (i = 0; i < 9; i++)
+    printf("%f\n", C[i]);
+
+  // lapack:
+  int ipiv[3];
+  int j;
+  int info;
+  int n = 1;
+  int nrhs = 1;
+  int lda = 3;
+  int ldb = 3;
+  dgesv_(&n,&nrhs, &m[0], &lda, ipiv, &x[0], &ldb, &info);
+  for (i=0; i<3; ++i)
+    printf("%5.1f\n", x[i]);
+
+  return 0;
+}
diff --git a/var/spack/repos/builtin/packages/atlas/test_cblas_dgemm.output b/var/spack/repos/builtin/packages/atlas/test_cblas_dgemm.output
new file mode 100644
index 0000000000..01404462c4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/atlas/test_cblas_dgemm.output
@@ -0,0 +1,12 @@
+11.000000
+-9.000000
+5.000000
+-9.000000
+21.000000
+-1.000000
+5.000000
+-1.000000
+3.000000
+ -0.3
+  3.0
+ -3.0
diff --git a/var/spack/repos/builtin/packages/atop/package.py b/var/spack/repos/builtin/packages/atop/package.py
index 9cacafc634..e3a9d464a9 100644
--- a/var/spack/repos/builtin/packages/atop/package.py
+++ b/var/spack/repos/builtin/packages/atop/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Atop(Package):
     """Atop is an ASCII full-screen performance monitor for Linux"""
     homepage = "http://www.atoptool.nl/index.php"
@@ -37,4 +38,4 @@ class Atop(Package):
         install("atop", join_path(prefix.bin, "atop"))
         mkdirp(join_path(prefix.man, "man1"))
         install(join_path("man", "atop.1"),
-        join_path(prefix.man, "man1", "atop.1"))
+                join_path(prefix.man, "man1", "atop.1"))
diff --git a/var/spack/repos/builtin/packages/automaded/package.py b/var/spack/repos/builtin/packages/automaded/package.py
index 2b4681778f..7e586b2991 100644
--- a/var/spack/repos/builtin/packages/automaded/package.py
+++ b/var/spack/repos/builtin/packages/automaded/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Automaded(Package):
     """AutomaDeD (Automata-based Debugging for Dissimilar parallel
        tasks) is a tool for automatic diagnosis of performance and
diff --git a/var/spack/repos/builtin/packages/bash/package.py b/var/spack/repos/builtin/packages/bash/package.py
index 5820595be9..e0cd114635 100644
--- a/var/spack/repos/builtin/packages/bash/package.py
+++ b/var/spack/repos/builtin/packages/bash/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Bash(Package):
     """The GNU Project's Bourne Again SHell."""
 
diff --git a/var/spack/repos/builtin/packages/bbcp/package.py b/var/spack/repos/builtin/packages/bbcp/package.py
index 09e897f34e..f69ed395a3 100644
--- a/var/spack/repos/builtin/packages/bbcp/package.py
+++ b/var/spack/repos/builtin/packages/bbcp/package.py
@@ -24,18 +24,22 @@
 ##############################################################################
 from spack import *
 
+
 class Bbcp(Package):
     """Securely and quickly copy data from source to target"""
     homepage = "http://www.slac.stanford.edu/~abh/bbcp/"
 
-    version('git', git='http://www.slac.stanford.edu/~abh/bbcp/bbcp.git', branch="master")
+    version('git', git='http://www.slac.stanford.edu/~abh/bbcp/bbcp.git',
+            branch="master")
 
     def install(self, spec, prefix):
         cd("src")
         make()
-        # BBCP wants to build the executable in a directory whose name depends on the system type
+        # BBCP wants to build the executable in a directory whose name depends
+        # on the system type
         makesname = Executable("../MakeSname")
-        bbcp_executable_path = "../bin/%s/bbcp" % makesname(output=str).rstrip("\n")
+        bbcp_executable_path = "../bin/%s/bbcp" % makesname(
+            output=str).rstrip("\n")
         destination_path = "%s/bin/" % prefix
         mkdirp(destination_path)
         install(bbcp_executable_path, destination_path)
diff --git a/var/spack/repos/builtin/packages/bcftools/package.py b/var/spack/repos/builtin/packages/bcftools/package.py
new file mode 100644
index 0000000000..a1b4a06dbb
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bcftools/package.py
@@ -0,0 +1,43 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Bcftools(Package):
+    """BCFtools is a set of utilities that manipulate variant calls in the
+       Variant Call Format (VCF) and its binary counterpart BCF. All
+       commands work transparently with both VCFs and BCFs, both
+       uncompressed and BGZF-compressed."""
+
+    homepage = "http://samtools.github.io/bcftools/"
+    url      = "https://github.com/samtools/bcftools/releases/download/1.3.1/bcftools-1.3.1.tar.bz2"
+
+    version('1.3.1', '575001e9fca37cab0c7a7287ad4b1cdb')
+
+    depends_on('zlib')
+
+    def install(self, spec, prefix):
+        make("prefix=%s" % prefix, "all")
+        make("prefix=%s" % prefix, "install")
diff --git a/var/spack/repos/builtin/packages/bdw-gc/package.py b/var/spack/repos/builtin/packages/bdw-gc/package.py
new file mode 100644
index 0000000000..5120266319
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bdw-gc/package.py
@@ -0,0 +1,53 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class BdwGc(Package):
+    """The Boehm-Demers-Weiser conservative garbage collector is a garbage
+    collecting replacement for C malloc or C++ new."""
+
+    homepage = "http://www.hboehm.info/gc/"
+    url      = "http://www.hboehm.info/gc/gc_source/gc-7.4.4.tar.gz"
+
+    version('7.4.4', '96d18b0448a841c88d56e4ab3d180297')
+
+    variant('libatomic-ops', default=True,
+            description='Use external libatomic-ops')
+
+    depends_on('libatomic-ops', when='+libatomic-ops')
+
+    def install(self, spec, prefix):
+        config_args = [
+            '--prefix={0}'.format(prefix),
+            '--with-libatomic-ops={0}'.format(
+                'yes' if '+libatomic-ops' in spec else 'no')
+        ]
+
+        configure(*config_args)
+
+        make()
+        make('check')
+        make('install')
diff --git a/var/spack/repos/builtin/packages/bear/package.py b/var/spack/repos/builtin/packages/bear/package.py
index a137fded08..f52050d7b9 100644
--- a/var/spack/repos/builtin/packages/bear/package.py
+++ b/var/spack/repos/builtin/packages/bear/package.py
@@ -24,8 +24,10 @@
 ##############################################################################
 from spack import *
 
+
 class Bear(Package):
-    """Bear is a tool that generates a compilation database for clang tooling from non-cmake build systems."""
+    """Bear is a tool that generates a compilation database for clang tooling
+    from non-cmake build systems."""
     homepage = "https://github.com/rizsotto/Bear"
     url      = "https://github.com/rizsotto/Bear/archive/2.0.4.tar.gz"
 
diff --git a/var/spack/repos/builtin/packages/bib2xhtml/package.py b/var/spack/repos/builtin/packages/bib2xhtml/package.py
index a9cbd204b6..b356038180 100644
--- a/var/spack/repos/builtin/packages/bib2xhtml/package.py
+++ b/var/spack/repos/builtin/packages/bib2xhtml/package.py
@@ -25,10 +25,11 @@
 from spack import *
 from glob import glob
 
+
 class Bib2xhtml(Package):
     """bib2xhtml is a program that converts BibTeX files into HTML."""
     homepage = "http://www.spinellis.gr/sw/textproc/bib2xhtml/"
-    url='http://www.spinellis.gr/sw/textproc/bib2xhtml/bib2xhtml-v3.0-15-gf506.tar.gz'
+    url = 'http://www.spinellis.gr/sw/textproc/bib2xhtml/bib2xhtml-v3.0-15-gf506.tar.gz'
 
     version('3.0-15-gf506', 'a26ba02fe0053bbbf2277bdf0acf8645')
 
diff --git a/var/spack/repos/builtin/packages/bison/package.py b/var/spack/repos/builtin/packages/bison/package.py
index c7a125df15..70795f05cc 100644
--- a/var/spack/repos/builtin/packages/bison/package.py
+++ b/var/spack/repos/builtin/packages/bison/package.py
@@ -24,9 +24,10 @@
 ##############################################################################
 from spack import *
 
+
 class Bison(Package):
-    """Bison is a general-purpose parser generator that converts 
-    an annotated context-free grammar into a deterministic LR or 
+    """Bison is a general-purpose parser generator that converts
+    an annotated context-free grammar into a deterministic LR or
     generalized LR (GLR) parser employing LALR(1) parser tables."""
 
     homepage = "http://www.gnu.org/software/bison/"
diff --git a/var/spack/repos/builtin/packages/boost/package.py b/var/spack/repos/builtin/packages/boost/package.py
index 67294fb9a1..690a05a150 100644
--- a/var/spack/repos/builtin/packages/boost/package.py
+++ b/var/spack/repos/builtin/packages/boost/package.py
@@ -102,13 +102,18 @@ class Boost(Package):
 
     for lib in all_libs:
         variant(lib, default=(lib not in default_noinstall_libs),
-            description="Compile with {0} library".format(lib))
-
-    variant('debug', default=False, description='Switch to the debug version of Boost')
-    variant('shared', default=True, description="Additionally build shared libraries")
-    variant('multithreaded', default=True, description="Build multi-threaded versions of libraries")
-    variant('singlethreaded', default=True, description="Build single-threaded versions of libraries")
-    variant('icu_support', default=False, description="Include ICU support (for regex/locale libraries)")
+                description="Compile with {0} library".format(lib))
+
+    variant('debug', default=False,
+            description='Switch to the debug version of Boost')
+    variant('shared', default=True,
+            description="Additionally build shared libraries")
+    variant('multithreaded', default=True,
+            description="Build multi-threaded versions of libraries")
+    variant('singlethreaded', default=True,
+            description="Build single-threaded versions of libraries")
+    variant('icu_support', default=False,
+            description="Include ICU support (for regex/locale libraries)")
     variant('graph', default=False, description="Build the Boost Graph library")
 
     depends_on('icu', when='+icu_support')
@@ -128,8 +133,7 @@ class Boost(Package):
         parts = [str(p) for p in Version(version)]
         dots = ".".join(parts)
         underscores = "_".join(parts)
-        return "http://downloads.sourceforge.net/project/boost" \
-               "/boost/%s/boost_%s.tar.bz2" % (dots, underscores)
+        return "http://downloads.sourceforge.net/project/boost/boost/%s/boost_%s.tar.bz2" % (dots, underscores)
 
     def determine_toolset(self, spec):
         if spec.satisfies("platform=darwin"):
@@ -158,7 +162,7 @@ class Boost(Package):
         with open('user-config.jam', 'w') as f:
             compiler_wrapper = join_path(spack.build_env_path, 'c++')
             f.write("using {0} : : {1} ;\n".format(boostToolsetId,
-                    compiler_wrapper))
+                                                   compiler_wrapper))
 
             if '+mpi' in spec:
                 f.write('using mpi : %s ;\n' %
diff --git a/var/spack/repos/builtin/packages/bowtie2/package.py b/var/spack/repos/builtin/packages/bowtie2/package.py
index 6d641da49b..a8a1a34ed4 100644
--- a/var/spack/repos/builtin/packages/bowtie2/package.py
+++ b/var/spack/repos/builtin/packages/bowtie2/package.py
@@ -24,12 +24,15 @@
 ##############################################################################
 from spack import *
 from glob import glob
+
+
 class Bowtie2(Package):
     """Description"""
     homepage = "bowtie-bio.sourceforge.net/bowtie2/index.shtml"
-    version('2.2.5','51fa97a862d248d7ee660efc1147c75f', url = "http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.2.5/bowtie2-2.2.5-source.zip")
+    version('2.2.5', '51fa97a862d248d7ee660efc1147c75f',
+            url="http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.2.5/bowtie2-2.2.5-source.zip")
 
-    patch('bowtie2-2.5.patch',when='@2.2.5', level=0)
+    patch('bowtie2-2.5.patch', when='@2.2.5', level=0)
 
     def install(self, spec, prefix):
         make()
@@ -45,4 +48,3 @@ class Bowtie2(Package):
         # install('bowtie2-inspect',prefix.bin)
         # install('bowtie2-inspect-l',prefix.bin)
         # install('bowtie2-inspect-s',prefix.bin)
-
diff --git a/var/spack/repos/builtin/packages/boxlib/package.py b/var/spack/repos/builtin/packages/boxlib/package.py
index 216ae1ec12..4f41aba6c6 100644
--- a/var/spack/repos/builtin/packages/boxlib/package.py
+++ b/var/spack/repos/builtin/packages/boxlib/package.py
@@ -24,12 +24,13 @@
 ##############################################################################
 from spack import *
 
+
 class Boxlib(Package):
     """BoxLib, a software framework for massively parallel
        block-structured adaptive mesh refinement (AMR) codes."""
 
     homepage = "https://ccse.lbl.gov/BoxLib/"
-    url = "https://ccse.lbl.gov/pub/Downloads/BoxLib.git";
+    url = "https://ccse.lbl.gov/pub/Downloads/BoxLib.git"
 
     # TODO: figure out how best to version this.  No tags in the repo!
     version('master', git='https://ccse.lbl.gov/pub/Downloads/BoxLib.git')
@@ -47,4 +48,3 @@ class Boxlib(Package):
         cmake('.', *args)
         make()
         make("install")
-
diff --git a/var/spack/repos/builtin/packages/bpp-core/package.py b/var/spack/repos/builtin/packages/bpp-core/package.py
new file mode 100644
index 0000000000..40360a03b3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bpp-core/package.py
@@ -0,0 +1,41 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class BppCore(Package):
+    """Bio++ core library."""
+
+    homepage = "http://biopp.univ-montp2.fr/wiki/index.php/Installation"
+    url      = "http://biopp.univ-montp2.fr/repos/sources/bpp-core-2.2.0.tar.gz"
+
+    version('2.2.0', '5789ed2ae8687d13664140cd77203477')
+
+    depends_on('cmake')
+
+    def install(self, spec, prefix):
+        cmake('-DBUILD_TESTING=FALSE', '.', *std_cmake_args)
+        make()
+        make('install')
diff --git a/var/spack/repos/builtin/packages/bpp-phyl/package.py b/var/spack/repos/builtin/packages/bpp-phyl/package.py
new file mode 100644
index 0000000000..62db8d5545
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bpp-phyl/package.py
@@ -0,0 +1,43 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class BppPhyl(Package):
+    """Bio++ phylogeny library."""
+
+    homepage = "http://biopp.univ-montp2.fr/wiki/index.php/Installation"
+    url      = "http://biopp.univ-montp2.fr/repos/sources/bpp-phyl-2.2.0.tar.gz"
+
+    version('2.2.0', '5c40667ec0bf37e0ecaba321be932770')
+
+    depends_on('cmake')
+    depends_on('bpp-core')
+    depends_on('bpp-seq')
+
+    def install(self, spec, prefix):
+        cmake('-DBUILD_TESTING=FALSE', '.', *std_cmake_args)
+        make()
+        make('install')
diff --git a/var/spack/repos/builtin/packages/bpp-seq/package.py b/var/spack/repos/builtin/packages/bpp-seq/package.py
new file mode 100644
index 0000000000..7132c668b3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bpp-seq/package.py
@@ -0,0 +1,42 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class BppSeq(Package):
+    """Bio++ seq library."""
+
+    homepage = "http://biopp.univ-montp2.fr/wiki/index.php/Installation"
+    url      = "http://biopp.univ-montp2.fr/repos/sources/bpp-seq-2.2.0.tar.gz"
+
+    version('2.2.0', '44adef0ff4d5ca4e69ccf258c9270633')
+
+    depends_on('cmake')
+    depends_on('bpp-core')
+
+    def install(self, spec, prefix):
+        cmake('-DBUILD_TESTING=FALSE', '.', *std_cmake_args)
+        make()
+        make('install')
diff --git a/var/spack/repos/builtin/packages/bpp-suite/package.py b/var/spack/repos/builtin/packages/bpp-suite/package.py
new file mode 100644
index 0000000000..41e90e375d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bpp-suite/package.py
@@ -0,0 +1,47 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class BppSuite(Package):
+    """BppSuite is a suite of ready-to-use programs for phylogenetic and
+       sequence analysis."""
+
+    homepage = "http://biopp.univ-montp2.fr/wiki/index.php/BppSuite"
+    url      = "http://biopp.univ-montp2.fr/repos/sources/bppsuite/bppsuite-2.2.0.tar.gz"
+
+    version('2.2.0', 'd8b29ad7ccf5bd3a7beb701350c9e2a4')
+
+    # FIXME: Add dependencies if required.
+    depends_on('cmake')
+    depends_on('texinfo')
+    depends_on('bpp-core')
+    depends_on('bpp-seq')
+    depends_on('bpp-phyl')
+
+    def install(self, spec, prefix):
+        cmake('.', *std_cmake_args)
+        make()
+        make('install')
diff --git a/var/spack/repos/builtin/packages/bwa/package.py b/var/spack/repos/builtin/packages/bwa/package.py
new file mode 100644
index 0000000000..bb6763629b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bwa/package.py
@@ -0,0 +1,52 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Bwa(Package):
+    """Burrow-Wheeler Aligner for pairwise alignment between DNA sequences."""
+
+    homepage = "http://github.com/lh3/bwa"
+    url      = "https://github.com/lh3/bwa/releases/download/v0.7.15/bwa-0.7.15.tar.bz2"
+
+    version('0.7.15', 'fcf470a46a1dbe2f96a1c5b87c530554')
+
+    depends_on('zlib')
+
+    def install(self, spec, prefix):
+        filter_file(r'^INCLUDES=',
+                    "INCLUDES=-I%s" % spec['zlib'].prefix.include, 'Makefile')
+        filter_file(r'^LIBS=', "LIBS=-L%s " % spec['zlib'].prefix.lib,
+                    'Makefile')
+        make()
+
+        mkdirp(prefix.bin)
+        install('bwa', join_path(prefix.bin, 'bwa'))
+        set_executable(join_path(prefix.bin, 'bwa'))
+        mkdirp(prefix.doc)
+        install('README.md', prefix.doc)
+        install('NEWS.md', prefix.doc)
+        mkdirp(prefix.man1)
+        install('bwa.1', prefix.man1)
diff --git a/var/spack/repos/builtin/packages/bzip2/package.py b/var/spack/repos/builtin/packages/bzip2/package.py
index 27303293d2..9e5894a6a8 100644
--- a/var/spack/repos/builtin/packages/bzip2/package.py
+++ b/var/spack/repos/builtin/packages/bzip2/package.py
@@ -51,15 +51,23 @@ class Bzip2(Package):
             kwargs = {'ignore_absent': False, 'backup': False, 'string': True}
 
             mf = FileFilter('Makefile-libbz2_so')
-            mf.filter('$(CC) -shared -Wl,-soname -Wl,libbz2.so.{0} -o libbz2.so.{1} $(OBJS)'.format(v2, v3),  # NOQA ignore=E501
-                      '$(CC) -dynamiclib -Wl,-install_name -Wl,@rpath/libbz2.{0}.dylib -current_version {1} -compatibility_version {2} -o libbz2.{3}.dylib $(OBJS)'.format(v1, v2, v3, v3), **kwargs)  # NOQA ignore=E501
+            mf.filter('$(CC) -shared -Wl,-soname -Wl,libbz2.so.{0} -o libbz2.so.{1} $(OBJS)'  # noqa
+                      .format(v2, v3),
+                      '$(CC) -dynamiclib -Wl,-install_name -Wl,@rpath/libbz2.{0}.dylib -current_version {1} -compatibility_version {2} -o libbz2.{3}.dylib $(OBJS)'  # noqa
+                      .format(v1, v2, v3, v3),
+                      **kwargs)
 
-            mf.filter('$(CC) $(CFLAGS) -o bzip2-shared bzip2.c libbz2.so.{0}'.format(v3),  # NOQA ignore=E501
-                      '$(CC) $(CFLAGS) -o bzip2-shared bzip2.c libbz2.{0}.dylib'.format(v3), **kwargs)  # NOQA ignore=E501
-            mf.filter('rm -f libbz2.so.{0}'.format(v2),
-                      'rm -f libbz2.{0}.dylib'.format(v2), **kwargs)
-            mf.filter('ln -s libbz2.so.{0} libbz2.so.{1}'.format(v3, v2),
-                      'ln -s libbz2.{0}.dylib libbz2.{1}.dylib'.format(v3, v2), **kwargs)  # NOQA ignore=E501
+            mf.filter(
+                '$(CC) $(CFLAGS) -o bzip2-shared bzip2.c libbz2.so.{0}'.format(v3),  # noqa
+                '$(CC) $(CFLAGS) -o bzip2-shared bzip2.c libbz2.{0}.dylib'
+                .format(v3), **kwargs)
+            mf.filter(
+                'rm -f libbz2.so.{0}'.format(v2),
+                'rm -f libbz2.{0}.dylib'.format(v2), **kwargs)
+            mf.filter(
+                'ln -s libbz2.so.{0} libbz2.so.{1}'.format(v3, v2),
+                'ln -s libbz2.{0}.dylib libbz2.{1}.dylib'.format(v3, v2),
+                **kwargs)
 
     def install(self, spec, prefix):
         # Build the dynamic library first
@@ -73,10 +81,12 @@ class Bzip2(Package):
         v1, v2, v3 = (self.spec.version.up_to(i) for i in (1, 2, 3))
         if 'darwin' in self.spec.architecture:
             lib = 'libbz2.dylib'
-            lib1, lib2, lib3 = ('libbz2.{0}.dylib'.format(v) for v in (v1, v2, v3))  # NOQA ignore=E501
+            lib1, lib2, lib3 = ('libbz2.{0}.dylib'.format(v)
+                                for v in (v1, v2, v3))
         else:
             lib = 'libbz2.so'
-            lib1, lib2, lib3 = ('libbz2.so.{0}'.format(v) for v in (v1, v2, v3))  # NOQA ignore=E501
+            lib1, lib2, lib3 = ('libbz2.so.{0}'.format(v)
+                                for v in (v1, v2, v3))
 
         install(lib3, join_path(prefix.lib, lib3))
         with working_dir(prefix.lib):
diff --git a/var/spack/repos/builtin/packages/c-blosc/package.py b/var/spack/repos/builtin/packages/c-blosc/package.py
index 49f9861126..4ebf3811a5 100644
--- a/var/spack/repos/builtin/packages/c-blosc/package.py
+++ b/var/spack/repos/builtin/packages/c-blosc/package.py
@@ -27,6 +27,7 @@ import sys
 
 from spack import *
 
+
 class CBlosc(Package):
     """Blosc, an extremely fast, multi-threaded, meta-compressor library"""
     homepage = "http://www.blosc.org"
diff --git a/var/spack/repos/builtin/packages/caliper/package.py b/var/spack/repos/builtin/packages/caliper/package.py
index 4a0fc54acc..e5aed5ed65 100644
--- a/var/spack/repos/builtin/packages/caliper/package.py
+++ b/var/spack/repos/builtin/packages/caliper/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Caliper(Package):
     """
     Caliper is a generic context annotation system. It gives programmers the
@@ -44,7 +45,7 @@ class Caliper(Package):
     depends_on('cmake', type='build')
 
     def install(self, spec, prefix):
-      with working_dir('build', create=True):
-        cmake('..', *std_cmake_args)
-        make()
-        make("install")
+        with working_dir('build', create=True):
+            cmake('..', *std_cmake_args)
+            make()
+            make("install")
diff --git a/var/spack/repos/builtin/packages/callpath/package.py b/var/spack/repos/builtin/packages/callpath/package.py
index 2f171fb9ce..f8227fa49e 100644
--- a/var/spack/repos/builtin/packages/callpath/package.py
+++ b/var/spack/repos/builtin/packages/callpath/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Callpath(Package):
     """Library for representing callpaths consistently in
        distributed-memory performance tools."""
diff --git a/var/spack/repos/builtin/packages/cantera/package.py b/var/spack/repos/builtin/packages/cantera/package.py
index 8e4f23046b..9c9c035325 100644
--- a/var/spack/repos/builtin/packages/cantera/package.py
+++ b/var/spack/repos/builtin/packages/cantera/package.py
@@ -35,11 +35,16 @@ class Cantera(Package):
 
     version('2.2.1', '9d1919bdef39ddec54485fc8a741a3aa')
 
-    variant('lapack',     default=True,  description='Build with external BLAS/LAPACK libraries')
-    variant('threadsafe', default=True,  description='Build threadsafe, requires Boost')
-    variant('sundials',   default=True,  description='Build with external Sundials')
-    variant('python',     default=False, description='Build the Cantera Python module')
-    variant('matlab',     default=False, description='Build the Cantera Matlab toolbox')
+    variant('lapack',     default=True,
+            description='Build with external BLAS/LAPACK libraries')
+    variant('threadsafe', default=True,
+            description='Build threadsafe, requires Boost')
+    variant('sundials',   default=True,
+            description='Build with external Sundials')
+    variant('python',     default=False,
+            description='Build the Cantera Python module')
+    variant('matlab',     default=False,
+            description='Build the Cantera Matlab toolbox')
 
     # Required dependencies
     depends_on('scons', type='build')
diff --git a/var/spack/repos/builtin/packages/cask/package.py b/var/spack/repos/builtin/packages/cask/package.py
new file mode 100644
index 0000000000..67cc48ab2a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cask/package.py
@@ -0,0 +1,53 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+#
+# Based on Homebrew's formula:
+# https://github.com/Homebrew/homebrew-core/blob/master/Formula/cask.rb
+#
+from spack import *
+from glob import glob
+
+
+class Cask(Package):
+    """Cask is a project management tool for Emacs Lisp to automate the package
+       development cycle; development, dependencies, testing, building,
+       packaging and more."""
+    homepage = "http://cask.readthedocs.io/en/latest/"
+    url      = "https://github.com/cask/cask/archive/v0.7.4.tar.gz"
+
+    version('0.7.4', 'c973a7db43bc980dd83759a5864a1260')
+
+    depends_on('emacs', type=nolink)
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('bin/cask', prefix.bin)
+        install_tree('templates', join_path(prefix, 'templates'))
+        for el_file in glob("*.el"):
+            install(el_file, prefix)
+        for misc_file in ['COPYING', 'cask.png', 'README.md']:
+            install(misc_file, prefix)
+        # disable cask's automatic upgrading feature
+        touch(join_path(prefix, ".no-upgrade"))
diff --git a/var/spack/repos/builtin/packages/cblas/package.py b/var/spack/repos/builtin/packages/cblas/package.py
index 0b85c5842a..0828141307 100644
--- a/var/spack/repos/builtin/packages/cblas/package.py
+++ b/var/spack/repos/builtin/packages/cblas/package.py
@@ -23,7 +23,7 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
-import os
+
 
 class Cblas(Package):
     """The BLAS (Basic Linear Algebra Subprograms) are routines that
@@ -42,11 +42,11 @@ class Cblas(Package):
     def patch(self):
         mf = FileFilter('Makefile.in')
 
-        mf.filter('^BLLIB =.*', 'BLLIB = %s/libblas.a' % self.spec['blas'].prefix.lib)
+        mf.filter('^BLLIB =.*', 'BLLIB = %s/libblas.a' %
+                  self.spec['blas'].prefix.lib)
         mf.filter('^CC =.*', 'CC = cc')
         mf.filter('^FC =.*', 'FC = f90')
 
-
     def install(self, spec, prefix):
         make('all')
         mkdirp(prefix.lib)
@@ -54,6 +54,5 @@ class Cblas(Package):
 
         # Rename the generated lib file to libcblas.a
         install('./lib/cblas_LINUX.a', '%s/libcblas.a' % prefix.lib)
-        install('./include/cblas.h','%s' % prefix.include)
-        install('./include/cblas_f77.h','%s' % prefix.include)
-
+        install('./include/cblas.h', '%s' % prefix.include)
+        install('./include/cblas_f77.h', '%s' % prefix.include)
diff --git a/var/spack/repos/builtin/packages/cbtf-argonavis/package.py b/var/spack/repos/builtin/packages/cbtf-argonavis/package.py
index 321d02b556..cbf36c3b61 100644
--- a/var/spack/repos/builtin/packages/cbtf-argonavis/package.py
+++ b/var/spack/repos/builtin/packages/cbtf-argonavis/package.py
@@ -22,7 +22,7 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-################################################################################
+##########################################################################
 # Copyright (c) 2015-2016 Krell Institute. All Rights Reserved.
 #
 # This program is free software; you can redistribute it and/or modify it under
@@ -38,20 +38,24 @@
 # You should have received a copy of the GNU General Public License along with
 # this program; if not, write to the Free Software Foundation, Inc., 59 Temple
 # Place, Suite 330, Boston, MA  02111-1307  USA
-################################################################################
+##########################################################################
 
 from spack import *
 
+
 class CbtfArgonavis(Package):
-    """CBTF Argo Navis project contains the CUDA collector and supporting 
-       libraries that was done as a result of a DOE SBIR grant."""
+    """CBTF Argo Navis project contains the CUDA collector and supporting
+       libraries that was done as a result of a DOE SBIR grant.
+
+    """
     homepage = "http://sourceforge.net/p/cbtf/wiki/Home/"
 
     # Mirror access template example
-    #url      = "file:/home/jeg/OpenSpeedShop_ROOT/SOURCES/cbtf-argonavis-1.6.tar.gz"
-    #version('1.6', '0fafa0008478405c2c2319450f174ed4')
+    # url = "file:/home/jeg/OpenSpeedShop_ROOT/SOURCES/cbtf-argonavis-1.6.tar.gz"
+    # version('1.6', '0fafa0008478405c2c2319450f174ed4')
 
-    version('1.6', branch='master', git='https://github.com/OpenSpeedShop/cbtf-argonavis.git')
+    version('1.6', branch='master',
+            git='https://github.com/OpenSpeedShop/cbtf-argonavis.git')
 
     depends_on("cmake@3.0.2", type='build')
     depends_on("boost@1.50.0:")
@@ -60,17 +64,19 @@ class CbtfArgonavis(Package):
     depends_on("cbtf")
     depends_on("cbtf-krell")
     depends_on("cuda@6.0.37")
-    #depends_on("cuda")
+    # depends_on("cuda")
 
     parallel = False
 
     def adjustBuildTypeParams_cmakeOptions(self, spec, cmakeOptions):
-        # Sets build type parameters into cmakeOptions the options that will enable the cbtf-krell built type settings
+        # Sets build type parameters into cmakeOptions the options that will
+        # enable the cbtf-krell built type settings
 
-        compile_flags="-O2 -g"
+        compile_flags = "-O2 -g"
         BuildTypeOptions = []
 
-        # Set CMAKE_BUILD_TYPE to what cbtf-krell wants it to be, not the stdcmakeargs
+        # Set CMAKE_BUILD_TYPE to what cbtf-krell wants it to be, not the
+        # stdcmakeargs
         for word in cmakeOptions[:]:
             if word.startswith('-DCMAKE_BUILD_TYPE'):
                 cmakeOptions.remove(word)
@@ -81,50 +87,54 @@ class CbtfArgonavis(Package):
             if word.startswith('-DCMAKE_VERBOSE_MAKEFILE'):
                 cmakeOptions.remove(word)
         BuildTypeOptions.extend([
-                 '-DCMAKE_VERBOSE_MAKEFILE=ON',
-                 '-DCMAKE_BUILD_TYPE=None',
-                 '-DCMAKE_CXX_FLAGS=%s'         % compile_flags,
-                 '-DCMAKE_C_FLAGS=%s'           % compile_flags
+            '-DCMAKE_VERBOSE_MAKEFILE=ON',
+            '-DCMAKE_BUILD_TYPE=None',
+            '-DCMAKE_CXX_FLAGS=%s'         % compile_flags,
+            '-DCMAKE_C_FLAGS=%s'           % compile_flags
         ])
 
         cmakeOptions.extend(BuildTypeOptions)
 
-
     def install(self, spec, prefix):
 
-       # Look for package installation information in the cbtf and cbtf-krell prefixes
-       cmake_prefix_path = join_path(spec['cbtf'].prefix) + ':' + join_path(spec['cbtf-krell'].prefix)
-
-       with working_dir('CUDA'):
-         with working_dir('build', create=True):
-
-             cmakeOptions = []
-             cmakeOptions.extend(['-DCMAKE_INSTALL_PREFIX=%s'   % prefix,
-                                  '-DCMAKE_PREFIX_PATH=%s'	% cmake_prefix_path,
-                                  '-DCUDA_DIR=%s'               % spec['cuda'].prefix,
-                                  '-DCUDA_INSTALL_PATH=%s'      % spec['cuda'].prefix,
-                                  '-DCUDA_TOOLKIT_ROOT_DIR=%s'  % spec['cuda'].prefix,
-                                  '-DCUPTI_DIR=%s'		% join_path(spec['cuda'].prefix + '/extras/CUPTI'),
-                                  '-DCUPTI_ROOT=%s'		% join_path(spec['cuda'].prefix + '/extras/CUPTI'),
-                                  '-DPAPI_ROOT=%s'		% spec['papi'].prefix,
-                                  '-DCBTF_DIR=%s'		% spec['cbtf'].prefix,
-                                  '-DCBTF_KRELL_DIR=%s'		% spec['cbtf-krell'].prefix,
-                                  '-DBOOST_ROOT=%s'             % spec['boost'].prefix,
-                                  '-DBoost_DIR=%s'		% spec['boost'].prefix,
-                                  '-DBOOST_LIBRARYDIR=%s'	% spec['boost'].prefix.lib,
-                                  '-DMRNET_DIR=%s'		% spec['mrnet'].prefix,
-                                  '-DBoost_NO_SYSTEM_PATHS=ON'
-                                 ])
-
-             # Add in the standard cmake arguments
-             cmakeOptions.extend(std_cmake_args)
-
-             # Adjust the standard cmake arguments to what we want the build type, etc to be
-             self.adjustBuildTypeParams_cmakeOptions(spec, cmakeOptions)
-             
-             # Invoke cmake
-             cmake('..', *cmakeOptions)
-
-             make("clean")
-             make()
-             make("install")
+        # Look for package installation information in the cbtf and cbtf-krell
+        # prefixes
+        cmake_prefix_path = join_path(
+            spec['cbtf'].prefix) + ':' + join_path(spec['cbtf-krell'].prefix)
+
+        with working_dir('CUDA'):
+            with working_dir('build', create=True):
+
+                cmakeOptions = []
+                cmakeOptions.extend(
+                    ['-DCMAKE_INSTALL_PREFIX=%s' % prefix,
+                     '-DCMAKE_PREFIX_PATH=%s' % cmake_prefix_path,
+                     '-DCUDA_DIR=%s' % spec['cuda'].prefix,
+                     '-DCUDA_INSTALL_PATH=%s' % spec['cuda'].prefix,
+                     '-DCUDA_TOOLKIT_ROOT_DIR=%s' % spec['cuda'].prefix,
+                     '-DCUPTI_DIR=%s' % join_path(
+                         spec['cuda'].prefix + '/extras/CUPTI'),
+                     '-DCUPTI_ROOT=%s' % join_path(
+                         spec['cuda'].prefix + '/extras/CUPTI'),
+                     '-DPAPI_ROOT=%s' % spec['papi'].prefix,
+                     '-DCBTF_DIR=%s' % spec['cbtf'].prefix,
+                     '-DCBTF_KRELL_DIR=%s' % spec['cbtf-krell'].prefix,
+                     '-DBOOST_ROOT=%s' % spec['boost'].prefix,
+                     '-DBoost_DIR=%s' % spec['boost'].prefix,
+                     '-DBOOST_LIBRARYDIR=%s' % spec['boost'].prefix.lib,
+                     '-DMRNET_DIR=%s' % spec['mrnet'].prefix,
+                     '-DBoost_NO_SYSTEM_PATHS=ON'])
+
+                # Add in the standard cmake arguments
+                cmakeOptions.extend(std_cmake_args)
+
+                # Adjust the standard cmake arguments to what we want the build
+                # type, etc to be
+                self.adjustBuildTypeParams_cmakeOptions(spec, cmakeOptions)
+
+                # Invoke cmake
+                cmake('..', *cmakeOptions)
+
+                make("clean")
+                make()
+                make("install")
diff --git a/var/spack/repos/builtin/packages/cbtf-krell/package.py b/var/spack/repos/builtin/packages/cbtf-krell/package.py
index acb78a7395..6f15c3f835 100644
--- a/var/spack/repos/builtin/packages/cbtf-krell/package.py
+++ b/var/spack/repos/builtin/packages/cbtf-krell/package.py
@@ -22,7 +22,7 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-################################################################################
+##########################################################################
 # Copyright (c) 2015-2016 Krell Institute. All Rights Reserved.
 #
 # This program is free software; you can redistribute it and/or modify it under
@@ -38,30 +38,40 @@
 # You should have received a copy of the GNU General Public License along with
 # this program; if not, write to the Free Software Foundation, Inc., 59 Temple
 # Place, Suite 330, Boston, MA  02111-1307  USA
-################################################################################
+##########################################################################
 
 from spack import *
 
+
 class CbtfKrell(Package):
-    """CBTF Krell project contains the Krell Institute contributions to the CBTF project. 
-       These contributions include many performance data collectors and support 
-       libraries as well as some example tools that drive the data collection at 
-       HPC levels of scale."""
+    """CBTF Krell project contains the Krell Institute contributions to the
+       CBTF project.  These contributions include many performance data
+       collectors and support libraries as well as some example tools
+       that drive the data collection at HPC levels of scale.
+
+    """
     homepage = "http://sourceforge.net/p/cbtf/wiki/Home/"
 
     # optional mirror access template
-    #url      = "file:/home/jeg/cbtf-krell-1.6.tar.gz"
-    #version('1.6', 'edeb61cd488f16e7b124f77db9ce762d')
+    # url      = "file:/home/jeg/cbtf-krell-1.6.tar.gz"
+    # version('1.6', 'edeb61cd488f16e7b124f77db9ce762d')
 
-    version('1.6', branch='master', git='https://github.com/OpenSpeedShop/cbtf-krell.git')
+    version('1.6', branch='master',
+            git='https://github.com/OpenSpeedShop/cbtf-krell.git')
 
     # MPI variants
-    variant('openmpi', default=False, description="Build mpi experiment collector for openmpi MPI when this variant is enabled.")
-    variant('mpt', default=False, description="Build mpi experiment collector for SGI MPT MPI when this variant is enabled.")
-    variant('mvapich2', default=False, description="Build mpi experiment collector for mvapich2 MPI when this variant is enabled.")
-    variant('mvapich', default=False, description="Build mpi experiment collector for mvapich MPI when this variant is enabled.")
-    variant('mpich2', default=False, description="Build mpi experiment collector for mpich2 MPI when this variant is enabled.")
-    variant('mpich', default=False, description="Build mpi experiment collector for mpich MPI when this variant is enabled.")
+    variant('openmpi', default=False,
+            description="Build mpi experiment collector for openmpi MPI..")
+    variant('mpt', default=False,
+            description="Build mpi experiment collector for SGI MPT MPI.")
+    variant('mvapich2', default=False,
+            description="Build mpi experiment collector for mvapich2 MPI.")
+    variant('mvapich', default=False,
+            description="Build mpi experiment collector for mvapich MPI.")
+    variant('mpich2', default=False,
+            description="Build mpi experiment collector for mpich2 MPI.")
+    variant('mpich', default=False,
+            description="Build mpi experiment collector for mpich MPI.")
 
     # Dependencies for cbtf-krell
     depends_on("cmake@3.0.2", type='build')
@@ -83,7 +93,8 @@ class CbtfKrell(Package):
     depends_on("papi")
 
     # MPI Installations
-    # These have not worked either for build or execution, commenting out for now
+    # These have not worked either for build or execution, commenting out for
+    # now
     depends_on("openmpi", when='+openmpi')
     depends_on("mpich", when='+mpich')
     depends_on("mpich2", when='+mpich2')
@@ -94,11 +105,13 @@ class CbtfKrell(Package):
     parallel = False
 
     def adjustBuildTypeParams_cmakeOptions(self, spec, cmakeOptions):
-        # Sets build type parameters into cmakeOptions the options that will enable the cbtf-krell built type settings
- 
-        compile_flags="-O2 -g"
+        # Sets build type parameters into cmakeOptions the options that will
+        # enable the cbtf-krell built type settings
+
+        compile_flags = "-O2 -g"
         BuildTypeOptions = []
-        # Set CMAKE_BUILD_TYPE to what cbtf-krell wants it to be, not the stdcmakeargs
+        # Set CMAKE_BUILD_TYPE to what cbtf-krell wants it to be, not the
+        # stdcmakeargs
         for word in cmakeOptions[:]:
             if word.startswith('-DCMAKE_BUILD_TYPE'):
                 cmakeOptions.remove(word)
@@ -109,75 +122,76 @@ class CbtfKrell(Package):
             if word.startswith('-DCMAKE_VERBOSE_MAKEFILE'):
                 cmakeOptions.remove(word)
         BuildTypeOptions.extend([
-                 '-DCMAKE_VERBOSE_MAKEFILE=ON',
-                 '-DCMAKE_BUILD_TYPE=None',
-                 '-DCMAKE_CXX_FLAGS=%s'         % compile_flags,
-                 '-DCMAKE_C_FLAGS=%s'           % compile_flags
+            '-DCMAKE_VERBOSE_MAKEFILE=ON',
+            '-DCMAKE_BUILD_TYPE=None',
+            '-DCMAKE_CXX_FLAGS=%s'         % compile_flags,
+            '-DCMAKE_C_FLAGS=%s'           % compile_flags
         ])
 
         cmakeOptions.extend(BuildTypeOptions)
 
-
-
     def set_mpi_cmakeOptions(self, spec, cmakeOptions):
-        # Appends to cmakeOptions the options that will enable the appropriate MPI implementations
- 
+        # Appends to cmakeOptions the options that will enable the appropriate
+        # MPI implementations
+
         MPIOptions = []
 
         # openmpi
         if '+openmpi' in spec:
             MPIOptions.extend([
-                 '-DOPENMPI_DIR=%s' % spec['openmpi'].prefix
+                '-DOPENMPI_DIR=%s' % spec['openmpi'].prefix
             ])
         # mpich
         if '+mpich' in spec:
             MPIOptions.extend([
-                 '-DMPICH_DIR=%s' % spec['mpich'].prefix
+                '-DMPICH_DIR=%s' % spec['mpich'].prefix
             ])
         # mpich2
         if '+mpich2' in spec:
             MPIOptions.extend([
-                 '-DMPICH2_DIR=%s' % spec['mpich2'].prefix
+                '-DMPICH2_DIR=%s' % spec['mpich2'].prefix
             ])
         # mvapich
         if '+mvapich' in spec:
             MPIOptions.extend([
-                 '-DMVAPICH_DIR=%s' % spec['mvapich'].prefix
+                '-DMVAPICH_DIR=%s' % spec['mvapich'].prefix
             ])
         # mvapich2
         if '+mvapich2' in spec:
             MPIOptions.extend([
-                 '-DMVAPICH2_DIR=%s' % spec['mvapich2'].prefix
+                '-DMVAPICH2_DIR=%s' % spec['mvapich2'].prefix
             ])
         # mpt
         if '+mpt' in spec:
             MPIOptions.extend([
-                 '-DMPT_DIR=%s' % spec['mpt'].prefix
+                '-DMPT_DIR=%s' % spec['mpt'].prefix
             ])
 
         cmakeOptions.extend(MPIOptions)
 
     def install(self, spec, prefix):
 
-        # Add in paths for finding package config files that tell us where to find these packages
-        #cmake_prefix_path = join_path(spec['cbtf'].prefix) + ':' + join_path(spec['dyninst'].prefix)
-                                 #'-DCMAKE_PREFIX_PATH=%s'	% cmake_prefix_path
+        # Add in paths for finding package config files that tell us
+        # where to find these packages
+        # cmake_prefix_path = \
+        #     join_path(spec['cbtf'].prefix) + ':' + \
+        #     join_path(spec['dyninst'].prefix)
+        # '-DCMAKE_PREFIX_PATH=%s' % cmake_prefix_path
 
-        # Build cbtf-krell with cmake 
+        # Build cbtf-krell with cmake
         with working_dir('build_cbtf_krell', create=True):
             cmakeOptions = []
-            cmakeOptions.extend(['-DCMAKE_INSTALL_PREFIX=%s'	% prefix,
-                                 '-DCBTF_DIR=%s' 		% spec['cbtf'].prefix,
-                                 '-DBINUTILS_DIR=%s'		% spec['binutils'].prefix,
-                                 '-DLIBMONITOR_DIR=%s'		% spec['libmonitor'].prefix,
-                                 '-DLIBUNWIND_DIR=%s'		% spec['libunwind'].prefix,
-                                 '-DPAPI_DIR=%s'		% spec['papi'].prefix,
-                                 '-DBOOST_DIR=%s'		% spec['boost'].prefix,
-                                 '-DMRNET_DIR=%s'		% spec['mrnet'].prefix,
-                                 '-DDYNINST_DIR=%s'		% spec['dyninst'].prefix,
-                                 '-DXERCESC_DIR=%s'		% spec['xerces-c'].prefix
-                                ])
-
+            cmakeOptions.extend(
+                ['-DCMAKE_INSTALL_PREFIX=%s' % prefix,
+                 '-DCBTF_DIR=%s' % spec['cbtf'].prefix,
+                 '-DBINUTILS_DIR=%s' % spec['binutils'].prefix,
+                 '-DLIBMONITOR_DIR=%s' % spec['libmonitor'].prefix,
+                 '-DLIBUNWIND_DIR=%s' % spec['libunwind'].prefix,
+                 '-DPAPI_DIR=%s' % spec['papi'].prefix,
+                 '-DBOOST_DIR=%s' % spec['boost'].prefix,
+                 '-DMRNET_DIR=%s' % spec['mrnet'].prefix,
+                 '-DDYNINST_DIR=%s' % spec['dyninst'].prefix,
+                 '-DXERCESC_DIR=%s' % spec['xerces-c'].prefix])
 
             # Add any MPI implementations coming from variant settings
             self.set_mpi_cmakeOptions(spec, cmakeOptions)
@@ -185,9 +199,10 @@ class CbtfKrell(Package):
             # Add in the standard cmake arguments
             cmakeOptions.extend(std_cmake_args)
 
-            # Adjust the standard cmake arguments to what we want the build type, etc to be
+            # Adjust the standard cmake arguments to what we want the build
+            # type, etc to be
             self.adjustBuildTypeParams_cmakeOptions(spec, cmakeOptions)
-             
+
             # Invoke cmake
             cmake('..', *cmakeOptions)
 
@@ -195,56 +210,54 @@ class CbtfKrell(Package):
             make()
             make("install")
 
-
-
-        #if '+cray' in spec:
-	#if 'cray' in self.spec.architecture:
+        # if '+cray' in spec:
+        # if 'cray' in self.spec.architecture:
         #    if '+runtime' in spec:
         #        with working_dir('build_cbtf_cray_runtime', create=True):
         #            python_vers='%d.%d' % spec['python'].version[:2]
         #            cmake .. \
-        #                    -DCMAKE_BUILD_TYPE=Debug \
-        #                    -DTARGET_OS="cray" \
-        #                    -DRUNTIME_ONLY="true" \
-        #                    -DCMAKE_INSTALL_PREFIX=${CBTF_KRELL_PREFIX} \
-        #                    -DCMAKE_PREFIX_PATH=${CBTF_ROOT} \
-        #                    -DCBTF_DIR=${CBTF_ROOT} \
-        #                    -DBOOST_ROOT=${BOOST_INSTALL_PREFIX} \
-        #                    -DXERCESC_DIR=${XERCESC_INSTALL_PREFIX} \
-        #                    -DBINUTILS_DIR=${KRELL_ROOT} \
-        #                    -DLIBMONITOR_DIR=${KRELL_ROOT_COMPUTE} \
-        #                    -DLIBUNWIND_DIR=${KRELL_ROOT_COMPUTE} \
-        #                    -DPAPI_DIR=${PAPI_ROOT} \
-        #                    -DDYNINST_DIR=${DYNINST_CN_ROOT} \
-        #                    -DMRNET_DIR=${MRNET_INSTALL_PREFIX} \
-        #                    -DMPICH2_DIR=/opt/cray/mpt/7.0.1/gni/mpich2-gnu/48
+        #                -DCMAKE_BUILD_TYPE=Debug \
+        #                -DTARGET_OS="cray" \
+        #                -DRUNTIME_ONLY="true" \
+        #                -DCMAKE_INSTALL_PREFIX=${CBTF_KRELL_PREFIX} \
+        #                -DCMAKE_PREFIX_PATH=${CBTF_ROOT} \
+        #                -DCBTF_DIR=${CBTF_ROOT} \
+        #                -DBOOST_ROOT=${BOOST_INSTALL_PREFIX} \
+        #                -DXERCESC_DIR=${XERCESC_INSTALL_PREFIX} \
+        #                -DBINUTILS_DIR=${KRELL_ROOT} \
+        #                -DLIBMONITOR_DIR=${KRELL_ROOT_COMPUTE} \
+        #                -DLIBUNWIND_DIR=${KRELL_ROOT_COMPUTE} \
+        #                -DPAPI_DIR=${PAPI_ROOT} \
+        #                -DDYNINST_DIR=${DYNINST_CN_ROOT} \
+        #                -DMRNET_DIR=${MRNET_INSTALL_PREFIX} \
+        #                -DMPICH2_DIR=/opt/cray/mpt/7.0.1/gni/mpich2-gnu/48
         #    else:
         #        with working_dir('build_cbtf_cray_frontend', create=True):
         #            python_vers='%d.%d' % spec['python'].version[:2]
         #            cmake .. \
-        #                    -DCMAKE_BUILD_TYPE=Debug \
-        #                    -DCMAKE_INSTALL_PREFIX=${CBTF_KRELL_PREFIX} \
-        #                    -DCMAKE_PREFIX_PATH=${CBTF_ROOT} \
-        #                    -DCBTF_DIR=${CBTF_ROOT} \
-        #                    -DRUNTIME_TARGET_OS="cray" \
-        #                    -DCBTF_KRELL_CN_RUNTIME_DIR=${CBTF_KRELL_CN_RUNTIME_ROOT} \
-        #                    -DCBTF_CN_RUNTIME_DIR=${CBTF_CN_RUNTIME_ROOT} \
-        #                    -DLIBMONITOR_CN_RUNTIME_DIR=${LIBMONITOR_CN_ROOT} \
-        #                    -DLIBUNWIND_CN_RUNTIME_DIR=${LIBUNWIND_CN_ROOT} \
-        #                    -DPAPI_CN_RUNTIME_DIR=${PAPI_CN_ROOT} \
-        #                    -DXERCESC_CN_RUNTIME_DIR=/${XERCESC_CN_ROOT} \
-        #                    -DMRNET_CN_RUNTIME_DIR=${MRNET_CN_ROOT} \
-        #                    -DBOOST_CN_RUNTIME_DIR=${BOOST_CN_ROOT} \
-        #                    -DDYNINST_CN_RUNTIME_DIR=${DYNINST_CN_ROOT} \
-        #                    -DBOOST_ROOT=/${KRELL_ROOT} \
-        #                    -DXERCESC_DIR=/${KRELL_ROOT} \
-        #                    -DBINUTILS_DIR=/${KRELL_ROOT} \
-        #                    -DLIBMONITOR_DIR=${KRELL_ROOT} \
-        #                    -DLIBUNWIND_DIR=${KRELL_ROOT} \
-        #                    -DPAPI_DIR=${PAPI_ROOT} \
-        #                    -DDYNINST_DIR=${KRELL_ROOT} \
-        #                    -DMRNET_DIR=${KRELL_ROOT} \
-        #                    -DMPICH2_DIR=/opt/cray/mpt/7.0.1/gni/mpich2-gnu/48
+        #            -DCMAKE_BUILD_TYPE=Debug \
+        #            -DCMAKE_INSTALL_PREFIX=${CBTF_KRELL_PREFIX} \
+        #            -DCMAKE_PREFIX_PATH=${CBTF_ROOT} \
+        #            -DCBTF_DIR=${CBTF_ROOT} \
+        #            -DRUNTIME_TARGET_OS="cray" \
+        #          -DCBTF_KRELL_CN_RUNTIME_DIR=${CBTF_KRELL_CN_RUNTIME_ROOT} \
+        #            -DCBTF_CN_RUNTIME_DIR=${CBTF_CN_RUNTIME_ROOT} \
+        #            -DLIBMONITOR_CN_RUNTIME_DIR=${LIBMONITOR_CN_ROOT} \
+        #            -DLIBUNWIND_CN_RUNTIME_DIR=${LIBUNWIND_CN_ROOT} \
+        #            -DPAPI_CN_RUNTIME_DIR=${PAPI_CN_ROOT} \
+        #            -DXERCESC_CN_RUNTIME_DIR=/${XERCESC_CN_ROOT} \
+        #            -DMRNET_CN_RUNTIME_DIR=${MRNET_CN_ROOT} \
+        #            -DBOOST_CN_RUNTIME_DIR=${BOOST_CN_ROOT} \
+        #            -DDYNINST_CN_RUNTIME_DIR=${DYNINST_CN_ROOT} \
+        #            -DBOOST_ROOT=/${KRELL_ROOT} \
+        #            -DXERCESC_DIR=/${KRELL_ROOT} \
+        #            -DBINUTILS_DIR=/${KRELL_ROOT} \
+        #            -DLIBMONITOR_DIR=${KRELL_ROOT} \
+        #            -DLIBUNWIND_DIR=${KRELL_ROOT} \
+        #            -DPAPI_DIR=${PAPI_ROOT} \
+        #            -DDYNINST_DIR=${KRELL_ROOT} \
+        #            -DMRNET_DIR=${KRELL_ROOT} \
+        #            -DMPICH2_DIR=/opt/cray/mpt/7.0.1/gni/mpich2-gnu/48
         #    fi
 #
 #                    make("clean")
@@ -264,22 +277,22 @@ class CbtfKrell(Package):
 #            fi
 #
 #        else:
-#            # Build cbtf-krell with cmake 
+#            # Build cbtf-krell with cmake
 #            with working_dir('build_cbtf_krell', create=True):
 #                cmake('..',
 #                      '-DCMAKE_BUILD_TYPE=Debug',
-#                      '-DCMAKE_INSTALL_PREFIX=%s'	% prefix,
-#                      '-DCBTF_DIR=%s' 			% spec['cbtf'].prefix,
-#                      '-DBINUTILS_DIR=%s'		% spec['binutils'].prefix,
-#                      '-DLIBMONITOR_DIR=%s'		% spec['libmonitor'].prefix,
-#                      '-DLIBUNWIND_DIR=%s'		% spec['libunwind'].prefix,
-#                      '-DPAPI_DIR=%s'			% spec['papi'].prefix,
-#                      '-DBOOST_DIR=%s'			% spec['boost'].prefix,
-#                      '-DMRNET_DIR=%s'			% spec['mrnet'].prefix,
-#                      '-DDYNINST_DIR=%s'		% spec['dyninst'].prefix,
-#                      '-DXERCESC_DIR=%s'		% spec['xerces-c'].prefix,
-#                      '-DOPENMPI_DIR=%s'		% openmpi_prefix_path,
-#                      '-DCMAKE_PREFIX_PATH=%s'		% cmake_prefix_path,
+#                      '-DCMAKE_INSTALL_PREFIX=%s' % prefix,
+#                      '-DCBTF_DIR=%s' % spec['cbtf'].prefix,
+#                      '-DBINUTILS_DIR=%s' % spec['binutils'].prefix,
+#                      '-DLIBMONITOR_DIR=%s' % spec['libmonitor'].prefix,
+#                      '-DLIBUNWIND_DIR=%s'% spec['libunwind'].prefix,
+#                      '-DPAPI_DIR=%s' % spec['papi'].prefix,
+#                      '-DBOOST_DIR=%s' % spec['boost'].prefix,
+#                      '-DMRNET_DIR=%s' % spec['mrnet'].prefix,
+#                      '-DDYNINST_DIR=%s' % spec['dyninst'].prefix,
+#                      '-DXERCESC_DIR=%s' % spec['xerces-c'].prefix,
+#                      '-DOPENMPI_DIR=%s' % openmpi_prefix_path,
+#                      '-DCMAKE_PREFIX_PATH=%s' % cmake_prefix_path,
 #                      *std_cmake_args)
 #
 #                make("clean")
diff --git a/var/spack/repos/builtin/packages/cbtf-lanl/package.py b/var/spack/repos/builtin/packages/cbtf-lanl/package.py
index 5694535fcc..b614a325f9 100644
--- a/var/spack/repos/builtin/packages/cbtf-lanl/package.py
+++ b/var/spack/repos/builtin/packages/cbtf-lanl/package.py
@@ -22,7 +22,7 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-################################################################################
+##########################################################################
 # Copyright (c) 2015-2016 Krell Institute. All Rights Reserved.
 #
 # This program is free software; you can redistribute it and/or modify it under
@@ -38,20 +38,22 @@
 # You should have received a copy of the GNU General Public License along with
 # this program; if not, write to the Free Software Foundation, Inc., 59 Temple
 # Place, Suite 330, Boston, MA  02111-1307  USA
-################################################################################
+##########################################################################
 
 from spack import *
 
+
 class CbtfLanl(Package):
-    """CBTF LANL project contains a memory tool and data center type system command monitoring tool."""
+    """CBTF LANL project contains a memory tool and data center type system
+       command monitoring tool."""
     homepage = "http://sourceforge.net/p/cbtf/wiki/Home/"
 
-
     # Mirror access template example
-    #url      = "file:/g/g24/jeg/cbtf-lanl-1.5.tar.gz"
-    #version('1.5', 'c3f78f967b0a42c6734ce4be0e602426')
+    # url      = "file:/g/g24/jeg/cbtf-lanl-1.5.tar.gz"
+    # version('1.5', 'c3f78f967b0a42c6734ce4be0e602426')
 
-    version('1.6', branch='master', git='http://git.code.sf.net/p/cbtf-lanl/cbtf-lanl')
+    version('1.6', branch='master',
+            git='http://git.code.sf.net/p/cbtf-lanl/cbtf-lanl')
 
     depends_on("cmake@3.0.2", type='build')
     # Dependencies for cbtf-krell
@@ -63,11 +65,13 @@ class CbtfLanl(Package):
     parallel = False
 
     def adjustBuildTypeParams_cmakeOptions(self, spec, cmakeOptions):
-        # Sets build type parameters into cmakeOptions the options that will enable the cbtf-krell built type settings
+        # Sets build type parameters into cmakeOptions the options that will
+        # enable the cbtf-krell built type settings
 
-        compile_flags="-O2 -g"
+        compile_flags = "-O2 -g"
         BuildTypeOptions = []
-        # Set CMAKE_BUILD_TYPE to what cbtf-krell wants it to be, not the stdcmakeargs
+        # Set CMAKE_BUILD_TYPE to what cbtf-krell wants it to be, not the
+        # stdcmakeargs
         for word in cmakeOptions[:]:
             if word.startswith('-DCMAKE_BUILD_TYPE'):
                 cmakeOptions.remove(word)
@@ -78,40 +82,43 @@ class CbtfLanl(Package):
             if word.startswith('-DCMAKE_VERBOSE_MAKEFILE'):
                 cmakeOptions.remove(word)
         BuildTypeOptions.extend([
-                 '-DCMAKE_VERBOSE_MAKEFILE=ON',
-                 '-DCMAKE_BUILD_TYPE=None',
-                 '-DCMAKE_CXX_FLAGS=%s'         % compile_flags,
-                 '-DCMAKE_C_FLAGS=%s'           % compile_flags
+            '-DCMAKE_VERBOSE_MAKEFILE=ON',
+            '-DCMAKE_BUILD_TYPE=None',
+            '-DCMAKE_CXX_FLAGS=%s'         % compile_flags,
+            '-DCMAKE_C_FLAGS=%s'           % compile_flags
         ])
 
         cmakeOptions.extend(BuildTypeOptions)
 
     def install(self, spec, prefix):
 
-     # Add in paths for finding package config files that tell us where to find these packages
-     cmake_prefix_path = join_path(spec['cbtf'].prefix) + ':' + join_path(spec['cbtf-krell'].prefix)
-
-     with working_dir('build', create=True):
-         cmakeOptions = []
-         cmakeOptions.extend(['-DCMAKE_INSTALL_PREFIX=%s'   % prefix,
-                              '-DCBTF_DIR=%s'               % spec['cbtf'].prefix,
-                              '-DCBTF_KRELL_DIR=%s'         % spec['cbtf-krell'].prefix,
-                              '-DMRNET_DIR=%s'              % spec['mrnet'].prefix,
-                              '-DXERCESC_DIR=%s'            % spec['xerces-c'].prefix,
-                              '-DCMAKE_PREFIX_PATH=%s'      % cmake_prefix_path,
-                              '-DCMAKE_MODULE_PATH=%s'      % join_path(prefix.share,'KrellInstitute','cmake')
-                             ])
-
-         # Add in the standard cmake arguments
-         cmakeOptions.extend(std_cmake_args)
-
-         # Adjust the standard cmake arguments to what we want the build type, etc to be
-         self.adjustBuildTypeParams_cmakeOptions(spec, cmakeOptions)
-             
-         # Invoke cmake
-         cmake('..', *cmakeOptions)
-
-         make("clean")
-         make()
-         make("install")
-
+        # Add in paths for finding package config files that tell us where to
+        # find these packages
+        cmake_prefix_path = join_path(
+            spec['cbtf'].prefix) + ':' + join_path(spec['cbtf-krell'].prefix)
+
+        with working_dir('build', create=True):
+            cmakeOptions = []
+            cmakeOptions.extend(
+                ['-DCMAKE_INSTALL_PREFIX=%s'   % prefix,
+                 '-DCBTF_DIR=%s'               % spec['cbtf'].prefix,
+                 '-DCBTF_KRELL_DIR=%s'         % spec['cbtf-krell'].prefix,
+                 '-DMRNET_DIR=%s'              % spec['mrnet'].prefix,
+                 '-DXERCESC_DIR=%s'            % spec['xerces-c'].prefix,
+                 '-DCMAKE_PREFIX_PATH=%s'      % cmake_prefix_path,
+                 '-DCMAKE_MODULE_PATH=%s'      % join_path(
+                     prefix.share, 'KrellInstitute', 'cmake')])
+
+            # Add in the standard cmake arguments
+            cmakeOptions.extend(std_cmake_args)
+
+            # Adjust the standard cmake arguments to what we want the build
+            # type, etc to be
+            self.adjustBuildTypeParams_cmakeOptions(spec, cmakeOptions)
+
+            # Invoke cmake
+            cmake('..', *cmakeOptions)
+
+            make("clean")
+            make()
+            make("install")
diff --git a/var/spack/repos/builtin/packages/cbtf/package.py b/var/spack/repos/builtin/packages/cbtf/package.py
index 017b897f3c..bc3116bf2a 100644
--- a/var/spack/repos/builtin/packages/cbtf/package.py
+++ b/var/spack/repos/builtin/packages/cbtf/package.py
@@ -22,7 +22,7 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-################################################################################
+##########################################################################
 # Copyright (c) 2015-2016 Krell Institute. All Rights Reserved.
 #
 # This program is free software; you can redistribute it and/or modify it under
@@ -38,24 +38,30 @@
 # You should have received a copy of the GNU General Public License along with
 # this program; if not, write to the Free Software Foundation, Inc., 59 Temple
 # Place, Suite 330, Boston, MA  02111-1307  USA
-################################################################################
+##########################################################################
 
 from spack import *
 
+
 class Cbtf(Package):
-    """CBTF project contains the base code for CBTF that supports creating components, 
-       component networks and the support to connect these components and component 
-       networks into sequential and distributed network tools."""
+    """CBTF project contains the base code for CBTF that supports creating
+       components, component networks and the support to connect these
+       components and component networks into sequential and distributed
+       network tools.
+
+    """
     homepage = "http://sourceforge.net/p/cbtf/wiki/Home"
 
     # Mirror access template example
-    #url      = "file:/home/jeg/cbtf-1.6.tar.gz"
-    #version('1.6', 'c1ef4e5aa4e470dffb042abdba0b9987')
+    # url      = "file:/home/jeg/cbtf-1.6.tar.gz"
+    # version('1.6', 'c1ef4e5aa4e470dffb042abdba0b9987')
 
     # Use when the git repository is available
-    version('1.6', branch='master', git='https://github.com/OpenSpeedShop/cbtf.git')
+    version('1.6', branch='master',
+            git='https://github.com/OpenSpeedShop/cbtf.git')
 
-    variant('runtime', default=False, description="build only the runtime libraries and collectors.")
+    variant('runtime', default=False,
+            description="build only the runtime libraries and collectors.")
 
     depends_on("cmake@3.0.2", type='build')
     depends_on("boost@1.50.0:")
@@ -67,11 +73,13 @@ class Cbtf(Package):
     parallel = False
 
     def adjustBuildTypeParams_cmakeOptions(self, spec, cmakeOptions):
-        # Sets build type parameters into cmakeOptions the options that will enable the cbtf-krell built type settings
- 
-        compile_flags="-O2 -g"
+        # Sets build type parameters into cmakeOptions the options that will
+        # enable the cbtf-krell built type settings
+
+        compile_flags = "-O2 -g"
         BuildTypeOptions = []
-        # Set CMAKE_BUILD_TYPE to what cbtf-krell wants it to be, not the stdcmakeargs
+        # Set CMAKE_BUILD_TYPE to what cbtf-krell wants it to be, not the
+        # stdcmakeargs
         for word in cmakeOptions[:]:
             if word.startswith('-DCMAKE_BUILD_TYPE'):
                 cmakeOptions.remove(word)
@@ -80,61 +88,66 @@ class Cbtf(Package):
             if word.startswith('-DCMAKE_C_FLAGS'):
                 cmakeOptions.remove(word)
         BuildTypeOptions.extend([
-                 '-DCMAKE_BUILD_TYPE=None',
-                 '-DCMAKE_CXX_FLAGS=%s'         % compile_flags,
-                 '-DCMAKE_C_FLAGS=%s'           % compile_flags
+            '-DCMAKE_BUILD_TYPE=None',
+            '-DCMAKE_CXX_FLAGS=%s'         % compile_flags,
+            '-DCMAKE_C_FLAGS=%s'           % compile_flags
         ])
 
         cmakeOptions.extend(BuildTypeOptions)
 
     def install(self, spec, prefix):
-      with working_dir('build', create=True):
-
-          # Boost_NO_SYSTEM_PATHS  Set to TRUE to suppress searching   
-          # in system paths (or other locations outside of BOOST_ROOT
-          # or BOOST_INCLUDEDIR).  Useful when specifying BOOST_ROOT. 
-          # Defaults to OFF.
-
-          if '+runtime' in spec:
-              # Install message tag include file for use in Intel MIC cbtf-krell build
-              # FIXME
-              cmakeOptions = []
-              cmakeOptions.extend(['-DCMAKE_INSTALL_PREFIX=%s'	% prefix,
-                                   '-DBoost_NO_SYSTEM_PATHS=TRUE',
-                                   '-DXERCESC_DIR=%s'         % spec['xerces-c'].prefix,
-                                   '-DBOOST_ROOT=%s'          % spec['boost'].prefix,
-                                   '-DMRNET_DIR=%s'           % spec['mrnet'].prefix,
-                                   '-DCMAKE_MODULE_PATH=%s'   % join_path(prefix.share,'KrellInstitute','cmake')
-                                  ])
-
-              # Add in the standard cmake arguments
-              cmakeOptions.extend(std_cmake_args)
-
-              # Adjust the standard cmake arguments to what we want the build type, etc to be
-              self.adjustBuildTypeParams_cmakeOptions(spec, cmakeOptions)
-             
-              # Invoke cmake
-              cmake('..', *cmakeOptions)
-
-          else:
-              cmakeOptions = []
-              cmakeOptions.extend(['-DCMAKE_INSTALL_PREFIX=%s'	% prefix,
-                                   '-DBoost_NO_SYSTEM_PATHS=TRUE',
-                                   '-DXERCESC_DIR=%s'         % spec['xerces-c'].prefix,
-                                   '-DBOOST_ROOT=%s'          % spec['boost'].prefix,
-                                   '-DMRNET_DIR=%s'           % spec['mrnet'].prefix,
-                                   '-DCMAKE_MODULE_PATH=%s'   % join_path(prefix.share,'KrellInstitute','cmake')
-                                  ])
-
-              # Add in the standard cmake arguments
-              cmakeOptions.extend(std_cmake_args)
-
-              # Adjust the standard cmake arguments to what we want the build type, etc to be
-              self.adjustBuildTypeParams_cmakeOptions(spec, cmakeOptions)
-             
-              # Invoke cmake
-              cmake('..', *cmakeOptions)
-
-          make("clean")
-          make()
-          make("install")
+        with working_dir('build', create=True):
+
+            # Boost_NO_SYSTEM_PATHS  Set to TRUE to suppress searching
+            # in system paths (or other locations outside of BOOST_ROOT
+            # or BOOST_INCLUDEDIR).  Useful when specifying BOOST_ROOT.
+            # Defaults to OFF.
+
+            if '+runtime' in spec:
+                # Install message tag include file for use in Intel MIC
+                # cbtf-krell build
+                # FIXME
+                cmakeOptions = []
+                cmakeOptions.extend(
+                    ['-DCMAKE_INSTALL_PREFIX=%s' % prefix,
+                     '-DBoost_NO_SYSTEM_PATHS=TRUE',
+                     '-DXERCESC_DIR=%s'         % spec['xerces-c'].prefix,
+                     '-DBOOST_ROOT=%s'          % spec['boost'].prefix,
+                     '-DMRNET_DIR=%s'           % spec['mrnet'].prefix,
+                     '-DCMAKE_MODULE_PATH=%s'   % join_path(
+                         prefix.share, 'KrellInstitute', 'cmake')])
+
+                # Add in the standard cmake arguments
+                cmakeOptions.extend(std_cmake_args)
+
+                # Adjust the standard cmake arguments to what we want the build
+                # type, etc to be
+                self.adjustBuildTypeParams_cmakeOptions(spec, cmakeOptions)
+
+                # Invoke cmake
+                cmake('..', *cmakeOptions)
+
+            else:
+                cmakeOptions = []
+                cmakeOptions.extend(
+                    ['-DCMAKE_INSTALL_PREFIX=%s' % prefix,
+                     '-DBoost_NO_SYSTEM_PATHS=TRUE',
+                     '-DXERCESC_DIR=%s'         % spec['xerces-c'].prefix,
+                     '-DBOOST_ROOT=%s'          % spec['boost'].prefix,
+                     '-DMRNET_DIR=%s'           % spec['mrnet'].prefix,
+                     '-DCMAKE_MODULE_PATH=%s'   % join_path(
+                         prefix.share, 'KrellInstitute', 'cmake')])
+
+                # Add in the standard cmake arguments
+                cmakeOptions.extend(std_cmake_args)
+
+                # Adjust the standard cmake arguments to what we want the build
+                # type, etc to be
+                self.adjustBuildTypeParams_cmakeOptions(spec, cmakeOptions)
+
+                # Invoke cmake
+                cmake('..', *cmakeOptions)
+
+            make("clean")
+            make()
+            make("install")
diff --git a/var/spack/repos/builtin/packages/cereal/package.py b/var/spack/repos/builtin/packages/cereal/package.py
index 41dc9a274b..716e0103d1 100644
--- a/var/spack/repos/builtin/packages/cereal/package.py
+++ b/var/spack/repos/builtin/packages/cereal/package.py
@@ -26,8 +26,16 @@ from spack import *
 import os
 import shutil
 
+
 class Cereal(Package):
-    """cereal is a header-only C++11 serialization library. cereal takes arbitrary data types and reversibly turns them into different representations, such as compact binary encodings, XML, or JSON. cereal was designed to be fast, light-weight, and easy to extend - it has no external dependencies and can be easily bundled with other code or used standalone."""
+    """cereal is a header-only C++11 serialization library. cereal takes
+       arbitrary data types and reversibly turns them into different
+       representations, such as compact binary encodings, XML, or
+       JSON. cereal was designed to be fast, light-weight, and easy to
+       extend - it has no external dependencies and can be easily bundled
+       with other code or used standalone.
+
+    """
     homepage = "http://uscilab.github.io/cereal/"
     url      = "https://github.com/USCiLab/cereal/archive/v1.1.2.tar.gz"
 
diff --git a/var/spack/repos/builtin/packages/cfitsio/package.py b/var/spack/repos/builtin/packages/cfitsio/package.py
index ed49ae5808..c68b3ffc0d 100644
--- a/var/spack/repos/builtin/packages/cfitsio/package.py
+++ b/var/spack/repos/builtin/packages/cfitsio/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Cfitsio(Package):
     """
     CFITSIO is a library of C and Fortran subroutines for reading and writing
diff --git a/var/spack/repos/builtin/packages/cgal/package.py b/var/spack/repos/builtin/packages/cgal/package.py
index 5c87978339..e522b4a5a0 100644
--- a/var/spack/repos/builtin/packages/cgal/package.py
+++ b/var/spack/repos/builtin/packages/cgal/package.py
@@ -27,10 +27,12 @@ from spack import *
 
 
 class Cgal(Package):
-    """
-    CGAL is a software project that provides easy access to efficient and reliable geometric algorithms in the form of
-    a C++ library. CGAL is used in various areas needing geometric computation, such as geographic information systems,
-    computer aided design, molecular biology, medical imaging, computer graphics, and robotics.
+    """CGAL is a software project that provides easy access to efficient and
+       reliable geometric algorithms in the form of a C++ library. CGAL
+       is used in various areas needing geometric computation, such as
+       geographic information systems, computer aided design, molecular
+       biology, medical imaging, computer graphics, and robotics.
+
     """
     homepage = 'http://www.cgal.org/'
     url = 'https://github.com/CGAL/cgal/archive/releases/CGAL-4.7.tar.gz'
@@ -38,9 +40,12 @@ class Cgal(Package):
     version('4.7', '4826714810f3b4c65cac96b90fb03b67')
     version('4.6.3', 'e8ee2ecc8d2b09b94a121c09257b576d')
 
-    # Installation instructions : http://doc.cgal.org/latest/Manual/installation.html
-    variant('shared', default=True, description='Enables the build of shared libraries')
-    variant('debug', default=False, description='Builds a debug version of the libraries')
+    # Installation instructions :
+    # http://doc.cgal.org/latest/Manual/installation.html
+    variant('shared', default=True,
+            description='Enables the build of shared libraries')
+    variant('debug', default=False,
+            description='Builds a debug version of the libraries')
 
     depends_on('boost')
     depends_on('mpfr')
@@ -55,7 +60,8 @@ class Cgal(Package):
 
         options = []
         options.extend(std_cmake_args)
-        # CGAL supports only Release and Debug build type. Any other build type will raise an error at configure time
+        # CGAL supports only Release and Debug build type. Any other build type
+        # will raise an error at configure time
         if '+debug' in spec:
             options.append('-DCMAKE_BUILD_TYPE:STRING=Debug')
         else:
diff --git a/var/spack/repos/builtin/packages/cgm/package.py b/var/spack/repos/builtin/packages/cgm/package.py
index c5da72d25a..5a998d471c 100644
--- a/var/spack/repos/builtin/packages/cgm/package.py
+++ b/var/spack/repos/builtin/packages/cgm/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Cgm(Package):
     """The Common Geometry Module, Argonne (CGMA) is a code library
        which provides geometry functionality used for mesh generation and
@@ -33,7 +34,7 @@ class Cgm(Package):
 
     version('13.1.1', '4e8dbc4ba8f65767b29f985f7a23b01f')
     version('13.1.0', 'a6c7b22660f164ce893fb974f9cb2028')
-    version('13.1'  , '95f724bda04919fc76818a5b7bc0b4ed')
+    version('13.1', '95f724bda04919fc76818a5b7bc0b4ed')
 
     depends_on("mpi")
 
@@ -42,7 +43,6 @@ class Cgm(Package):
                     '//\1',
                     'geom/parallel/CGMReadParallel.cpp')
 
-
     def install(self, spec, prefix):
         configure("--with-mpi",
                   "--prefix=%s" % prefix,
diff --git a/var/spack/repos/builtin/packages/cityhash/package.py b/var/spack/repos/builtin/packages/cityhash/package.py
index caa15780e3..d6d7f51558 100644
--- a/var/spack/repos/builtin/packages/cityhash/package.py
+++ b/var/spack/repos/builtin/packages/cityhash/package.py
@@ -25,16 +25,18 @@
 from spack import *
 from spack.util.environment import *
 
+
 class Cityhash(Package):
     homepage = "https://github.com/google/cityhash"
     url      = "https://github.com/google/cityhash"
 
-    version('2013-07-31', git='https://github.com/google/cityhash.git', commit='8af9b8c2b889d80c22d6bc26ba0df1afb79a30db')
-    version('master', branch='master', git='https://github.com/google/cityhash.git')
+    version('2013-07-31', git='https://github.com/google/cityhash.git',
+            commit='8af9b8c2b889d80c22d6bc26ba0df1afb79a30db')
+    version('master', branch='master',
+            git='https://github.com/google/cityhash.git')
 
     def install(self, spec, prefix):
         configure('--enable-sse4.2', '--prefix=%s' % prefix)
 
         make()
         make("install")
-
diff --git a/var/spack/repos/builtin/packages/cleverleaf/package.py b/var/spack/repos/builtin/packages/cleverleaf/package.py
index c258e89514..61e6dca433 100644
--- a/var/spack/repos/builtin/packages/cleverleaf/package.py
+++ b/var/spack/repos/builtin/packages/cleverleaf/package.py
@@ -24,18 +24,21 @@
 ##############################################################################
 from spack import *
 
+
 class Cleverleaf(Package):
-    """
-    CleverLeaf is a hydrodynamics mini-app that extends CloverLeaf with Adaptive
-    Mesh Refinement using the SAMRAI toolkit from Lawrence Livermore National
-    Laboratory. The primary goal of CleverLeaf is to evaluate the application of
-    AMR to the Lagrangian-Eulerian hydrodynamics scheme used by CloverLeaf.
+    """CleverLeaf is a hydrodynamics mini-app that extends CloverLeaf with
+       Adaptive Mesh Refinement using the SAMRAI toolkit from Lawrence
+       Livermore National Laboratory. The primary goal of CleverLeaf is
+       to evaluate the application of AMR to the Lagrangian-Eulerian
+       hydrodynamics scheme used by CloverLeaf.
+
     """
 
     homepage = "http://uk-mac.github.io/CleverLeaf/"
     url      = "https://github.com/UK-MAC/CleverLeaf/tarball/master"
 
-    version('develop', git='https://github.com/UK-MAC/CleverLeaf_ref.git', branch='develop')
+    version('develop', git='https://github.com/UK-MAC/CleverLeaf_ref.git',
+            branch='develop')
 
     depends_on("SAMRAI@3.8.0:")
     depends_on("hdf5+mpi")
diff --git a/var/spack/repos/builtin/packages/cloog/package.py b/var/spack/repos/builtin/packages/cloog/package.py
index db3d2ac928..a979ae83fc 100644
--- a/var/spack/repos/builtin/packages/cloog/package.py
+++ b/var/spack/repos/builtin/packages/cloog/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Cloog(Package):
     """CLooG is a free software and library to generate code for
     scanning Z-polyhedra. That is, it finds a code (e.g. in C,
diff --git a/var/spack/repos/builtin/packages/cmake/package.py b/var/spack/repos/builtin/packages/cmake/package.py
index bfb8764feb..90a7c20d19 100644
--- a/var/spack/repos/builtin/packages/cmake/package.py
+++ b/var/spack/repos/builtin/packages/cmake/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Cmake(Package):
     """A cross-platform, open-source build system. CMake is a family of
        tools designed to build, test and package software."""
@@ -40,10 +41,13 @@ class Cmake(Package):
     version('3.0.2',    'db4c687a31444a929d2fdc36c4dfb95f')
     version('2.8.10.2', '097278785da7182ec0aea8769d06860c')
 
-    variant('ncurses', default=True, description='Enables the build of the ncurses gui')
-    variant('openssl', default=True, description="Enables CMake's OpenSSL features")
+    variant('ncurses', default=True,
+            description='Enables the build of the ncurses gui')
+    variant('openssl', default=True,
+            description="Enables CMake's OpenSSL features")
     variant('qt', default=False, description='Enables the build of cmake-gui')
-    variant('doc', default=False, description='Enables the generation of html and man page documentation')
+    variant('doc', default=False,
+            description='Enables the generation of html and man page docs')
 
     depends_on('ncurses', when='+ncurses')
     depends_on('openssl', when='+openssl')
@@ -53,7 +57,8 @@ class Cmake(Package):
 
     def url_for_version(self, version):
         """Handle CMake's version-based custom URLs."""
-        return 'https://cmake.org/files/v%s/cmake-%s.tar.gz' % (version.up_to(2), version)
+        return 'https://cmake.org/files/v%s/cmake-%s.tar.gz' % (
+            version.up_to(2), version)
 
     def validate(self, spec):
         """
diff --git a/var/spack/repos/builtin/packages/cmocka/package.py b/var/spack/repos/builtin/packages/cmocka/package.py
index aa2b3cc3bb..274b78379a 100644
--- a/var/spack/repos/builtin/packages/cmocka/package.py
+++ b/var/spack/repos/builtin/packages/cmocka/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Cmocka(Package):
     """Unit-testing framework in pure C"""
     homepage = "https://cmocka.org/"
@@ -36,7 +37,7 @@ class Cmocka(Package):
 
     def install(self, spec, prefix):
         with working_dir('spack-build', create=True):
-	    cmake('..', *std_cmake_args)
+            cmake('..', *std_cmake_args)
 
-	    make()
-	    make("install")
+            make()
+            make("install")
diff --git a/var/spack/repos/builtin/packages/cnmem/package.py b/var/spack/repos/builtin/packages/cnmem/package.py
index f4c05f5b5f..0c62023952 100644
--- a/var/spack/repos/builtin/packages/cnmem/package.py
+++ b/var/spack/repos/builtin/packages/cnmem/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Cnmem(Package):
     """CNMem mempool for CUDA devices"""
     homepage = "https://github.com/NVIDIA/cnmem"
@@ -31,6 +32,6 @@ class Cnmem(Package):
     version('git', git='https://github.com/NVIDIA/cnmem.git', branch="master")
 
     def install(self, spec, prefix):
-            cmake('.',*std_cmake_args)
-            make()
-            make('install')
+        cmake('.', *std_cmake_args)
+        make()
+        make('install')
diff --git a/var/spack/repos/builtin/packages/coreutils/package.py b/var/spack/repos/builtin/packages/coreutils/package.py
index cb8f596b41..94cfa11341 100644
--- a/var/spack/repos/builtin/packages/coreutils/package.py
+++ b/var/spack/repos/builtin/packages/coreutils/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Coreutils(Package):
     """The GNU Core Utilities are the basic file, shell and text
        manipulation utilities of the GNU operating system.  These are
diff --git a/var/spack/repos/builtin/packages/cp2k/package.py b/var/spack/repos/builtin/packages/cp2k/package.py
new file mode 100644
index 0000000000..5f59286323
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cp2k/package.py
@@ -0,0 +1,178 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+import os
+import shutil
+import copy
+
+from spack import *
+
+
+class Cp2k(Package):
+    """CP2K is a quantum chemistry and solid state physics software package
+    that can perform atomistic simulations of solid state, liquid, molecular,
+    periodic, material, crystal, and biological systems
+    """
+    homepage = 'https://www.cp2k.org'
+    url = 'https://sourceforge.net/projects/cp2k/files/cp2k-3.0.tar.bz2'
+
+    version('3.0', 'c05bc47335f68597a310b1ed75601d35')
+
+    variant('mpi', default=True, description='Enable MPI support')
+    variant('plumed', default=False, description='Enable PLUMED support')
+
+    depends_on('python')  # Build dependency
+
+    depends_on('lapack')
+    depends_on('blas')
+    depends_on('fftw')
+
+    depends_on('mpi', when='+mpi')
+    depends_on('scalapack', when='+mpi')
+    depends_on('plumed+shared+mpi', when='+plumed+mpi')
+    depends_on('plumed+shared~mpi', when='+plumed~mpi')
+
+    # TODO : add dependency on libint
+    # TODO : add dependency on libsmm, libxsmm
+    # TODO : add dependency on elpa
+    # TODO : add dependency on CUDA
+    # TODO : add dependency on PEXSI
+    # TODO : add dependency on QUIP
+    # TODO : add dependency on libwannier90
+
+    parallel = False
+
+    def install(self, spec, prefix):
+        # Construct a proper filename for the architecture file
+        cp2k_architecture = '{0.architecture}-{0.compiler.name}'.format(spec)
+        cp2k_version = 'sopt' if '~mpi' in spec else 'popt'
+        makefile_basename = '.'.join([cp2k_architecture, cp2k_version])
+        makefile = join_path('arch', makefile_basename)
+
+        # Write the custom makefile
+        with open(makefile, 'w') as mkf:
+            # Optimization flags
+            optflags = {
+                'gcc': ['-O2',
+                        '-ffast-math',
+                        '-ffree-form',
+                        '-ffree-line-length-none',
+                        '-ftree-vectorize',
+                        '-funroll-loops',
+                        '-mtune=native'],
+                'intel': ['-O2',
+                          '-pc64',
+                          '-unroll',
+                          '-heap-arrays 64']
+            }
+            cppflags = [
+                '-D__FFTW3',
+                '-I' + spec['fftw'].prefix.include
+            ]
+            fcflags = copy.deepcopy(optflags[self.spec.compiler.name])
+            fcflags.extend([
+                '-I' + spec['fftw'].prefix.include
+            ])
+            ldflags = ['-L' + spec['fftw'].prefix.lib]
+            libs = []
+            if '+plumed' in self.spec:
+                # Include Plumed.inc in the Makefile
+                mkf.write('include {0}\n'.format(
+                    join_path(self.spec['plumed'].prefix.lib,
+                              'plumed',
+                              'src',
+                              'lib',
+                              'Plumed.inc')
+                ))
+                # Add required macro
+                cppflags.extend(['-D__PLUMED2'])
+                libs.extend([
+                    join_path(self.spec['plumed'].prefix.lib, 'libplumed.so')
+                ])
+
+            mkf.write('CC = {0.compiler.cc}\n'.format(self))
+            if '%intel' in self.spec:
+                # CPP is a commented command in Intel arch of CP2K
+                # This is the hack through which cp2k developers avoid doing :
+                #
+                # ${CPP} <file>.F > <file>.f90
+                #
+                # and use `-fpp` instead
+                mkf.write('CPP = # {0.compiler.cc} -P\n'.format(self))
+                mkf.write('AR = xiar -r\n')
+            else:
+                mkf.write('CPP = {0.compiler.cc} -E\n'.format(self))
+                mkf.write('AR = ar -r\n')
+            fc = self.compiler.fc if '~mpi' in spec else self.spec['mpi'].mpifc
+            mkf.write('FC = {0}\n'.format(fc))
+            mkf.write('LD = {0}\n'.format(fc))
+            # Intel
+            if '%intel' in self.spec:
+                cppflags.extend([
+                    '-D__INTEL_COMPILER',
+                    '-D__MKL'
+                ])
+                fcflags.extend([
+                    '-diag-disable 8290,8291,10010,10212,11060',
+                    '-free',
+                    '-fpp'
+                ])
+            # MPI
+            if '+mpi' in self.spec:
+                cppflags.extend([
+                    '-D__parallel',
+                    '-D__SCALAPACK'
+                ])
+                ldflags.extend([
+                    '-L' + spec['scalapack'].prefix.lib
+                ])
+                libs.extend(spec['scalapack'].scalapack_shared_libs)
+
+            # LAPACK / BLAS
+            ldflags.extend([
+                '-L' + spec['lapack'].prefix.lib,
+                '-L' + spec['blas'].prefix.lib
+            ])
+            libs.extend([
+                join_path(spec['fftw'].prefix.lib, 'libfftw3.so'),
+                spec['lapack'].lapack_shared_lib,
+                spec['blas'].blas_shared_lib
+            ])
+
+            # Write compiler flags to file
+            mkf.write('CPPFLAGS = {0}\n'.format(' '.join(cppflags)))
+            mkf.write('FCFLAGS = {0}\n'.format(' '.join(fcflags)))
+            mkf.write('LDFLAGS = {0}\n'.format(' '.join(ldflags)))
+            mkf.write('LIBS = {0}\n'.format(' '.join(libs)))
+
+        with working_dir('makefiles'):
+            # Apparently the Makefile bases its paths on PWD
+            # so we need to set PWD = os.getcwd()
+            pwd_backup = env['PWD']
+            env['PWD'] = os.getcwd()
+            make('ARCH={0}'.format(cp2k_architecture),
+                 'VERSION={0}'.format(cp2k_version))
+            env['PWD'] = pwd_backup
+        exe_dir = join_path('exe', cp2k_architecture)
+        shutil.copytree(exe_dir, self.prefix.bin)
diff --git a/var/spack/repos/builtin/packages/cppcheck/package.py b/var/spack/repos/builtin/packages/cppcheck/package.py
index 16f052ef2f..fd48fcb7e3 100644
--- a/var/spack/repos/builtin/packages/cppcheck/package.py
+++ b/var/spack/repos/builtin/packages/cppcheck/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Cppcheck(Package):
     """A tool for static C/C++ code analysis."""
     homepage = "http://cppcheck.sourceforge.net/"
diff --git a/var/spack/repos/builtin/packages/cram/package.py b/var/spack/repos/builtin/packages/cram/package.py
index 283bc5adea..bef26cdcbd 100644
--- a/var/spack/repos/builtin/packages/cram/package.py
+++ b/var/spack/repos/builtin/packages/cram/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Cram(Package):
     """Cram runs many small MPI jobs inside one large MPI job."""
     homepage = "https://github.com/llnl/cram"
diff --git a/var/spack/repos/builtin/packages/cryptopp/package.py b/var/spack/repos/builtin/packages/cryptopp/package.py
index 77895a7331..e9294a14a6 100644
--- a/var/spack/repos/builtin/packages/cryptopp/package.py
+++ b/var/spack/repos/builtin/packages/cryptopp/package.py
@@ -25,12 +25,15 @@
 import glob
 from spack import *
 
+
 class Cryptopp(Package):
     """Crypto++ is an open-source C++ library of cryptographic schemes. The
-       library supports a number of different cryptography algorithms, including
-       authenticated encryption schemes (GCM, CCM), hash functions (SHA-1, SHA2),
-       public-key encryption (RSA, DSA), and a few obsolete/historical encryption
-       algorithms (MD5, Panama)."""
+       library supports a number of different cryptography algorithms,
+       including authenticated encryption schemes (GCM, CCM), hash
+       functions (SHA-1, SHA2), public-key encryption (RSA, DSA), and a
+       few obsolete/historical encryption algorithms (MD5, Panama).
+
+    """
 
     homepage = "http://www.cryptopp.com"
     base_url = "http://www.cryptopp.com"
diff --git a/var/spack/repos/builtin/packages/cscope/package.py b/var/spack/repos/builtin/packages/cscope/package.py
index 88d522f486..f21226cce1 100644
--- a/var/spack/repos/builtin/packages/cscope/package.py
+++ b/var/spack/repos/builtin/packages/cscope/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Cscope(Package):
     """Cscope is a developer's tool for browsing source code."""
     homepage = "http://http://cscope.sourceforge.net/"
diff --git a/var/spack/repos/builtin/packages/cube/package.py b/var/spack/repos/builtin/packages/cube/package.py
index 40c2cc6893..09237f87c3 100644
--- a/var/spack/repos/builtin/packages/cube/package.py
+++ b/var/spack/repos/builtin/packages/cube/package.py
@@ -28,8 +28,8 @@ from spack import *
 
 class Cube(Package):
     """
-    Cube the profile viewer for Score-P and Scalasca profiles. It displays a multi-dimensional performance space
-    consisting of the dimensions:
+    Cube the profile viewer for Score-P and Scalasca profiles. It displays a
+    multi-dimensional performance space consisting of the dimensions:
     - performance metric
     - call path
     - system resource
@@ -38,14 +38,17 @@ class Cube(Package):
     homepage = "http://www.scalasca.org/software/cube-4.x/download.html"
     url = "http://apps.fz-juelich.de/scalasca/releases/cube/4.2/dist/cube-4.2.3.tar.gz"
 
+    version('4.3.4', '50f73060f55311cb12c5b3cb354d59fa',
+            url='http://apps.fz-juelich.de/scalasca/releases/cube/4.3/dist/cube-4.3.4.tar.gz')
     version('4.3.3', '07e109248ed8ffc7bdcce614264a2909',
             url='http://apps.fz-juelich.de/scalasca/releases/cube/4.3/dist/cube-4.3.3.tar.gz')
-
     version('4.2.3', '8f95b9531f5a8f8134f279c2767c9b20',
             url="http://apps.fz-juelich.de/scalasca/releases/cube/4.2/dist/cube-4.2.3.tar.gz")
 
     # TODO : add variant that builds GUI on top of Qt
 
+    depends_on('zlib')
+
     def install(self, spec, prefix):
         configure_args = ["--prefix=%s" % prefix,
                           "--without-paraver",
diff --git a/var/spack/repos/builtin/packages/cuda/package.py b/var/spack/repos/builtin/packages/cuda/package.py
index 96694670ad..558535bec6 100644
--- a/var/spack/repos/builtin/packages/cuda/package.py
+++ b/var/spack/repos/builtin/packages/cuda/package.py
@@ -26,22 +26,27 @@ from spack import *
 from glob import glob
 import os
 
+
 class Cuda(Package):
-    """CUDA is a parallel computing platform and programming model invented by
-    NVIDIA. It enables dramatic increases in computing performance by harnessing
-    the power of the graphics processing unit (GPU).
+    """CUDA is a parallel computing platform and programming model invented
+    by NVIDIA. It enables dramatic increases in computing performance by
+    harnessing the power of the graphics processing unit (GPU).
+
+    Note: NVIDIA does not provide a download URL for CUDA so you will
+    need to download it yourself. Go to
+    https://developer.nvidia.com/cuda-downloads and select your Operating
+    System, Architecture, Distribution, and Version.  For the Installer
+    Type, select runfile and click Download. Spack will search your
+    current directory for this file. Alternatively, add this file to a
+    mirror so that Spack can find it. For instructions on how to set up a
+    mirror, see http://software.llnl.gov/spack/mirrors.html
 
-    Note: NVIDIA does not provide a download URL for CUDA so you will need to
-    download it yourself. Go to https://developer.nvidia.com/cuda-downloads
-    and select your Operating System, Architecture, Distribution, and Version.
-    For the Installer Type, select runfile and click Download. Spack will search
-    your current directory for this file. Alternatively, add this file to a
-    mirror so that Spack can find it. For instructions on how to set up a mirror,
-    see http://software.llnl.gov/spack/mirrors.html
+    Note: This package does not currently install the drivers necessary
+    to run CUDA. These will need to be installed manually. See:
+    http://docs.nvidia.com/cuda/cuda-getting-started-guide-for-linux for
+    details.
 
-    Note: This package does not currently install the drivers necessary to run
-    CUDA. These will need to be installed manually. See:
-    http://docs.nvidia.com/cuda/cuda-getting-started-guide-for-linux for details."""
+    """
 
     homepage = "http://www.nvidia.com/object/cuda_home_new.html"
 
@@ -50,15 +55,15 @@ class Cuda(Package):
     version('6.5.14', '90b1b8f77313600cc294d9271741f4da', expand=False,
             url="file://%s/cuda_6.5.14_linux_64.run" % os.getcwd())
 
-
     def install(self, spec, prefix):
         runfile = glob(os.path.join(self.stage.path, 'cuda*.run'))[0]
         chmod = which('chmod')
         chmod('+x', runfile)
         runfile = which(runfile)
 
-        # Note: NVIDIA does not officially support many newer versions of compilers.
-        # For example, on CentOS 6, you must use GCC 4.4.7 or older. See:
+        # Note: NVIDIA does not officially support many newer versions of
+        # compilers.  For example, on CentOS 6, you must use GCC 4.4.7 or
+        # older. See:
         # http://docs.nvidia.com/cuda/cuda-installation-guide-linux/#system-requirements
         # for details.
 
@@ -68,4 +73,3 @@ class Cuda(Package):
             '--toolkit',  # install CUDA Toolkit
             '--toolkitpath=%s' % prefix
         )
-
diff --git a/var/spack/repos/builtin/packages/czmq/package.py b/var/spack/repos/builtin/packages/czmq/package.py
index a251a94470..ef6374619b 100644
--- a/var/spack/repos/builtin/packages/czmq/package.py
+++ b/var/spack/repos/builtin/packages/czmq/package.py
@@ -25,12 +25,14 @@
 from spack import *
 import os
 
+
 class Czmq(Package):
     """ A C interface to the ZMQ library """
     homepage = "http://czmq.zeromq.org"
     url      = "https://github.com/zeromq/czmq/archive/v3.0.2.tar.gz"
 
-    version('3.0.2', '23e9885f7ee3ce88d99d0425f52e9be1', url='https://github.com/zeromq/czmq/archive/v3.0.2.tar.gz')
+    version('3.0.2', '23e9885f7ee3ce88d99d0425f52e9be1',
+            url='https://github.com/zeromq/czmq/archive/v3.0.2.tar.gz')
 
     depends_on('libtool', type='build')
     depends_on('automake', type='build')
@@ -39,19 +41,21 @@ class Czmq(Package):
     depends_on('zeromq')
 
     def install(self, spec, prefix):
-        bash = which("bash")
         # Work around autogen.sh oddities
+        # bash = which("bash")
         # bash("./autogen.sh")
         mkdirp("config")
         autoreconf = which("autoreconf")
         autoreconf("--install", "--verbose", "--force",
-        "-I", "config",
-        "-I", os.path.join(spec['pkg-config'].prefix, "share", "aclocal"),
-        "-I", os.path.join(spec['automake'].prefix, "share", "aclocal"),
-        "-I", os.path.join(spec['libtool'].prefix, "share", "aclocal"),
-        )
+                   "-I", "config",
+                   "-I", os.path.join(spec['pkg-config'].prefix,
+                                      "share", "aclocal"),
+                   "-I", os.path.join(spec['automake'].prefix,
+                                      "share", "aclocal"),
+                   "-I", os.path.join(spec['libtool'].prefix,
+                                      "share", "aclocal"),
+                   )
         configure("--prefix=%s" % prefix)
 
         make()
         make("install")
-
diff --git a/var/spack/repos/builtin/packages/dakota/package.py b/var/spack/repos/builtin/packages/dakota/package.py
index d0d22d9728..e8f7d0889b 100644
--- a/var/spack/repos/builtin/packages/dakota/package.py
+++ b/var/spack/repos/builtin/packages/dakota/package.py
@@ -26,17 +26,22 @@ from spack import *
 
 
 class Dakota(Package):
-    """
-    The Dakota toolkit provides a flexible, extensible interface between analysis codes and iterative systems
-    analysis methods. Dakota contains algorithms for:
+    """The Dakota toolkit provides a flexible, extensible interface between
+    analysis codes and iterative systems analysis methods. Dakota
+    contains algorithms for:
 
     - optimization with gradient and non gradient-based methods;
-    - uncertainty quantification with sampling, reliability, stochastic expansion, and epistemic methods;
+    - uncertainty quantification with sampling, reliability, stochastic
+    - expansion, and epistemic methods;
     - parameter estimation with nonlinear least squares methods;
-    - sensitivity/variance analysis with design of experiments and parameter study methods.
+    - sensitivity/variance analysis with design of experiments and
+    - parameter study methods.
+
+    These capabilities may be used on their own or as components within
+    advanced strategies such as hybrid optimization, surrogate-based
+    optimization, mixed integer nonlinear programming, or optimization
+    under uncertainty.
 
-    These capabilities may be used on their own or as components within advanced strategies such as hybrid optimization,
-    surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty.
     """
 
     homepage = 'https://dakota.sandia.gov/'
@@ -45,8 +50,10 @@ class Dakota(Package):
 
     version('6.3', '05a58d209fae604af234c894c3f73f6d')
 
-    variant('debug', default=False, description='Builds a debug version of the libraries')
-    variant('shared', default=True, description='Enables the build of shared libraries')
+    variant('debug', default=False,
+            description='Builds a debug version of the libraries')
+    variant('shared', default=True,
+            description='Enables the build of shared libraries')
     variant('mpi', default=True, description='Activates MPI support')
 
     depends_on('blas')
@@ -64,12 +71,17 @@ class Dakota(Package):
         options = []
         options.extend(std_cmake_args)
 
-        options.extend(['-DCMAKE_BUILD_TYPE:STRING=%s' % ('Debug' if '+debug' in spec else 'Release'),
-                        '-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if '+shared' in spec else 'OFF')])
+        options.extend([
+            '-DCMAKE_BUILD_TYPE:STRING=%s' % (
+                'Debug' if '+debug' in spec else 'Release'),
+            '-DBUILD_SHARED_LIBS:BOOL=%s' % (
+                'ON' if '+shared' in spec else 'OFF')])
 
         if '+mpi' in spec:
-            options.extend(['-DDAKOTA_HAVE_MPI:BOOL=ON',
-                            '-DMPI_CXX_COMPILER:STRING=%s' % join_path(spec['mpi'].prefix.bin, 'mpicxx')])
+            options.extend([
+                '-DDAKOTA_HAVE_MPI:BOOL=ON',
+                '-DMPI_CXX_COMPILER:STRING=%s' % join_path(
+                    spec['mpi'].prefix.bin, 'mpicxx')])
 
         build_directory = join_path(self.stage.path, 'spack-build')
         source_directory = self.stage.source_path
diff --git a/var/spack/repos/builtin/packages/damselfly/package.py b/var/spack/repos/builtin/packages/damselfly/package.py
index 427997072c..a37728c92b 100644
--- a/var/spack/repos/builtin/packages/damselfly/package.py
+++ b/var/spack/repos/builtin/packages/damselfly/package.py
@@ -24,17 +24,19 @@
 ##############################################################################
 from spack import *
 
+
 class Damselfly(Package):
     """Damselfly is a model-based parallel network simulator."""
     homepage = "https://github.com/llnl/damselfly"
     url      = "https://github.com/llnl/damselfly"
 
-    version('1.0', '05cf7e2d8ece4408c0f2abb7ab63fd74c0d62895', git='https://github.com/llnl/damselfly.git', tag='v1.0')
+    version('1.0', '05cf7e2d8ece4408c0f2abb7ab63fd74c0d62895',
+            git='https://github.com/llnl/damselfly.git', tag='v1.0')
 
     depends_on('cmake', type='build')
 
     def install(self, spec, prefix):
         with working_dir('spack-build', create=True):
-	    cmake('-DCMAKE_BUILD_TYPE=release', '..', *std_cmake_args)
-	    make()
-	    make('install')
+            cmake('-DCMAKE_BUILD_TYPE=release', '..', *std_cmake_args)
+            make()
+            make('install')
diff --git a/var/spack/repos/builtin/packages/datamash/package.py b/var/spack/repos/builtin/packages/datamash/package.py
new file mode 100644
index 0000000000..ef30c50ebe
--- /dev/null
+++ b/var/spack/repos/builtin/packages/datamash/package.py
@@ -0,0 +1,45 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Datamash(Package):
+    """
+    GNU datamash is a command-line program which performs basic numeric,
+    textual and statistical operations on input textual data files.
+    """
+
+    homepage = "https://www.gnu.org/software/datamash/"
+    url      = "http://ftp.gnu.org/gnu/datamash/datamash-1.0.5.tar.gz"
+
+    version('1.1.0', '79a6affca08107a095e97e4237fc8775')
+    version('1.0.7', '9f317bab07454032ba9c068e7f17b04b')
+    version('1.0.6', 'ff26fdef0f343cb695cf1853e14a1a5b')
+    version('1.0.5', '9a29549dc7feca49fdc5fab696614e11')
+
+    def install(self, spec, prefix):
+        configure('--prefix=%s' % prefix)
+        make()
+        make("install")
diff --git a/var/spack/repos/builtin/packages/dbus/package.py b/var/spack/repos/builtin/packages/dbus/package.py
index 130ba2ea1f..fdca68f53f 100644
--- a/var/spack/repos/builtin/packages/dbus/package.py
+++ b/var/spack/repos/builtin/packages/dbus/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Dbus(Package):
     """D-Bus is a message bus system, a simple way for applications to
        talk to one another. D-Bus supplies both a system daemon (for
diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py
index 54604d351f..939d8fc013 100644
--- a/var/spack/repos/builtin/packages/dealii/package.py
+++ b/var/spack/repos/builtin/packages/dealii/package.py
@@ -40,25 +40,48 @@ class Dealii(Package):
     version('develop', git='https://github.com/dealii/dealii.git')
 
     variant('mpi',      default=True,  description='Compile with MPI')
-    variant('arpack',   default=True,  description='Compile with Arpack and PArpack (only with MPI)')
-    variant('doc',      default=False, description='Compile with documentation')
+    variant('arpack',   default=True,
+            description='Compile with Arpack and PArpack (only with MPI)')
+    variant('doc',      default=False,
+            description='Compile with documentation')
     variant('gsl',      default=True,  description='Compile with GSL')
-    variant('hdf5',     default=True,  description='Compile with HDF5 (only with MPI)')
+    variant('hdf5',     default=True,
+            description='Compile with HDF5 (only with MPI)')
     variant('metis',    default=True,  description='Compile with Metis')
-    variant('netcdf',   default=True,  description='Compile with Netcdf (only with MPI)')
+    variant('netcdf',   default=True,
+            description='Compile with Netcdf (only with MPI)')
     variant('oce',      default=True,  description='Compile with OCE')
-    variant('p4est',    default=True,  description='Compile with P4est (only with MPI)')
-    variant('petsc',    default=True,  description='Compile with Petsc (only with MPI)')
-    variant('slepc',    default=True,  description='Compile with Slepc (only with Petsc and MPI)')
-    variant('trilinos', default=True,  description='Compile with Trilinos (only with MPI)')
+    variant('p4est',    default=True,
+            description='Compile with P4est (only with MPI)')
+    variant('petsc',    default=True,
+            description='Compile with Petsc (only with MPI)')
+    variant('slepc',    default=True,
+            description='Compile with Slepc (only with Petsc and MPI)')
+    variant('trilinos', default=True,
+            description='Compile with Trilinos (only with MPI)')
+    variant('python',   default=True,
+            description='Compile with Python bindings')
 
     # required dependencies, light version
     depends_on("blas")
     # Boost 1.58 is blacklisted, see
     # https://github.com/dealii/dealii/issues/1591
     # Require at least 1.59
-    depends_on("boost@1.59.0:+thread+system+serialization+iostreams",     when='~mpi')  # NOQA: ignore=E501
-    depends_on("boost@1.59.0:+mpi+thread+system+serialization+iostreams", when='+mpi')  # NOQA: ignore=E501
+    # +python won't affect @:8.4.1
+    depends_on("boost@1.59.0:+thread+system+serialization+iostreams",
+               when='@:8.4.1~mpi')
+    depends_on("boost@1.59.0:+thread+system+serialization+iostreams+mpi",
+               when='@:8.4.1+mpi')
+    # since @8.5.0: (and @develop) python bindings are introduced:
+    depends_on("boost@1.59.0:+thread+system+serialization+iostreams",
+               when='@8.5.0:~mpi~python')
+    depends_on("boost@1.59.0:+thread+system+serialization+iostreams+mpi",
+               when='@8.5.0:+mpi~python')
+    depends_on("boost@1.59.0:+thread+system+serialization+iostreams+python",
+               when='@8.5.0:~mpi+python')
+    depends_on(
+        "boost@1.59.0:+thread+system+serialization+iostreams+mpi+python",
+        when='@8.5.0:+mpi+python')
     depends_on("bzip2")
     depends_on("cmake", type='build')
     depends_on("lapack")
@@ -120,6 +143,12 @@ class Dealii(Package):
             '-DZLIB_DIR=%s' % spec['zlib'].prefix
         ])
 
+        if spec.satisfies('@8.5.0:'):
+            options.extend([
+                '-DDEAL_II_COMPONENT_PYTHON_BINDINGS=%s' %
+                ('ON' if '+python' in spec else 'OFF')
+            ])
+
         # Set directory structure:
         if spec.satisfies('@:8.2.1'):
             options.extend(['-DDEAL_II_COMPONENT_COMPAT_FILES=OFF'])
@@ -145,7 +174,8 @@ class Dealii(Package):
 
         # Optional dependencies for which librariy names are the same as CMake
         # variables:
-        for library in ('gsl', 'hdf5', 'p4est', 'petsc', 'slepc', 'trilinos', 'metis'):  # NOQA: ignore=E501
+        for library in (
+                'gsl', 'hdf5', 'p4est', 'petsc', 'slepc', 'trilinos', 'metis'):
             if library in spec:
                 options.extend([
                     '-D%s_DIR=%s' % (library.upper(), spec[library].prefix),
@@ -276,15 +306,20 @@ class Dealii(Package):
                     print('=== Step-40 Trilinos SuperluDist ====')
                     print('=====================================')
                     # change to direct solvers
-                    filter_file(r'(LA::SolverCG solver\(solver_control\);)',  ('TrilinosWrappers::SolverDirect::AdditionalData data(false,"Amesos_Superludist"); TrilinosWrappers::SolverDirect solver(solver_control,data);'), 'step-40.cc')  # NOQA: ignore=E501
-                    filter_file(r'(LA::MPI::PreconditionAMG preconditioner;)',
-                                (''), 'step-40.cc')
-                    filter_file(r'(LA::MPI::PreconditionAMG::AdditionalData data;)',  # NOQA: ignore=E501
-                                (''), 'step-40.cc')
-                    filter_file(r'(preconditioner.initialize\(system_matrix, data\);)',  # NOQA: ignore=E501
-                                (''), 'step-40.cc')
-                    filter_file(r'(solver\.solve \(system_matrix, completely_distributed_solution, system_rhs,)',  ('solver.solve (system_matrix, completely_distributed_solution, system_rhs);'), 'step-40.cc')  # NOQA: ignore=E501
-                    filter_file(r'(preconditioner\);)',  (''), 'step-40.cc')
+                    filter_file(r'(LA::SolverCG solver\(solver_control\);)',  ('TrilinosWrappers::SolverDirect::AdditionalData data(false,"Amesos_Superludist"); TrilinosWrappers::SolverDirect solver(solver_control,data);'), 'step-40.cc')  # noqa
+                    filter_file(
+                        r'(LA::MPI::PreconditionAMG preconditioner;)',
+                        (''), 'step-40.cc')
+                    filter_file(
+                        r'(LA::MPI::PreconditionAMG::AdditionalData data;)',
+                        (''), 'step-40.cc')
+                    filter_file(
+                        r'(preconditioner.initialize\(system_matrix, data\);)',
+                        (''), 'step-40.cc')
+                    filter_file(
+                        r'(solver\.solve \(system_matrix, completely_distributed_solution, system_rhs,)',  ('solver.solve (system_matrix, completely_distributed_solution, system_rhs);'), 'step-40.cc')  # noqa
+                    filter_file(
+                        r'(preconditioner\);)',  (''), 'step-40.cc')
                     if '^trilinos+superlu-dist' in spec:
                         make('release')
                         make('run', paralle=False)
diff --git a/var/spack/repos/builtin/packages/dia/package.py b/var/spack/repos/builtin/packages/dia/package.py
index 1685f0009f..94cd75656d 100644
--- a/var/spack/repos/builtin/packages/dia/package.py
+++ b/var/spack/repos/builtin/packages/dia/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Dia(Package):
     """Dia is a program for drawing structured diagrams."""
     homepage  = 'https://wiki.gnome.org/Apps/Dia'
@@ -34,7 +35,7 @@ class Dia(Package):
     depends_on('intltool', type='build')
     depends_on('gtkplus@2.6.0:')
     depends_on('cairo')
-    #depends_on('libart') # optional dependency, not yet supported by spack.
+    # depends_on('libart') # optional dependency, not yet supported by spack.
     depends_on('libpng')
     depends_on('libxslt')
     depends_on('python')
diff --git a/var/spack/repos/builtin/packages/doxygen/package.py b/var/spack/repos/builtin/packages/doxygen/package.py
index 267ba61756..f29110ac1d 100644
--- a/var/spack/repos/builtin/packages/doxygen/package.py
+++ b/var/spack/repos/builtin/packages/doxygen/package.py
@@ -24,8 +24,6 @@
 ##############################################################################
 from spack import *
 
-import sys
-
 
 class Doxygen(Package):
     """Doxygen is the de facto standard tool for generating documentation
@@ -41,7 +39,8 @@ class Doxygen(Package):
     version('1.8.10', '79767ccd986f12a0f949015efb5f058f')
 
     # graphviz appears to be a run-time optional dependency
-    variant('graphviz', default=True, description='Build with dot command support from Graphviz.')  # NOQA: ignore=E501
+    variant('graphviz', default=True,
+            description='Build with dot command support from Graphviz.')
 
     depends_on("cmake@2.8.12:", type='build')
     depends_on("flex", type='build')
diff --git a/var/spack/repos/builtin/packages/dri2proto/package.py b/var/spack/repos/builtin/packages/dri2proto/package.py
index 25ea783c0c..65b86714f1 100644
--- a/var/spack/repos/builtin/packages/dri2proto/package.py
+++ b/var/spack/repos/builtin/packages/dri2proto/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Dri2proto(Package):
     """DRI2 Protocol Headers."""
     homepage = "http://http://cgit.freedesktop.org/xorg/proto/dri2proto/"
diff --git a/var/spack/repos/builtin/packages/dtcmp/package.py b/var/spack/repos/builtin/packages/dtcmp/package.py
index b50b2ae3ae..e59e246d47 100644
--- a/var/spack/repos/builtin/packages/dtcmp/package.py
+++ b/var/spack/repos/builtin/packages/dtcmp/package.py
@@ -22,9 +22,9 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import os
 from spack import *
 
+
 class Dtcmp(Package):
     """The Datatype Comparison Library provides comparison operations and
        parallel sort algorithms for MPI applications."""
diff --git a/var/spack/repos/builtin/packages/dyninst/package.py b/var/spack/repos/builtin/packages/dyninst/package.py
index efe4de4abf..90c83bdc3a 100644
--- a/var/spack/repos/builtin/packages/dyninst/package.py
+++ b/var/spack/repos/builtin/packages/dyninst/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Dyninst(Package):
     """API for dynamic binary instrumentation.  Modify programs while they
     are executing without recompiling, re-linking, or re-executing."""
@@ -55,16 +56,18 @@ class Dyninst(Package):
                   '-DBoost_INCLUDE_DIR=%s'    % spec['boost'].prefix.include,
                   '-DBoost_LIBRARY_DIR=%s'    % spec['boost'].prefix.lib,
                   '-DBoost_NO_SYSTEM_PATHS=TRUE',
-                  '-DLIBELF_INCLUDE_DIR=%s'   % join_path(libelf.include, 'libelf'),
-                  '-DLIBELF_LIBRARIES=%s'     % join_path(libelf.lib, 'libelf.so'),
+                  '-DLIBELF_INCLUDE_DIR=%s'   % join_path(
+                      libelf.include, 'libelf'),
+                  '-DLIBELF_LIBRARIES=%s'     % join_path(
+                      libelf.lib, 'libelf.so'),
                   '-DLIBDWARF_INCLUDE_DIR=%s' % libdwarf.include,
-                  '-DLIBDWARF_LIBRARIES=%s'   % join_path(libdwarf.lib, 'libdwarf.so'),
+                  '-DLIBDWARF_LIBRARIES=%s'   % join_path(
+                      libdwarf.lib, 'libdwarf.so'),
                   *std_cmake_args)
 
             make()
             make("install")
 
-
     @when('@:8.1')
     def install(self, spec, prefix):
         configure("--prefix=" + prefix)
diff --git a/var/spack/repos/builtin/packages/eigen/package.py b/var/spack/repos/builtin/packages/eigen/package.py
index 97343f499b..36d6850c1a 100644
--- a/var/spack/repos/builtin/packages/eigen/package.py
+++ b/var/spack/repos/builtin/packages/eigen/package.py
@@ -22,7 +22,6 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-
 from spack import *
 
 
@@ -36,15 +35,19 @@ class Eigen(Package):
     homepage = 'http://eigen.tuxfamily.org/'
     url = 'http://bitbucket.org/eigen/eigen/get/3.2.7.tar.bz2'
 
-    version('3.2.7', 'cc1bacbad97558b97da6b77c9644f184', url='http://bitbucket.org/eigen/eigen/get/3.2.7.tar.bz2')
+    version('3.2.7', 'cc1bacbad97558b97da6b77c9644f184',
+            url='http://bitbucket.org/eigen/eigen/get/3.2.7.tar.bz2')
 
-    variant('debug', default=False, description='Builds the library in debug mode')
+    variant('debug', default=False,
+            description='Builds the library in debug mode')
 
     variant('metis', default=True, description='Enables metis backend')
     variant('scotch', default=True, description='Enables scotch backend')
     variant('fftw', default=True, description='Enables FFTW backend')
-    variant('suitesparse', default=True, description='Enables SuiteSparse support')
-    variant('mpfr', default=True, description='Enables support for multi-precisions floating points via mpfr')
+    variant('suitesparse', default=True,
+            description='Enables SuiteSparse support')
+    variant('mpfr', default=True,
+            description='Enables support for multi-precisions FP via mpfr')
 
     # TODO : dependency on googlehash, superlu, adolc missing
     depends_on('cmake', type='build')
diff --git a/var/spack/repos/builtin/packages/elfutils/package.py b/var/spack/repos/builtin/packages/elfutils/package.py
index ecb5759ddc..ef8c2433c9 100644
--- a/var/spack/repos/builtin/packages/elfutils/package.py
+++ b/var/spack/repos/builtin/packages/elfutils/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Elfutils(Package):
     """elfutils is a collection of various binary tools such as
     eu-objdump, eu-readelf, and other utilities that allow you to
@@ -47,4 +48,3 @@ class Elfutils(Package):
         configure('--prefix=%s' % prefix, '--enable-maintainer-mode')
         make()
         make("install")
-
diff --git a/var/spack/repos/builtin/packages/elpa/package.py b/var/spack/repos/builtin/packages/elpa/package.py
index ae81422495..f28d63f6c3 100644
--- a/var/spack/repos/builtin/packages/elpa/package.py
+++ b/var/spack/repos/builtin/packages/elpa/package.py
@@ -34,7 +34,8 @@ class Elpa(Package):
     homepage = 'http://elpa.mpcdf.mpg.de/'
     url = 'http://elpa.mpcdf.mpg.de/elpa-2015.11.001.tar.gz'
 
-    version('2015.11.001', 'de0f35b7ee7c971fd0dca35c900b87e6', url='http://elpa.mpcdf.mpg.de/elpa-2015.11.001.tar.gz')
+    version('2015.11.001', 'de0f35b7ee7c971fd0dca35c900b87e6',
+            url='http://elpa.mpcdf.mpg.de/elpa-2015.11.001.tar.gz')
 
     variant('openmp', default=False, description='Activates OpenMP support')
 
diff --git a/var/spack/repos/builtin/packages/emacs/package.py b/var/spack/repos/builtin/packages/emacs/package.py
index a9ebd6d42f..94d42a3c9f 100644
--- a/var/spack/repos/builtin/packages/emacs/package.py
+++ b/var/spack/repos/builtin/packages/emacs/package.py
@@ -35,7 +35,8 @@ class Emacs(Package):
     version('24.5', 'd74b597503a68105e61b5b9f6d065b44')
 
     variant('X', default=True, description="Enable a X toolkit (GTK+)")
-    variant('gtkplus', default=False, description="Enable a GTK+ as X toolkit (this variant is ignored if ~X)")
+    variant('gtkplus', default=False,
+            description="Enable a GTK+ as X toolkit (ignored if ~X)")
 
     depends_on('ncurses')
     depends_on('libtiff', when='+X')
diff --git a/var/spack/repos/builtin/packages/environment-modules/package.py b/var/spack/repos/builtin/packages/environment-modules/package.py
index 5d5bb3be02..85594bab47 100644
--- a/var/spack/repos/builtin/packages/environment-modules/package.py
+++ b/var/spack/repos/builtin/packages/environment-modules/package.py
@@ -46,17 +46,18 @@ class EnvironmentModules(Package):
             "--without-tclx",
             "--with-tclx-ver=0.0",
             "--prefix=%s" % prefix,
-            "--with-tcl=%s" % join_path(tcl_spec.prefix, 'lib'),    # It looks for tclConfig.sh
-            "--with-tcl-ver=%d.%d" % (tcl_spec.version.version[0], tcl_spec.version.version[1]),
+            # It looks for tclConfig.sh
+            "--with-tcl=%s" % join_path(tcl_spec.prefix, 'lib'),
+            "--with-tcl-ver=%d.%d" % (tcl_spec.version.version[
+                                      0], tcl_spec.version.version[1]),
             '--disable-debug',
             '--disable-dependency-tracking',
             '--disable-silent-rules',
-            '--disable-versioning', 
+            '--disable-versioning',
             '--datarootdir=%s' % prefix.share,
             'CPPFLAGS=%s' % ' '.join(CPPFLAGS)
         ]
 
-
         configure(*config_args)
         make()
         make('install')
diff --git a/var/spack/repos/builtin/packages/exodusii/package.py b/var/spack/repos/builtin/packages/exodusii/package.py
index eb6c23afeb..15fe1e89a6 100644
--- a/var/spack/repos/builtin/packages/exodusii/package.py
+++ b/var/spack/repos/builtin/packages/exodusii/package.py
@@ -32,17 +32,22 @@ from spack import *
 # TODO: Create installation options for NetCDF that support larger page size
 # TODO: suggested by Exodus (see the repository "README" file).
 
+
 class Exodusii(Package):
-    """Exodus II is a C++/Fortran library developed to store and retrieve data for
-       finite element analyses. It's used for preprocessing (problem definition),
-       postprocessing (results visualization), and data transfer between codes.
-       An Exodus II data file is a random access, machine independent, binary
-       file that is written and read via C, C++, or Fortran API routines."""
+    """Exodus II is a C++/Fortran library developed to store and retrieve
+       data for finite element analyses. It's used for preprocessing
+       (problem definition), postprocessing (results visualization), and
+       data transfer between codes.  An Exodus II data file is a random
+       access, machine independent, binary file that is written and read
+       via C, C++, or Fortran API routines.
+
+    """
 
     homepage = "https://github.com/gsjaardema/seacas"
     url      = "https://github.com/gsjaardema/seacas/archive/master.zip"
 
-    version('2016-02-08', git='https://github.com/gsjaardema/seacas.git', commit='dcf3529')
+    version('2016-02-08',
+            git='https://github.com/gsjaardema/seacas.git', commit='dcf3529')
 
     depends_on('cmake@2.8.7:', type='build')
     depends_on('hdf5~shared~mpi')
@@ -54,11 +59,14 @@ class Exodusii(Package):
         ff = FileFilter('cmake-exodus')
 
         ff.filter('CMAKE_INSTALL_PREFIX:PATH=${ACCESS}',
-            'CMAKE_INSTALL_PREFIX:PATH=%s' % self.spec.prefix, string=True)
+                  'CMAKE_INSTALL_PREFIX:PATH=%s' % self.spec.prefix,
+                  string=True)
         ff.filter('NetCDF_DIR:PATH=${TPL}',
-            'NetCDF_DIR:PATH=%s' % self.spec['netcdf'].prefix, string=True)
+                  'NetCDF_DIR:PATH=%s' % self.spec['netcdf'].prefix,
+                  string=True)
         ff.filter('HDF5_ROOT:PATH=${TPL}',
-            'HDF5_ROOT:PATH=%s' % self.spec['hdf5'].prefix, string=True)
+                  'HDF5_ROOT:PATH=%s' % self.spec['hdf5'].prefix,
+                  string=True)
 
     def install(self, spec, prefix):
         mkdirp('build')
diff --git a/var/spack/repos/builtin/packages/exonerate/package.py b/var/spack/repos/builtin/packages/exonerate/package.py
new file mode 100644
index 0000000000..7921e64058
--- /dev/null
+++ b/var/spack/repos/builtin/packages/exonerate/package.py
@@ -0,0 +1,45 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Exonerate(Package):
+    """Pairwise sequence alignment of DNA and proteins"""
+
+    homepage = "http://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate"
+    url      = "http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/exonerate-2.2.0.tar.gz"
+
+    version('2.4.0', '126fbade003b80b663a1d530c56f1904')
+
+    depends_on('pkg-config', type="build")
+    depends_on('glib')
+
+    parallel = False
+
+    def install(self, spec, prefix):
+        configure('--prefix={0}'.format(prefix), '--disable-debug',
+                  '--disable-dependency-tracking')
+        make()
+        make('install')
diff --git a/var/spack/repos/builtin/packages/expat/package.py b/var/spack/repos/builtin/packages/expat/package.py
index 2a9ac123f3..7d0fdae1d4 100644
--- a/var/spack/repos/builtin/packages/expat/package.py
+++ b/var/spack/repos/builtin/packages/expat/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Expat(Package):
     """<eXpat/> is an XML parser library written in C"""
     homepage = "http://expat.sourceforge.net/"
@@ -39,4 +40,3 @@ class Expat(Package):
             cmake('..', *std_cmake_args)
             make()
             make('install')
-
diff --git a/var/spack/repos/builtin/packages/extrae/package.py b/var/spack/repos/builtin/packages/extrae/package.py
index 84c410e4ba..72bfbe6326 100644
--- a/var/spack/repos/builtin/packages/extrae/package.py
+++ b/var/spack/repos/builtin/packages/extrae/package.py
@@ -25,7 +25,23 @@
 from spack import *
 
 # typical working line with extrae 3.0.1
-# ./configure --prefix=/usr/local --with-mpi=/usr/lib64/mpi/gcc/openmpi --with-unwind=/usr/local --with-papi=/usr --with-dwarf=/usr --with-elf=/usr --with-dyninst=/usr --with-binutils=/usr --with-xml-prefix=/usr --enable-openmp --enable-nanos --enable-pthread --disable-parallel-merge LDFLAGS=-pthread
+# ./configure
+#   --prefix=/usr/local
+#   --with-mpi=/usr/lib64/mpi/gcc/openmpi
+#   --with-unwind=/usr/local
+#   --with-papi=/usr
+#   --with-dwarf=/usr
+#   --with-elf=/usr
+#   --with-dyninst=/usr
+#   --with-binutils=/usr
+#   --with-xml-prefix=/usr
+#   --enable-openmp
+#   --enable-nanos
+#   --enable-pthread
+#   --disable-parallel-merge
+#
+# LDFLAGS=-pthread
+
 
 class Extrae(Package):
     """Extrae is the package devoted to generate tracefiles which can
@@ -55,16 +71,16 @@ class Extrae(Package):
         elif 'mvapich2' in spec:
             mpi = spec['mvapich2']
 
-        configure("--prefix=%s"				% prefix,
-	            "--with-mpi=%s"				% mpi.prefix,
-	            "--with-unwind=%s"			% spec['libunwind'].prefix,
-	            "--with-dyninst=%s"			% spec['dyninst'].prefix,
-	            "--with-boost=%s"			% spec['boost'].prefix,
-	            "--with-dwarf=%s"			% spec['libdwarf'].prefix,
-	            "--with-papi=%s"			% spec['papi'].prefix,
-	            "--with-dyninst-headers=%s"	% spec['dyninst'].prefix.include,
-	            "--with-dyninst-libs=%s"	% spec['dyninst'].prefix.lib)
+        configure("--prefix=%s" % prefix,
+                  "--with-mpi=%s" % mpi.prefix,
+                  "--with-unwind=%s" % spec['libunwind'].prefix,
+                  "--with-dyninst=%s" % spec['dyninst'].prefix,
+                  "--with-boost=%s" % spec['boost'].prefix,
+                  "--with-dwarf=%s" % spec['libdwarf'].prefix,
+                  "--with-papi=%s" % spec['papi'].prefix,
+                  "--with-dyninst-headers=%s" % spec[
+                      'dyninst'].prefix.include,
+                  "--with-dyninst-libs=%s" % spec['dyninst'].prefix.lib)
 
         make()
         make("install", parallel=False)
-
diff --git a/var/spack/repos/builtin/packages/exuberant-ctags/package.py b/var/spack/repos/builtin/packages/exuberant-ctags/package.py
index c49d0624f6..10be30ab8b 100644
--- a/var/spack/repos/builtin/packages/exuberant-ctags/package.py
+++ b/var/spack/repos/builtin/packages/exuberant-ctags/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class ExuberantCtags(Package):
     """The canonical ctags generator"""
     homepage = "ctags.sourceforge.net"
diff --git a/var/spack/repos/builtin/packages/fastx_toolkit/package.py b/var/spack/repos/builtin/packages/fastx_toolkit/package.py
new file mode 100644
index 0000000000..04b4d24b39
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fastx_toolkit/package.py
@@ -0,0 +1,43 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class FastxToolkit(Package):
+    """The FASTX-Toolkit is a collection of command line tools for
+       Short-Reads FASTA/FASTQ files preprocessing."""
+
+    homepage = "http://hannonlab.cshl.edu/fastx_toolkit/"
+    url      = "https://github.com/agordon/fastx_toolkit/releases/download/0.0.14/fastx_toolkit-0.0.14.tar.bz2"
+
+    version('0.0.14', 'bf1993c898626bb147de3d6695c20b40')
+
+    depends_on('libgtextutils')
+
+    def install(self, spec, prefix):
+        configure('--prefix={0}'.format(prefix))
+
+        make()
+        make('install')
diff --git a/var/spack/repos/builtin/packages/fenics/package.py b/var/spack/repos/builtin/packages/fenics/package.py
index 465ab651be..eeeefc540d 100644
--- a/var/spack/repos/builtin/packages/fenics/package.py
+++ b/var/spack/repos/builtin/packages/fenics/package.py
@@ -36,7 +36,7 @@ class Fenics(Package):
     homepage = "http://fenicsproject.org/"
     url      = "https://bitbucket.org/fenics-project/dolfin/downloads/dolfin-1.6.0.tar.gz"
 
-    base_url = "https://bitbucket.org/fenics-project/{pkg}/downloads/{pkg}-{version}.tar.gz"  # NOQA: ignore E501
+    base_url = "https://bitbucket.org/fenics-project/{pkg}/downloads/{pkg}-{version}.tar.gz"
 
     variant('hdf5',         default=True,  description='Compile with HDF5')
     variant('parmetis',     default=True,  description='Compile with ParMETIS')
@@ -44,13 +44,18 @@ class Fenics(Package):
     variant('petsc',        default=True,  description='Compile with PETSc')
     variant('slepc',        default=True,  description='Compile with SLEPc')
     variant('trilinos',     default=True,  description='Compile with Trilinos')
-    variant('suite-sparse', default=True,  description='Compile with SuiteSparse solvers')
+    variant('suite-sparse', default=True,
+            description='Compile with SuiteSparse solvers')
     variant('vtk',          default=False, description='Compile with VTK')
     variant('qt',           default=False, description='Compile with QT')
-    variant('mpi',          default=True,  description='Enables the distributed memory support')
-    variant('openmp',       default=True,  description='Enables the shared memory support')
-    variant('shared',       default=True,  description='Enables the build of shared libraries')
-    variant('debug',        default=False, description='Builds a debug version of the libraries')
+    variant('mpi',          default=True,
+            description='Enables the distributed memory support')
+    variant('openmp',       default=True,
+            description='Enables the shared memory support')
+    variant('shared',       default=True,
+            description='Enables the build of shared libraries')
+    variant('debug',        default=False,
+            description='Builds a debug version of the libraries')
 
     # not part of spack list for now
     # variant('petsc4py',     default=True,  description='Uses PETSc4py')
@@ -109,7 +114,8 @@ class Fenics(Package):
     ]
 
     for release in releases:
-        version(release['version'], release['md5'], url=base_url.format(pkg='dolfin', version=release['version']))
+        version(release['version'], release['md5'], url=base_url.format(
+            pkg='dolfin', version=release['version']))
         for name, md5 in release['resources'].items():
             resource(name=name,
                      url=base_url.format(pkg=name, **release),
diff --git a/var/spack/repos/builtin/packages/fftw/package.py b/var/spack/repos/builtin/packages/fftw/package.py
index 434aeea616..570cd1bbdd 100644
--- a/var/spack/repos/builtin/packages/fftw/package.py
+++ b/var/spack/repos/builtin/packages/fftw/package.py
@@ -28,26 +28,36 @@ from spack import *
 
 
 class Fftw(Package):
-    """
-    FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of
-    arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine
-    transforms or DCT/DST). We believe that FFTW, which is free software, should become the FFT library of choice for
-    most applications.
+    """FFTW is a C subroutine library for computing the discrete Fourier
+       transform (DFT) in one or more dimensions, of arbitrary input
+       size, and of both real and complex data (as well as of even/odd
+       data, i.e. the discrete cosine/sine transforms or DCT/DST). We
+       believe that FFTW, which is free software, should become the FFT
+       library of choice for most applications.
+
     """
     homepage = "http://www.fftw.org"
     url      = "http://www.fftw.org/fftw-3.3.4.tar.gz"
 
     version('3.3.4', '2edab8c06b24feeb3b82bbb3ebf3e7b3')
 
-    variant('float', default=True, description='Produces a single precision version of the library')
-    variant('long_double', default=True, description='Produces a long double precision version of the library')
-    variant('quad', default=False, description='Produces a quad precision version of the library (works only with GCC and libquadmath)')
+    variant(
+        'float', default=True,
+        description='Produces a single precision version of the library')
+    variant(
+        'long_double', default=True,
+        description='Produces a long double precision version of the library')
+    variant(
+        'quad', default=False,
+        description='Produces a quad precision version of the library '
+                    '(works only with GCC and libquadmath)')
     variant('openmp', default=False, description="Enable OpenMP support.")
     variant('mpi', default=False, description='Activate MPI support')
 
     depends_on('mpi', when='+mpi')
 
-    # TODO : add support for architecture specific optimizations as soon as targets are supported
+    # TODO : add support for architecture specific optimizations as soon as
+    # targets are supported
 
     def install(self, spec, prefix):
         options = ['--prefix=%s' % prefix,
@@ -57,9 +67,9 @@ class Fftw(Package):
         if '+openmp' in spec:
             # Note: Apple's Clang does not support OpenMP.
             if spec.satisfies('%clang'):
-              ver = str(self.compiler.version)
-              if ver.endswith('-apple'):
-                raise InstallError("Apple's clang does not support OpenMP")
+                ver = str(self.compiler.version)
+                if ver.endswith('-apple'):
+                    raise InstallError("Apple's clang does not support OpenMP")
             options.append('--enable-openmp')
         if not self.compiler.f77 or not self.compiler.fc:
             options.append("--disable-fortran")
diff --git a/var/spack/repos/builtin/packages/fish/package.py b/var/spack/repos/builtin/packages/fish/package.py
index 9d23a3d63d..0e85f410c1 100644
--- a/var/spack/repos/builtin/packages/fish/package.py
+++ b/var/spack/repos/builtin/packages/fish/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Fish(Package):
     """fish is a smart and user-friendly command line shell for OS X, Linux, and
     the rest of the family.
diff --git a/var/spack/repos/builtin/packages/fltk/package.py b/var/spack/repos/builtin/packages/fltk/package.py
index f8ac5bc2a4..f29b64b02b 100644
--- a/var/spack/repos/builtin/packages/fltk/package.py
+++ b/var/spack/repos/builtin/packages/fltk/package.py
@@ -26,13 +26,16 @@ from spack import *
 
 
 class Fltk(Package):
-    """
-    FLTK (pronounced "fulltick") is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and
-    MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its
-    built-in GLUT emulation.
+    """FLTK (pronounced "fulltick") is a cross-platform C++ GUI toolkit for
+       UNIX/Linux (X11), Microsoft Windows, and MacOS X. FLTK provides
+       modern GUI functionality without the bloat and supports 3D
+       graphics via OpenGL and its built-in GLUT emulation.
+
+       FLTK is designed to be small and modular enough to be statically
+       linked, but works fine as a shared library. FLTK also includes an
+       excellent UI builder called FLUID that can be used to create
+       applications in minutes.
 
-    FLTK is designed to be small and modular enough to be statically linked, but works fine as a shared library. FLTK
-    also includes an excellent UI builder called FLUID that can be used to create applications in minutes.
     """
     homepage = 'http://www.fltk.org/'
     url = 'http://fltk.org/pub/fltk/1.3.3/fltk-1.3.3-source.tar.gz'
@@ -41,7 +44,8 @@ class Fltk(Package):
 
     patch('font.patch', when='@1.3.3')
 
-    variant('shared', default=True, description='Enables the build of shared libraries')
+    variant('shared', default=True,
+            description='Enables the build of shared libraries')
 
     def install(self, spec, prefix):
         options = ['--prefix=%s' % prefix,
diff --git a/var/spack/repos/builtin/packages/flux/package.py b/var/spack/repos/builtin/packages/flux/package.py
index dec339a6af..2fd2392b5e 100644
--- a/var/spack/repos/builtin/packages/flux/package.py
+++ b/var/spack/repos/builtin/packages/flux/package.py
@@ -25,13 +25,15 @@
 from spack import *
 import os
 
+
 class Flux(Package):
     """ A next-generation resource manager (pre-alpha) """
 
     homepage = "https://github.com/flux-framework/flux-core"
     url      = "https://github.com/flux-framework/flux-core"
 
-    version('master', branch='master', git='https://github.com/flux-framework/flux-core')
+    version('master', branch='master',
+            git='https://github.com/flux-framework/flux-core')
 
     # Also needs autotools, but should use the system version if available
     depends_on("zeromq@4.0.4:")
@@ -52,12 +54,11 @@ class Flux(Package):
         # Bootstrap with autotools
         bash = which('bash')
         bash('./autogen.sh')
-        bash('./autogen.sh') #yes, twice, intentionally
+        bash('./autogen.sh')  # yes, twice, intentionally
 
         # Fix asciidoc dependency on xml style sheets and whatnot
-        os.environ['XML_CATALOG_FILES'] = os.path.join(spec['docbook-xml'].prefix,
-                                                       'catalog.xml')
+        os.environ['XML_CATALOG_FILES'] = os.path.join(
+            spec['docbook-xml'].prefix, 'catalog.xml')
         # Configure, compile & install
         configure("--prefix=" + prefix)
         make("install", "V=1")
-
diff --git a/var/spack/repos/builtin/packages/foam-extend/package.py b/var/spack/repos/builtin/packages/foam-extend/package.py
index 0ff5765895..6b3b87a110 100644
--- a/var/spack/repos/builtin/packages/foam-extend/package.py
+++ b/var/spack/repos/builtin/packages/foam-extend/package.py
@@ -16,12 +16,24 @@ class FoamExtend(Package):
     version('3.0', git='http://git.code.sf.net/p/foam-extend/foam-extend-3.0')
 
     variant('paraview', default=False, description='Enable ParaFOAM')
-    variant('scotch', default=True, description='Activate Scotch as a possible decomposition library')
-    variant('ptscotch', default=True, description='Activate PT-Scotch as a possible decomposition library')
-    variant('metis', default=True, description='Activate Metis as a possible decomposition library')
-    variant('parmetis', default=True, description='Activate Parmetis as a possible decomposition library')
-    variant('parmgridgen', default=True, description='Activate Parmgridgen support')
-    variant('source', default=True, description='Installs also the source folder')
+    variant(
+        'scotch', default=True,
+        description='Activate Scotch as a possible decomposition library')
+    variant(
+        'ptscotch', default=True,
+        description='Activate PT-Scotch as a possible decomposition library')
+    variant(
+        'metis', default=True,
+        description='Activate Metis as a possible decomposition library')
+    variant(
+        'parmetis', default=True,
+        description='Activate Parmetis as a possible decomposition library')
+    variant(
+        'parmgridgen', default=True,
+        description='Activate Parmgridgen support')
+    variant(
+        'source', default=True,
+        description='Installs also the source folder')
 
     supported_compilers = {'clang': 'Clang', 'gcc': 'Gcc', 'intel': 'Icc'}
 
@@ -80,7 +92,7 @@ class FoamExtend(Package):
             filter_file(
                 r'-lMGridGen',
                 r'-lmgrid',
-                'src/fvAgglomerationMethods/MGridGenGamgAgglomeration/Make/options')  # NOQA: ignore=501
+                'src/fvAgglomerationMethods/MGridGenGamgAgglomeration/Make/options')  # noqa
 
         # Get the wmake arch and compiler
         (arch, foam_compiler) = self.set_arch()
diff --git a/var/spack/repos/builtin/packages/fontconfig/package.py b/var/spack/repos/builtin/packages/fontconfig/package.py
index 76e9d8cb3f..0d7e47f228 100644
--- a/var/spack/repos/builtin/packages/fontconfig/package.py
+++ b/var/spack/repos/builtin/packages/fontconfig/package.py
@@ -24,12 +24,13 @@
 ##############################################################################
 from spack import *
 
+
 class Fontconfig(Package):
     """Fontconfig customizing font access"""
     homepage = "http://www.freedesktop.org/wiki/Software/fontconfig/"
     url      = "http://www.freedesktop.org/software/fontconfig/release/fontconfig-2.11.1.tar.gz"
 
-    version('2.11.1' , 'e75e303b4f7756c2b16203a57ac87eba')
+    version('2.11.1', 'e75e303b4f7756c2b16203a57ac87eba')
 
     depends_on('freetype')
     depends_on('libxml2')
diff --git a/var/spack/repos/builtin/packages/gasnet/package.py b/var/spack/repos/builtin/packages/gasnet/package.py
index b3bd6c25f2..12ecd9fd6f 100644
--- a/var/spack/repos/builtin/packages/gasnet/package.py
+++ b/var/spack/repos/builtin/packages/gasnet/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Gasnet(Package):
     """GASNet is a language-independent, low-level networking layer
        that provides network-independent, high-performance communication
@@ -36,24 +37,24 @@ class Gasnet(Package):
 
     version('1.24.0', 'c8afdf48381e8b5a7340bdb32ca0f41a')
 
-
     def install(self, spec, prefix):
         # TODO: don't use paths with @ in them.
         change_sed_delimiter('@', ';', 'configure')
 
-        configure("--prefix=%s" % prefix,
-                  # TODO: factor IB suport out into architecture description.
-                  "--enable-ibv",
-                  "--enable-udp",
-                  "--disable-mpi",
-                  "--enable-par",
-                  "--enable-mpi-compat",
-                  "--enable-segment-fast",
-                  "--disable-aligned-segments",
-                  # TODO: make an option so that Legion can request builds with/without this.
-                  # See the Legion webpage for details on when to/not to use.
-                  "--disable-pshm",
-                  "--with-segment-mmap-max=64MB")
+        configure(
+            "--prefix=%s" % prefix,
+            # TODO: factor IB suport out into architecture description.
+            "--enable-ibv",
+            "--enable-udp",
+            "--disable-mpi",
+            "--enable-par",
+            "--enable-mpi-compat",
+            "--enable-segment-fast",
+            "--disable-aligned-segments",
+            # TODO: make option so Legion can request builds with/without this.
+            # See the Legion webpage for details on when to/not to use.
+            "--disable-pshm",
+            "--with-segment-mmap-max=64MB")
 
         make()
         make("install")
diff --git a/var/spack/repos/builtin/packages/gcc/package.py b/var/spack/repos/builtin/packages/gcc/package.py
index 224105ea0f..72a5cb22f8 100644
--- a/var/spack/repos/builtin/packages/gcc/package.py
+++ b/var/spack/repos/builtin/packages/gcc/package.py
@@ -15,6 +15,7 @@ class Gcc(Package):
     list_depth = 2
 
     version('6.1.0', '8fb6cb98b8459f5863328380fbf06bd1')
+    version('5.4.0', '4c626ac2a83ef30dfb9260e6f59c2b30')
     version('5.3.0', 'c9616fd448f980259c31de613e575719')
     version('5.2.0', 'a51bcfeb3da7dd4c623e27207ed43467')
     version('4.9.3', '6f831b4d251872736e8e9cc09746f327')
diff --git a/var/spack/repos/builtin/packages/gdal/package.py b/var/spack/repos/builtin/packages/gdal/package.py
index 9ed83bc3be..4fdfafc992 100644
--- a/var/spack/repos/builtin/packages/gdal/package.py
+++ b/var/spack/repos/builtin/packages/gdal/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Gdal(Package):
     """
     GDAL is a translator library for raster and vector geospatial
diff --git a/var/spack/repos/builtin/packages/gdb/package.py b/var/spack/repos/builtin/packages/gdb/package.py
index 78ad4b307d..9145009fa4 100644
--- a/var/spack/repos/builtin/packages/gdb/package.py
+++ b/var/spack/repos/builtin/packages/gdb/package.py
@@ -27,9 +27,10 @@ from spack import *
 
 
 class Gdb(Package):
-    """
-    GDB, the GNU Project debugger, allows you to see what is going on `inside' another program while it executes
-    -- or what another program was doing at the moment it crashed.
+    """GDB, the GNU Project debugger, allows you to see what is going on
+       `inside' another program while it executes -- or what another
+       program was doing at the moment it crashed.
+
     """
     homepage = "https://www.gnu.org/software/gdb"
     url = "http://ftp.gnu.org/gnu/gdb/gdb-7.10.tar.gz"
diff --git a/var/spack/repos/builtin/packages/gdk-pixbuf/package.py b/var/spack/repos/builtin/packages/gdk-pixbuf/package.py
index daf43f3256..d7a0200395 100644
--- a/var/spack/repos/builtin/packages/gdk-pixbuf/package.py
+++ b/var/spack/repos/builtin/packages/gdk-pixbuf/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class GdkPixbuf(Package):
     """The Gdk Pixbuf is a toolkit for image loading and pixel buffer
        manipulation. It is used by GTK+ 2 and GTK+ 3 to load and
diff --git a/var/spack/repos/builtin/packages/geos/package.py b/var/spack/repos/builtin/packages/geos/package.py
index 88438b0a99..324186cfbc 100644
--- a/var/spack/repos/builtin/packages/geos/package.py
+++ b/var/spack/repos/builtin/packages/geos/package.py
@@ -23,7 +23,7 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
-import os
+
 
 class Geos(Package):
     """GEOS (Geometry Engine - Open Source) is a C++ port of the Java
diff --git a/var/spack/repos/builtin/packages/gettext/package.py b/var/spack/repos/builtin/packages/gettext/package.py
index df301aea3c..cf260c3f8a 100644
--- a/var/spack/repos/builtin/packages/gettext/package.py
+++ b/var/spack/repos/builtin/packages/gettext/package.py
@@ -24,31 +24,80 @@
 ##############################################################################
 from spack import *
 
+
 class Gettext(Package):
     """GNU internationalization (i18n) and localization (l10n) library."""
     homepage = "https://www.gnu.org/software/gettext/"
     url      = "http://ftpmirror.gnu.org/gettext/gettext-0.19.7.tar.xz"
 
-    version('0.19.7', 'f81e50556da41b44c1d59ac93474dca5')
+    version('0.19.8.1', 'df3f5690eaa30fd228537b00cb7b7590')
+    version('0.19.7',   'f81e50556da41b44c1d59ac93474dca5')
+
+    # Recommended variants
+    variant('curses',   default=True, description='Use libncurses')
+    variant('libxml2',  default=True, description='Use libxml2')
+    variant('git',      default=True, description='Enable git support')
+    variant('tar',      default=True, description='Enable tar support')
+    variant('bzip2',    default=True, description='Enable bzip2 support')
+    variant('xz',       default=True, description='Enable xz support')
+
+    # Optional variants
+    variant('libunistring', default=False, description='Use libunistring')
+
+    # Recommended dependencies
+    depends_on('ncurses',  when='+curses')
+    depends_on('libxml2',  when='+libxml2')
+    # Java runtime and compiler (e.g. GNU gcj or kaffe)
+    # C# runtime and compiler (e.g. pnet or mono)
+    depends_on('tar',      when='+tar')
+    # depends_on('gzip',     when='+gzip')
+    depends_on('bzip2',    when='+bzip2')
+    depends_on('xz',       when='+xz')
+
+    # Optional dependencies
+    # depends_on('glib')  # circular dependency?
+    # depends_on('libcroco@0.6.1:')
+    depends_on('libunistring', when='+libunistring')
+    # depends_on('cvs')
 
     def install(self, spec, prefix):
-        options = ['--disable-dependency-tracking',
-                   '--disable-silent-rules',
-                   '--disable-debug',
-                   '--prefix=%s' % prefix,
-                   '--with-included-gettext',
-                   '--with-included-glib',
-                   '--with-included-libcroco',
-                   '--with-included-libunistring',
-                   '--with-emacs',
-                   '--with-lispdir=%s/emacs/site-lisp/gettext' % prefix.share,
-                   '--disable-java',
-                   '--disable-csharp',
-                   '--without-git', # Don't use VCS systems to create these archives
-                   '--without-cvs',
-                   '--without-xz']
-
-        configure(*options)
+        config_args = [
+            '--prefix={0}'.format(prefix),
+            '--disable-java',
+            '--disable-csharp',
+            '--with-included-glib',
+            '--with-included-gettext',
+            '--with-included-libcroco',
+            '--without-emacs',
+            '--with-lispdir=%s/emacs/site-lisp/gettext' % prefix.share,
+            '--without-cvs'
+        ]
+
+        if '+curses' in spec:
+            config_args.append('--with-ncurses-prefix={0}'.format(
+                spec['ncurses'].prefix))
+        else:
+            config_args.append('--disable-curses')
+
+        if '+libxml2' in spec:
+            config_args.append('--with-libxml2-prefix={0}'.format(
+                spec['libxml2'].prefix))
+        else:
+            config_args.append('--with-included-libxml')
+
+        if '+bzip2' not in spec:
+            config_args.append('--without-bzip2')
+
+        if '+xz' not in spec:
+            config_args.append('--without-xz')
+
+        if '+libunistring' in spec:
+            config_args.append('--with-libunistring-prefix={0}'.format(
+                spec['libunistring'].prefix))
+        else:
+            config_args.append('--with-included-libunistring')
+
+        configure(*config_args)
 
         make()
         make("install")
diff --git a/var/spack/repos/builtin/packages/gflags/package.py b/var/spack/repos/builtin/packages/gflags/package.py
index 47bbf369ef..7e04c9b682 100644
--- a/var/spack/repos/builtin/packages/gflags/package.py
+++ b/var/spack/repos/builtin/packages/gflags/package.py
@@ -22,9 +22,9 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import os
 from spack import *
 
+
 class Gflags(Package):
     """The gflags package contains a C++ library that implements
     commandline flags processing. It includes built-in support for
diff --git a/var/spack/repos/builtin/packages/git/package.py b/var/spack/repos/builtin/packages/git/package.py
index 4cbbaac342..3cc879088d 100644
--- a/var/spack/repos/builtin/packages/git/package.py
+++ b/var/spack/repos/builtin/packages/git/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Git(Package):
     """Git is a free and open source distributed version control
        system designed to handle everything from small to very large
@@ -36,40 +37,36 @@ class Git(Package):
     version('2.7.3', 'fa1c008b56618c355a32ba4a678305f6')
     version('2.7.1', 'bf0706b433a8dedd27a63a72f9a66060')
 
-
     # See here for info on vulnerable Git versions:
     # http://www.theregister.co.uk/2016/03/16/git_server_client_patch_now/
     # All the following are vulnerable
-    #version('2.6.3', 'b711be7628a4a2c25f38d859ee81b423')
-    #version('2.6.2', 'da293290da69f45a86a311ad3cd43dc8')
-    #version('2.6.1', '4c62ee9c5991fe93d99cf2a6b68397fd')
-    #version('2.6.0', 'eb76a07148d94802a1745d759716a57e')
-    #version('2.5.4', '3eca2390cf1fa698b48e2a233563a76b')
-    #version('2.2.1', 'ff41fdb094eed1ec430aed8ee9b9849c')
-
+    # version('2.6.3', 'b711be7628a4a2c25f38d859ee81b423')
+    # version('2.6.2', 'da293290da69f45a86a311ad3cd43dc8')
+    # version('2.6.1', '4c62ee9c5991fe93d99cf2a6b68397fd')
+    # version('2.6.0', 'eb76a07148d94802a1745d759716a57e')
+    # version('2.5.4', '3eca2390cf1fa698b48e2a233563a76b')
+    # version('2.2.1', 'ff41fdb094eed1ec430aed8ee9b9849c')
 
     depends_on("openssl")
     depends_on("autoconf", type='build')
     depends_on("curl")
     depends_on("expat")
-
-    # Also depends_on gettext: apt-get install gettext (Ubuntu)
-
-    # Use system perl for now.
-    # depends_on("perl")
-    # depends_on("pcre")
-
+    depends_on("gettext")
     depends_on("zlib")
+    depends_on("pcre")
+    depends_on("perl")
 
     def install(self, spec, prefix):
+        env['LDFLAGS'] = "-L%s" % spec['gettext'].prefix.lib + " -lintl"
         configure_args = [
             "--prefix=%s" % prefix,
-            "--without-pcre",
+            "--with-libpcre=%s" % spec['pcre'].prefix,
             "--with-openssl=%s" % spec['openssl'].prefix,
             "--with-zlib=%s" % spec['zlib'].prefix,
             "--with-curl=%s" % spec['curl'].prefix,
             "--with-expat=%s" % spec['expat'].prefix,
-            ]
+            "--with-perl=%s" % join_path(spec['perl'].prefix.bin, 'perl'),
+        ]
 
         which('autoreconf')('-i')
         configure(*configure_args)
diff --git a/var/spack/repos/builtin/packages/gl2ps/package.py b/var/spack/repos/builtin/packages/gl2ps/package.py
index 25172bd544..d5e7b00027 100644
--- a/var/spack/repos/builtin/packages/gl2ps/package.py
+++ b/var/spack/repos/builtin/packages/gl2ps/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Gl2ps(Package):
     """GL2PS is a C library providing high quality vector output for any
     OpenGL application."""
diff --git a/var/spack/repos/builtin/packages/glib/package.py b/var/spack/repos/builtin/packages/glib/package.py
index 0a0a02f464..2720831e4f 100644
--- a/var/spack/repos/builtin/packages/glib/package.py
+++ b/var/spack/repos/builtin/packages/glib/package.py
@@ -23,7 +23,6 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
-import sys
 
 
 class Glib(Package):
@@ -32,17 +31,24 @@ class Glib(Package):
        and interfaces for such runtime functionality as an event loop,
        threads, dynamic loading and an object system."""
     homepage = "https://developer.gnome.org/glib/"
-    url = "http://ftp.gnome.org/pub/gnome/sources/glib/2.42/glib-2.42.1.tar.xz"
+    url      = "http://ftp.gnome.org/pub/gnome/sources/glib/2.42/glib-2.42.1.tar.xz"
 
+    version('2.49.4', 'e2c87c03017b0cd02c4c73274b92b148')
     version('2.42.1', '89c4119e50e767d3532158605ee9121a')
 
-    depends_on("libffi")
-    depends_on("zlib")
-    depends_on("pkg-config", type='build')
-    depends_on('gettext', when=sys.platform == 'darwin')
+    depends_on('libffi')
+    depends_on('zlib')
+    depends_on('pkg-config', type='build')
+    depends_on('gettext')
+    depends_on('pcre+utf', when='@2.49:')
 
     # The following patch is needed for gcc-6.1
-    patch('g_date_strftime.patch')
+    patch('g_date_strftime.patch', when='@2.42.1')
+
+    def url_for_version(self, version):
+        """Handle glib's version-based custom URLs."""
+        url = 'http://ftp.gnome.org/pub/gnome/sources/glib'
+        return url + '/%s/glib-%s.tar.xz' % (version.up_to(2), version)
 
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
diff --git a/var/spack/repos/builtin/packages/glm/package.py b/var/spack/repos/builtin/packages/glm/package.py
index 442c1cdf40..c565b3cae7 100644
--- a/var/spack/repos/builtin/packages/glm/package.py
+++ b/var/spack/repos/builtin/packages/glm/package.py
@@ -26,9 +26,10 @@ from spack import *
 
 
 class Glm(Package):
-    """
-    OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics software based on
-    the OpenGL Shading Language (GLSL) specification.
+    """OpenGL Mathematics (GLM) is a header only C++ mathematics library for
+       graphics software based on the OpenGL Shading Language (GLSL)
+       specification.
+
     """
 
     homepage = "https://github.com/g-truc/glm"
diff --git a/var/spack/repos/builtin/packages/glog/package.py b/var/spack/repos/builtin/packages/glog/package.py
index 03ee092429..14f042732b 100644
--- a/var/spack/repos/builtin/packages/glog/package.py
+++ b/var/spack/repos/builtin/packages/glog/package.py
@@ -22,9 +22,9 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import os
 from spack import *
 
+
 class Glog(Package):
     """C++ implementation of the Google logging module."""
 
diff --git a/var/spack/repos/builtin/packages/glpk/package.py b/var/spack/repos/builtin/packages/glpk/package.py
index 2ab3c38150..1b52643e59 100644
--- a/var/spack/repos/builtin/packages/glpk/package.py
+++ b/var/spack/repos/builtin/packages/glpk/package.py
@@ -22,22 +22,23 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-
 from spack import *
 
 
 class Glpk(Package):
-    """
-    The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear programming (LP), mixed
-    integer programming (MIP), and other related problems. It is a set of routines written in ANSI C and organized in
-    the form of a callable library
+    """The GLPK (GNU Linear Programming Kit) package is intended for solving
+       large-scale linear programming (LP), mixed integer programming
+       (MIP), and other related problems. It is a set of routines written
+       in ANSI C and organized in the form of a callable library
+
     """
     homepage = "https://www.gnu.org/software/glpk"
     url = "http://ftp.gnu.org/gnu/glpk/glpk-4.57.tar.gz"
 
     version('4.57', '237531a54f73155842f8defe51aedb0f')
 
-    variant('gmp', default=False, description='Activates support for GMP library')
+    variant('gmp', default=False,
+            description='Activates support for GMP library')
 
     depends_on('gmp', when='+gmp')
 
diff --git a/var/spack/repos/builtin/packages/gmp/package.py b/var/spack/repos/builtin/packages/gmp/package.py
index 9bec5a14c9..bd1f653bd7 100644
--- a/var/spack/repos/builtin/packages/gmp/package.py
+++ b/var/spack/repos/builtin/packages/gmp/package.py
@@ -32,8 +32,9 @@ class Gmp(AutotoolsPackage):
     homepage = "https://gmplib.org"
     url = "https://gmplib.org/download/gmp/gmp-6.0.0a.tar.bz2"
 
-    version('6.1.0' , '86ee6e54ebfc4a90b643a65e402c4048')
+    version('6.1.1',  '4c175f86e11eb32d8bf9872ca3a8e11d')
+    version('6.1.0',  '86ee6e54ebfc4a90b643a65e402c4048')
     version('6.0.0a', 'b7ff2d88cae7f8085bd5006096eed470')
-    version('6.0.0' , '6ef5869ae735db9995619135bd856b84')
+    version('6.0.0',  '6ef5869ae735db9995619135bd856b84')
 
     depends_on("m4", type='build')
diff --git a/var/spack/repos/builtin/packages/gmsh/package.py b/var/spack/repos/builtin/packages/gmsh/package.py
index fe26cb3bf2..72f490e2f4 100644
--- a/var/spack/repos/builtin/packages/gmsh/package.py
+++ b/var/spack/repos/builtin/packages/gmsh/package.py
@@ -41,15 +41,21 @@ class Gmsh(Package):
     version('2.12.0', '7fbd2ec8071e79725266e72744d21e902d4fe6fa9e7c52340ad5f4be5c159d09')
     version('2.11.0', 'f15b6e7ac9ca649c9a74440e1259d0db')
 
-    variant('shared',      default=True,  description='Enables the build of shared libraries')
-    variant('debug',       default=False, description='Builds the library in debug mode')
-    variant('mpi',         default=False, description='Builds MPI support for parser and solver')
-    variant('fltk',        default=False, description='Enables the build of the FLTK GUI')
+    variant('shared',      default=True,
+            description='Enables the build of shared libraries')
+    variant('debug',       default=False,
+            description='Builds the library in debug mode')
+    variant('mpi',         default=False,
+            description='Builds MPI support for parser and solver')
+    variant('fltk',        default=False,
+            description='Enables the build of the FLTK GUI')
     variant('hdf5',        default=False, description='Enables HDF5 support')
-    variant('compression', default=True,  description='Enables IO compression through zlib')
+    variant('compression', default=True,
+            description='Enables IO compression through zlib')
     variant('oce',         default=False, description='Build with OCE')
     variant('petsc',       default=False, description='Build with PETSc')
-    variant('slepc',       default=False, description='Build with SLEPc (only when PETSc is enabled)')
+    variant('slepc',       default=False,
+            description='Build with SLEPc (only when PETSc is enabled)')
 
     depends_on('blas')
     depends_on('lapack')
diff --git a/var/spack/repos/builtin/packages/gnu-prolog/package.py b/var/spack/repos/builtin/packages/gnu-prolog/package.py
index f497ed3001..1e0487c654 100644
--- a/var/spack/repos/builtin/packages/gnu-prolog/package.py
+++ b/var/spack/repos/builtin/packages/gnu-prolog/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class GnuProlog(Package):
     """A free Prolog compiler with constraint solving over finite domains."""
     homepage = "http://www.gprolog.org/"
diff --git a/var/spack/repos/builtin/packages/gnuplot/package.py b/var/spack/repos/builtin/packages/gnuplot/package.py
index a76677e066..600b6d285f 100644
--- a/var/spack/repos/builtin/packages/gnuplot/package.py
+++ b/var/spack/repos/builtin/packages/gnuplot/package.py
@@ -27,13 +27,18 @@ from spack import *
 
 import os
 
+
 class Gnuplot(Package):
-    """
-    Gnuplot is a portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other
-    platforms. The source code is copyrighted but freely distributed (i.e., you don't have to pay for it). It was
-    originally created to allow scientists and students to visualize mathematical functions and data interactively,
-    but has grown to support many non-interactive uses such as web scripting. It is also used as a plotting engine by
-    third-party applications like Octave. Gnuplot has been supported and under active development since 1986
+    """Gnuplot is a portable command-line driven graphing utility for Linux,
+       OS/2, MS Windows, OSX, VMS, and many other platforms. The source
+       code is copyrighted but freely distributed (i.e., you don't have
+       to pay for it). It was originally created to allow scientists and
+       students to visualize mathematical functions and data
+       interactively, but has grown to support many non-interactive uses
+       such as web scripting. It is also used as a plotting engine by
+       third-party applications like Octave. Gnuplot has been supported
+       and under active development since 1986
+
     """
     homepage = "http://www.gnuplot.info"
     url      = "http://downloads.sourceforge.net/project/gnuplot/gnuplot/5.0.1/gnuplot-5.0.1.tar.gz"
diff --git a/var/spack/repos/builtin/packages/gnutls/package.py b/var/spack/repos/builtin/packages/gnutls/package.py
index 71b571bc88..5f7b0daf9b 100644
--- a/var/spack/repos/builtin/packages/gnutls/package.py
+++ b/var/spack/repos/builtin/packages/gnutls/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Gnutls(Package):
     """GnuTLS is a secure communications library implementing the SSL,
        TLS and DTLS protocols and technologies around them. It
diff --git a/var/spack/repos/builtin/packages/googletest/package.py b/var/spack/repos/builtin/packages/googletest/package.py
index 1dc74fbcf4..6f3cafec06 100644
--- a/var/spack/repos/builtin/packages/googletest/package.py
+++ b/var/spack/repos/builtin/packages/googletest/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Googletest(Package):
     """Google test framework for C++.  Also called gtest."""
     homepage = "https://github.com/google/googletest"
@@ -40,9 +41,8 @@ class Googletest(Package):
 
         # Google Test doesn't have a make install
         # We have to do our own install here.
-	install_tree('include', prefix.include)
+        install_tree('include', prefix.include)
 
         mkdirp(prefix.lib)
-	install('./libgtest.a', '%s' % prefix.lib)
-	install('./libgtest_main.a', '%s' % prefix.lib)
-
+        install('./libgtest.a', '%s' % prefix.lib)
+        install('./libgtest_main.a', '%s' % prefix.lib)
diff --git a/var/spack/repos/builtin/packages/gperf/package.py b/var/spack/repos/builtin/packages/gperf/package.py
index af176afcf6..0e54d0e037 100644
--- a/var/spack/repos/builtin/packages/gperf/package.py
+++ b/var/spack/repos/builtin/packages/gperf/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Gperf(Package):
     """GNU gperf is a perfect hash function generator. For a given
     list of strings, it produces a hash function and hash table, in
diff --git a/var/spack/repos/builtin/packages/gperftools/package.py b/var/spack/repos/builtin/packages/gperftools/package.py
index 1f17ab71a4..c6ca6c8057 100644
--- a/var/spack/repos/builtin/packages/gperftools/package.py
+++ b/var/spack/repos/builtin/packages/gperftools/package.py
@@ -24,14 +24,20 @@
 ##############################################################################
 from spack import *
 
+
 class Gperftools(Package):
-    """Google's fast malloc/free implementation, especially for multi-threaded applications.
-       Contains tcmalloc, heap-checker, heap-profiler, and cpu-profiler."""
+    """Google's fast malloc/free implementation, especially for
+       multi-threaded applications.  Contains tcmalloc, heap-checker,
+       heap-profiler, and cpu-profiler.
+
+    """
     homepage = "https://code.google.com/p/gperftools"
     url      = "https://googledrive.com/host/0B6NtGsLhIcf7MWxMMF9JdTN3UVk/gperftools-2.3.tar.gz"
 
-    version('2.4', '2171cea3bbe053036fb5d5d25176a160', url="https://github.com/gperftools/gperftools/releases/download/gperftools-2.4/gperftools-2.4.tar.gz")
-    version('2.3', 'f54dd119f0e46ac1f13264f8d97adf90', url="https://googledrive.com/host/0B6NtGsLhIcf7MWxMMF9JdTN3UVk/gperftools-2.3.tar.gz")
+    version('2.4', '2171cea3bbe053036fb5d5d25176a160',
+            url="https://github.com/gperftools/gperftools/releases/download/gperftools-2.4/gperftools-2.4.tar.gz")
+    version('2.3', 'f54dd119f0e46ac1f13264f8d97adf90',
+            url="https://googledrive.com/host/0B6NtGsLhIcf7MWxMMF9JdTN3UVk/gperftools-2.3.tar.gz")
 
     depends_on("libunwind")
 
diff --git a/var/spack/repos/builtin/packages/graphlib/package.py b/var/spack/repos/builtin/packages/graphlib/package.py
index 087a322acc..0c3cd9b649 100644
--- a/var/spack/repos/builtin/packages/graphlib/package.py
+++ b/var/spack/repos/builtin/packages/graphlib/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Graphlib(Package):
     """Library to create, manipulate, and export graphs Graphlib."""
     homepage = "http://https://github.com/lee218llnl/graphlib"
diff --git a/var/spack/repos/builtin/packages/graphviz/package.py b/var/spack/repos/builtin/packages/graphviz/package.py
index e5898a6e59..b37121248c 100644
--- a/var/spack/repos/builtin/packages/graphviz/package.py
+++ b/var/spack/repos/builtin/packages/graphviz/package.py
@@ -37,7 +37,9 @@ class Graphviz(Package):
     # related to missing Perl packages. If spack begins support for Perl in the
     # future, this package can be updated to depend_on('perl') and the
     # ncecessary devel packages.
-    variant('perl', default=False, description='Enable if you need the optional Perl language bindings.')  # NOQA: ignore=E501
+    variant(
+        'perl', default=False,
+        description='Enable if you need the optional Perl language bindings.')
 
     parallel = False
 
diff --git a/var/spack/repos/builtin/packages/gromacs/package.py b/var/spack/repos/builtin/packages/gromacs/package.py
index 55eacc8d38..d39c9738ef 100644
--- a/var/spack/repos/builtin/packages/gromacs/package.py
+++ b/var/spack/repos/builtin/packages/gromacs/package.py
@@ -22,19 +22,21 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
+
 from spack import *
 
 
 class Gromacs(Package):
-    """
-    GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics package primarily designed for
-    simulations of proteins, lipids and nucleic acids. It was originally developed in the Biophysical Chemistry
-    department of University of Groningen, and is now maintained by contributors in universities and research centers
-    across the world.
-
-    GROMACS is one of the fastest and most popular software packages available and can run on CPUs as well as GPUs.
-    It is free, open source released under the GNU General Public License. Starting from version 4.6, GROMACS is
-    released under the GNU Lesser General Public License.
+    """GROMACS (GROningen MAchine for Chemical Simulations) is a molecular
+    dynamics package primarily designed for simulations of proteins, lipids
+    and nucleic acids. It was originally developed in the Biophysical
+    Chemistry department of University of Groningen, and is now maintained
+    by contributors in universities and research centers across the world.
+
+    GROMACS is one of the fastest and most popular software packages
+    available and can run on CPUs as well as GPUs. It is free, open source
+    released under the GNU General Public License. Starting from version 4.6,
+    GROMACS is released under the GNU Lesser General Public License.
     """
 
     homepage = 'http://www.gromacs.org'
@@ -43,17 +45,26 @@ class Gromacs(Package):
     version('5.1.2', '614d0be372f1a6f1f36382b7a6fcab98')
 
     variant('mpi', default=True, description='Activate MPI support')
-    variant('shared', default=True, description='Enables the build of shared libraries')
+    variant('shared', default=True,
+            description='Enables the build of shared libraries')
     variant('debug', default=False, description='Enables debug mode')
-    variant('double', default=False, description='Produces a double precision version of the executables')
+    variant(
+        'double', default=False,
+        description='Produces a double precision version of the executables')
+    variant('plumed', default=False, description='Enable PLUMED support')
 
     depends_on('mpi', when='+mpi')
-
+    depends_on('plumed+mpi', when='+plumed+mpi')
+    depends_on('plumed~mpi', when='+plumed~mpi')
     depends_on('fftw')
     depends_on('cmake', type='build')
 
     # TODO : add GPU support
 
+    def patch(self):
+        if '+plumed' in self.spec:
+            self.spec['plumed'].package.apply_patch(self)
+
     def install(self, spec, prefix):
 
         options = []
diff --git a/var/spack/repos/builtin/packages/gsl/package.py b/var/spack/repos/builtin/packages/gsl/package.py
index c1695a6f02..574d3b9402 100644
--- a/var/spack/repos/builtin/packages/gsl/package.py
+++ b/var/spack/repos/builtin/packages/gsl/package.py
@@ -27,17 +27,19 @@ from spack import *
 
 
 class Gsl(Package):
-    """
-    The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. It is free software under the
-    GNU General Public License. The library provides a wide range of mathematical routines such as random number
-    generators, special functions and least-squares fitting. There are over 1000 functions in total with an extensive
-    test suite.
+    """The GNU Scientific Library (GSL) is a numerical library for C and C++
+       programmers. It is free software under the GNU General Public
+       License. The library provides a wide range of mathematical
+       routines such as random number generators, special functions and
+       least-squares fitting. There are over 1000 functions in total with
+       an extensive test suite.
+
     """
     homepage = "http://www.gnu.org/software/gsl"
     url      = "http://mirror.switch.ch/ftp/mirror/gnu/gsl/gsl-2.1.tar.gz"
 
-    version('2.1' , 'd8f70abafd3e9f0bae03c52d1f4e8de5')
-    version('2.0' , 'ae44cdfed78ece40e73411b63a78c375')
+    version('2.1', 'd8f70abafd3e9f0bae03c52d1f4e8de5')
+    version('2.0', 'ae44cdfed78ece40e73411b63a78c375')
     version('1.16', 'e49a664db13d81c968415cd53f62bc8b')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/gtkplus/package.py b/var/spack/repos/builtin/packages/gtkplus/package.py
index c135e89f78..c85bbe4094 100644
--- a/var/spack/repos/builtin/packages/gtkplus/package.py
+++ b/var/spack/repos/builtin/packages/gtkplus/package.py
@@ -24,12 +24,15 @@
 ##############################################################################
 from spack import *
 
+
 class Gtkplus(Package):
-    """The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications."""
+    """The GTK+ 2 package contains libraries used for creating graphical user
+       interfaces for applications."""
     homepage = "http://www.gtk.org"
 
-    version('2.24.25', '612350704dd3aacb95355a4981930c6f',
-            url="http://ftp.gnome.org/pub/gnome/sources/gtk+/2.24/gtk+-2.24.25.tar.xz")
+    version(
+        '2.24.25', '612350704dd3aacb95355a4981930c6f',
+        url="http://ftp.gnome.org/pub/gnome/sources/gtk+/2.24/gtk+-2.24.25.tar.xz")
 
     depends_on("atk")
     depends_on("gdk-pixbuf")
diff --git a/var/spack/repos/builtin/packages/guile/package.py b/var/spack/repos/builtin/packages/guile/package.py
new file mode 100644
index 0000000000..22aff1bddf
--- /dev/null
+++ b/var/spack/repos/builtin/packages/guile/package.py
@@ -0,0 +1,68 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Guile(Package):
+    """Guile is the GNU Ubiquitous Intelligent Language for Extensions,
+    the official extension language for the GNU operating system."""
+
+    homepage = "https://www.gnu.org/software/guile/"
+    url      = "ftp://ftp.gnu.org/gnu/guile/guile-2.0.11.tar.gz"
+
+    version('2.0.11', 'e532c68c6f17822561e3001136635ddd')
+
+    variant('readline', default=True, description='Use the readline library')
+
+    depends_on('gmp@4.2:')
+    depends_on('gettext')
+    depends_on('libtool@1.5.6:')
+    depends_on('libunistring@0.9.3:')
+    depends_on('bdw-gc@7.0:')
+    depends_on('libffi')
+    depends_on('readline', when='+readline')
+    depends_on('pkg-config', type='build')
+
+    def install(self, spec, prefix):
+        config_args = [
+            '--prefix={0}'.format(prefix),
+            '--with-libunistring-prefix={0}'.format(
+                spec['libunistring'].prefix),
+            '--with-libltdl-prefix={0}'.format(spec['libtool'].prefix),
+            '--with-libgmp-prefix={0}'.format(spec['gmp'].prefix),
+            '--with-libintl-prefix={0}'.format(spec['gettext'].prefix)
+        ]
+
+        if '+readline' in spec:
+            config_args.append('--with-libreadline-prefix={0}'.format(
+                spec['readline'].prefix))
+        else:
+            config_args.append('--without-libreadline-prefix')
+
+        configure(*config_args)
+
+        make()
+        make('check')
+        make('install')
diff --git a/var/spack/repos/builtin/packages/harminv/package.py b/var/spack/repos/builtin/packages/harminv/package.py
new file mode 100644
index 0000000000..184535ebb0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/harminv/package.py
@@ -0,0 +1,54 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Harminv(Package):
+    """Harminv is a free program (and accompanying library) to solve the
+    problem of harmonic inversion - given a discrete-time, finite-length
+    signal that consists of a sum of finitely-many sinusoids (possibly
+    exponentially decaying) in a given bandwidth, it determines the
+    frequencies, decay constants, amplitudes, and phases of those sinusoids."""
+
+    homepage = "http://ab-initio.mit.edu/wiki/index.php/Harminv"
+    url      = "http://ab-initio.mit.edu/harminv/harminv-1.4.tar.gz"
+
+    version('1.4', 'b95e24a9bc7e07d3d2202d1605e9e86f')
+
+    depends_on('blas')
+    depends_on('lapack')
+
+    def install(self, spec, prefix):
+        config_args = [
+            '--prefix={0}'.format(prefix),
+            '--with-blas={0}'.format(spec['blas'].prefix.lib),
+            '--with-lapack={0}'.format(spec['lapack'].prefix.lib),
+            '--enable-shared'
+        ]
+
+        configure(*config_args)
+
+        make()
+        make('install')
diff --git a/var/spack/repos/builtin/packages/hdf/package.py b/var/spack/repos/builtin/packages/hdf/package.py
index 7ad4df2fde..aafb345be6 100644
--- a/var/spack/repos/builtin/packages/hdf/package.py
+++ b/var/spack/repos/builtin/packages/hdf/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Hdf(Package):
     """HDF4 (also known as HDF) is a library and multi-object
     file format for storing and managing data between machines."""
@@ -41,10 +42,9 @@ class Hdf(Package):
     depends_on("szip", when='+szip')
     depends_on("zlib")
 
-
     def url_for_version(self, version):
-       return "https://www.hdfgroup.org/ftp/HDF/releases/HDF" + str(version) + "/src/hdf-" + str(version) + ".tar.gz"
-
+        return "https://www.hdfgroup.org/ftp/HDF/releases/HDF" + str(
+            version) + "/src/hdf-" + str(version) + ".tar.gz"
 
     def install(self, spec, prefix):
         config_args = [
@@ -52,9 +52,9 @@ class Hdf(Package):
             '--prefix=%s' % prefix,
             '--with-jpeg=%s' % spec['jpeg'].prefix,
             '--with-zlib=%s' % spec['zlib'].prefix,
-            '--disable-netcdf',  # must be disabled to build NetCDF with HDF4 support
+            '--disable-netcdf',  # must be disabled to build NetCDF with HDF4
             '--enable-fortran',
-            '--disable-shared',  # fortran and shared libraries are not compatible
+            '--disable-shared',  # fortran and shared libs are not compatible
             '--enable-static',
             '--enable-production'
         ]
diff --git a/var/spack/repos/builtin/packages/hdf5-blosc/package.py b/var/spack/repos/builtin/packages/hdf5-blosc/package.py
index 28b65711b0..b9c19dff62 100644
--- a/var/spack/repos/builtin/packages/hdf5-blosc/package.py
+++ b/var/spack/repos/builtin/packages/hdf5-blosc/package.py
@@ -29,6 +29,7 @@ import sys
 
 from spack import *
 
+
 def _install_shlib(name, src, dst):
     """Install a shared library from directory src to directory dst"""
     if sys.platform == "darwin":
@@ -44,6 +45,7 @@ def _install_shlib(name, src, dst):
         os.symlink(shlib000, join_path(dst, shlib0))
         os.symlink(shlib0, join_path(dst, shlib))
 
+
 class Hdf5Blosc(Package):
     """Blosc filter for HDF5"""
     homepage = "https://github.com/Blosc/hdf5-blosc"
@@ -60,18 +62,21 @@ class Hdf5Blosc(Package):
     def install(self, spec, prefix):
         # The included cmake recipe doesn"t work for Darwin
         # cmake(".", *std_cmake_args)
-        # 
+        #
         # make()
         # make("install")
         # if sys.platform == "darwin":
         #     fix_darwin_install_name(prefix.lib)
 
         libtool = Executable(join_path(spec["libtool"].prefix.bin, "libtool"))
-        if "+mpi" in spec["hdf5"]:
-            cc = "mpicc"
-        else:
-            cc = "cc"
-        shlibext = "so" if sys.platform!="darwin" else "dylib"
+
+        # TODO: these vars are not used.
+        # if "+mpi" in spec["hdf5"]:
+        #     cc = "mpicc"
+        # else:
+        #     cc = "cc"
+        # shlibext = "so" if sys.platform != "darwin" else "dylib"
+
         mkdirp(prefix.include)
         mkdirp(prefix.lib)
 
@@ -118,7 +123,7 @@ class Hdf5Blosc(Package):
 #include <stdio.h>
 #include <stdlib.h>
 
-#define FILTER_BLOSC 32001   /* Blosc filter ID registered with the HDF group */
+#define FILTER_BLOSC 32001 /* Blosc filter ID registered with the HDF group */
 
 int main(int argc, char **argv) {
   herr_t herr;
@@ -184,13 +189,13 @@ Done.
             if not success:
                 print "Produced output does not match expected output."
                 print "Expected output:"
-                print "-"*80
+                print "-" * 80
                 print expected
-                print "-"*80
+                print "-" * 80
                 print "Produced output:"
-                print "-"*80
+                print "-" * 80
                 print output
-                print "-"*80
+                print "-" * 80
                 print "Environment:"
                 env = which("env")
                 env()
diff --git a/var/spack/repos/builtin/packages/hdf5/package.py b/var/spack/repos/builtin/packages/hdf5/package.py
index 3b2600e671..a7c4b2d85e 100644
--- a/var/spack/repos/builtin/packages/hdf5/package.py
+++ b/var/spack/repos/builtin/packages/hdf5/package.py
@@ -40,19 +40,22 @@ class Hdf5(AutotoolsPackage):
 
     version('1.10.0-patch1', '9180ff0ef8dc2ef3f61bd37a7404f295')
     version('1.10.0', 'bdc935337ee8282579cd6bc4270ad199')
-    version('1.8.16', 'b8ed9a36ae142317f88b0c7ef4b9c618', preferred=True)
+    version('1.8.16', 'b8ed9a36ae142317f88b0c7ef4b9c618')
     version('1.8.15', '03cccb5b33dbe975fdcd8ae9dc021f24')
     version('1.8.13', 'c03426e9e77d7766944654280b467289')
 
-    variant('debug', default=False, description='Builds a debug version of the library')
-    variant('shared', default=True, description='Builds a shared version of the library')
+    variant('debug', default=False,
+            description='Builds a debug version of the library')
+    variant('shared', default=True,
+            description='Builds a shared version of the library')
 
     variant('cxx', default=True, description='Enable C++ support')
     variant('fortran', default=True, description='Enable Fortran support')
 
     variant('mpi', default=False, description='Enable MPI support')
     variant('szip', default=False, description='Enable szip support')
-    variant('threadsafe', default=False, description='Enable thread-safe capabilities')
+    variant('threadsafe', default=False,
+            description='Enable thread-safe capabilities')
 
     depends_on('mpi', when='+mpi')
     depends_on('szip', when='+szip')
diff --git a/var/spack/repos/builtin/packages/hoomd-blue/package.py b/var/spack/repos/builtin/packages/hoomd-blue/package.py
index 060cd0b713..79e99e7b89 100644
--- a/var/spack/repos/builtin/packages/hoomd-blue/package.py
+++ b/var/spack/repos/builtin/packages/hoomd-blue/package.py
@@ -25,6 +25,7 @@
 from spack import *
 import os
 
+
 class HoomdBlue(Package):
     """HOOMD-blue is a general-purpose particle simulation toolkit. It scales
     from a single CPU core to thousands of GPUs.
@@ -56,7 +57,7 @@ class HoomdBlue(Package):
 
         cmake_args = [
             '-DPYTHON_EXECUTABLE=%s/python' % spec['python'].prefix.bin,
-            '-DBOOST_ROOT=%s'               % spec['boost' ].prefix
+            '-DBOOST_ROOT=%s'               % spec['boost'].prefix
         ]
 
         # MPI support
@@ -73,9 +74,9 @@ class HoomdBlue(Package):
             cmake_args.append('-DENABLE_CUDA=OFF')
 
         # CUDA-aware MPI library support
-        #if '+cuda' in spec and '+mpi' in spec:
+        # if '+cuda' in spec and '+mpi' in spec:
         #    cmake_args.append('-DENABLE_MPI_CUDA=ON')
-        #else:
+        # else:
         #    cmake_args.append('-DENABLE_MPI_CUDA=OFF')
 
         # There may be a bug in the MPI-CUDA code. See:
diff --git a/var/spack/repos/builtin/packages/hpx5/package.py b/var/spack/repos/builtin/packages/hpx5/package.py
index cd0c0b7a7b..686e959719 100644
--- a/var/spack/repos/builtin/packages/hpx5/package.py
+++ b/var/spack/repos/builtin/packages/hpx5/package.py
@@ -25,6 +25,7 @@
 from spack import *
 import os
 
+
 class Hpx5(Package):
     """The HPX-5 Runtime System. HPX-5 (High Performance ParalleX) is an
     open source, portable, performance-oriented runtime developed at
diff --git a/var/spack/repos/builtin/packages/htslib/package.py b/var/spack/repos/builtin/packages/htslib/package.py
new file mode 100644
index 0000000000..1a8b8fd2f5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/htslib/package.py
@@ -0,0 +1,41 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Htslib(Package):
+    """C library for high-throughput sequencing data formats."""
+
+    homepage = "https://github.com/samtools/htslib"
+    url      = "https://github.com/samtools/htslib/releases/download/1.3.1/htslib-1.3.1.tar.bz2"
+
+    version('1.3.1', '16d78f90b72f29971b042e8da8be6843')
+
+    depends_on('zlib')
+
+    def install(self, spec, prefix):
+        configure('--prefix={0}'.format(prefix))
+        make()
+        make('install')
diff --git a/var/spack/repos/builtin/packages/hwloc/package.py b/var/spack/repos/builtin/packages/hwloc/package.py
index ee0168c38e..c163628840 100644
--- a/var/spack/repos/builtin/packages/hwloc/package.py
+++ b/var/spack/repos/builtin/packages/hwloc/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Hwloc(Package):
     """The Portable Hardware Locality (hwloc) software package
        provides a portable abstraction (across OS, versions,
diff --git a/var/spack/repos/builtin/packages/hydra/package.py b/var/spack/repos/builtin/packages/hydra/package.py
index 3d56056022..eee346ba49 100644
--- a/var/spack/repos/builtin/packages/hydra/package.py
+++ b/var/spack/repos/builtin/packages/hydra/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Hydra(Package):
     """Hydra is a process management system for starting parallel jobs.
     Hydra is designed to natively work with existing launcher daemons
@@ -37,7 +38,6 @@ class Hydra(Package):
 
     version('3.2', '4d670916695bf7e3a869cc336a881b39')
 
-
     def install(self, spec, prefix):
         configure('--prefix=%s' % prefix)
 
diff --git a/var/spack/repos/builtin/packages/hypre/package.py b/var/spack/repos/builtin/packages/hypre/package.py
index 65fef57559..fdc236dcf4 100644
--- a/var/spack/repos/builtin/packages/hypre/package.py
+++ b/var/spack/repos/builtin/packages/hypre/package.py
@@ -39,9 +39,11 @@ class Hypre(Package):
     version('2.10.0b', '768be38793a35bb5d055905b271f5b8e')
 
     # hypre does not know how to build shared libraries on Darwin
-    variant('shared', default=(sys.platform != 'darwin'), description="Build shared library version (disables static library)")
+    variant('shared', default=(sys.platform != 'darwin'),
+            description="Build shared library (disables static library)")
     # SuperluDist have conflicting headers with those in Hypre
-    variant('internal-superlu', default=True, description="Use internal Superlu routines")
+    variant('internal-superlu', default=True,
+            description="Use internal Superlu routines")
 
     depends_on("mpi")
     depends_on("blas")
@@ -62,10 +64,10 @@ class Hypre(Package):
             '--prefix=%s' % prefix,
             '--with-lapack-libs=%s' % to_lib_name(
                 spec['lapack'].lapack_shared_lib),
-            '--with-lapack-lib-dirs=%s/lib' % spec['lapack'].prefix,
+            '--with-lapack-lib-dirs=%s' % spec['lapack'].prefix.lib,
             '--with-blas-libs=%s' % to_lib_name(
                 spec['blas'].blas_shared_lib),
-            '--with-blas-lib-dirs=%s/lib' % spec['blas'].prefix
+            '--with-blas-lib-dirs=%s' % spec['blas'].prefix.lib
         ]
 
         if '+shared' in self.spec:
diff --git a/var/spack/repos/builtin/packages/ibmisc/package.py b/var/spack/repos/builtin/packages/ibmisc/package.py
index 2c7ed4f2a7..dbfa09bc20 100644
--- a/var/spack/repos/builtin/packages/ibmisc/package.py
+++ b/var/spack/repos/builtin/packages/ibmisc/package.py
@@ -1,5 +1,6 @@
 from spack import *
 
+
 class Ibmisc(CMakePackage):
     """Misc. reusable utilities used by IceBin."""
 
@@ -8,14 +9,22 @@ class Ibmisc(CMakePackage):
 
     version('0.1.0', '12f2a32432a11db48e00217df18e59fa')
 
-    variant('everytrace', default=False, description='Report errors through Everytrace')
-    variant('proj', default=True, description='Compile utilities for PROJ.4 library')
-    variant('blitz', default=True, description='Compile utilities for Blitz library')
-    variant('netcdf', default=True, description='Compile utilities for NetCDF library')
-    variant('boost', default=True, description='Compile utilities for Boost library')
-    variant('udunits2', default=True, description='Compile utilities for UDUNITS2 library')
-    variant('googletest', default=True, description='Compile utilities for Google Test library')
-    variant('python', default=True, description='Compile utilities for use with Python/Cython')
+    variant('everytrace', default=False,
+            description='Report errors through Everytrace')
+    variant('proj', default=True,
+            description='Compile utilities for PROJ.4 library')
+    variant('blitz', default=True,
+            description='Compile utilities for Blitz library')
+    variant('netcdf', default=True,
+            description='Compile utilities for NetCDF library')
+    variant('boost', default=True,
+            description='Compile utilities for Boost library')
+    variant('udunits2', default=True,
+            description='Compile utilities for UDUNITS2 library')
+    variant('googletest', default=True,
+            description='Compile utilities for Google Test library')
+    variant('python', default=True,
+            description='Compile utilities for use with Python/Cython')
 
     extends('python')
 
diff --git a/var/spack/repos/builtin/packages/icu/package.py b/var/spack/repos/builtin/packages/icu/package.py
index c7cabb5d95..b8d366b905 100644
--- a/var/spack/repos/builtin/packages/icu/package.py
+++ b/var/spack/repos/builtin/packages/icu/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Icu(Package):
     """The International Components for Unicode (ICU) package is a
        mature, widely used set of C/C++ libraries providing Unicode and
@@ -36,12 +37,10 @@ class Icu(Package):
 
     version('54.1', 'e844caed8f2ca24c088505b0d6271bc0')
 
-
     def url_for_version(self, version):
         return "http://download.icu-project.org/files/icu4c/%s/icu4c-%s-src.tgz" % (
             version, str(version).replace('.', '_'))
 
-
     def install(self, spec, prefix):
         with working_dir("source"):
             configure("--prefix=%s" % prefix)
diff --git a/var/spack/repos/builtin/packages/icu4c/package.py b/var/spack/repos/builtin/packages/icu4c/package.py
index 6cfec99c3f..2bcf86cd13 100644
--- a/var/spack/repos/builtin/packages/icu4c/package.py
+++ b/var/spack/repos/builtin/packages/icu4c/package.py
@@ -24,9 +24,12 @@
 ##############################################################################
 from spack import *
 
+
 class Icu4c(Package):
-    """ICU is a mature, widely used set of C/C++ and Java libraries 
-    providing Unicode and Globalization support for software applications."""
+    """ICU is a mature, widely used set of C/C++ and Java libraries providing
+       Unicode and Globalization support for software applications.
+
+    """
 
     homepage = "http://site.icu-project.org/"
     url      = "http://downloads.sourceforge.net/project/icu/ICU4C/54.1/icu4c-54_1-src.tgz"
diff --git a/var/spack/repos/builtin/packages/ilmbase/package.py b/var/spack/repos/builtin/packages/ilmbase/package.py
new file mode 100644
index 0000000000..873c830623
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ilmbase/package.py
@@ -0,0 +1,42 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Ilmbase(Package):
+    """OpenEXR ILM Base libraries (high dynamic-range image file format)"""
+
+    homepage = "http://www.openexr.com/"
+    url      = "http://download.savannah.nongnu.org/releases/openexr/ilmbase-2.2.0.tar.gz"
+
+    version('2.2.0', 'b540db502c5fa42078249f43d18a4652')
+    version('2.1.0', 'af1115f4d759c574ce84efcde9845d29')
+    version('2.0.1', '74c0d0d2873960bd0dc1993f8e03f0ae')
+    version('1.0.2', '26c133ee8ca48e1196fbfb3ffe292ab4')
+    version('0.9.0', '4df45f8116cb7a013b286caf6da30a2e')
+
+    def install(self, spec, prefix):
+        configure('--prefix={0}'.format(prefix))
+        make('install')
diff --git a/var/spack/repos/builtin/packages/intel-parallel-studio/package.py b/var/spack/repos/builtin/packages/intel-parallel-studio/package.py
index 493ca16417..65db3351a1 100644
--- a/var/spack/repos/builtin/packages/intel-parallel-studio/package.py
+++ b/var/spack/repos/builtin/packages/intel-parallel-studio/package.py
@@ -17,19 +17,19 @@ class IntelParallelStudio(IntelInstaller):
 
     # TODO: can also try the online installer (will download files on demand)
     version('composer.2016.2', '1133fb831312eb519f7da897fec223fa',
-        url="file://%s/parallel_studio_xe_2016_composer_edition_update2.tgz"  # NOQA: ignore=E501
+        url="file://%s/parallel_studio_xe_2016_composer_edition_update2.tgz"
         % os.getcwd())
     version('professional.2016.2', '70be832f2d34c9bf596a5e99d5f2d832',
-        url="file://%s/parallel_studio_xe_2016_update2.tgz" % os.getcwd())  # NOQA: ignore=E501
+        url="file://%s/parallel_studio_xe_2016_update2.tgz" % os.getcwd())
     version('cluster.2016.2', '70be832f2d34c9bf596a5e99d5f2d832',
-        url="file://%s/parallel_studio_xe_2016_update2.tgz" % os.getcwd())  # NOQA: ignore=E501
+        url="file://%s/parallel_studio_xe_2016_update2.tgz" % os.getcwd())
     version('composer.2016.3', '3208eeabee951fc27579177b593cefe9',
-        url="file://%s/parallel_studio_xe_2016_composer_edition_update3.tgz"  # NOQA: ignore=E501
+        url="file://%s/parallel_studio_xe_2016_composer_edition_update3.tgz"
         % os.getcwd())
     version('professional.2016.3', 'eda19bb0d0d19709197ede58f13443f3',
-        url="file://%s/parallel_studio_xe_2016_update3.tgz" % os.getcwd())  # NOQA: ignore=E501
+        url="file://%s/parallel_studio_xe_2016_update3.tgz" % os.getcwd())
     version('cluster.2016.3', 'eda19bb0d0d19709197ede58f13443f3',
-        url="file://%s/parallel_studio_xe_2016_update3.tgz" % os.getcwd())  # NOQA: ignore=E501
+        url="file://%s/parallel_studio_xe_2016_update3.tgz" % os.getcwd())
 
     variant('rpath', default=True, description="Add rpath to .cfg files")
     variant('newdtags', default=False,
@@ -42,15 +42,32 @@ class IntelParallelStudio(IntelInstaller):
     variant('daal',
             default=True, description="Install the Intel DAAL libraries")
     variant('ipp', default=True, description="Install the Intel IPP libraries")
-    variant('tools', default=True, description="""Install the Intel Advisor,\
-VTune Amplifier, and Inspector tools""")
+    variant('tools', default=True, description="Install the Intel Advisor, "
+            "VTune Amplifier, and Inspector tools")
 
     provides('mpi', when='@cluster:+mpi')
     provides('mkl', when='+mkl')
     provides('daal', when='+daal')
     provides('ipp', when='+ipp')
 
+    # virtual dependency
+    provides('blas', when='+mkl')
+    provides('lapack', when='+mkl')
+    # TODO: MKL also provides implementation of Scalapack.
+
+    def check_variants(self, spec):
+        error_message = '\t{variant} can not be turned off if "+all" is set'
+
+        if self.spec.satisfies('+all'):
+            errors = [error_message.format(variant=x)
+                      for x in ('mpi', 'mkl', 'daal', 'ipp', 'tools')
+                      if ('~' + x) in self.spec]
+            if errors:
+                errors = ['incompatible variants given'] + errors
+                raise InstallError('\n'.join(errors))
+
     def install(self, spec, prefix):
+        self.check_variants(spec)
 
         base_components = "ALL"  # when in doubt, install everything
         mpi_components = ""
@@ -58,14 +75,12 @@ VTune Amplifier, and Inspector tools""")
         daal_components = ""
         ipp_components = ""
 
-        if spec.satisfies('+all'):
-            base_components = "ALL"
-        else:
+        if not spec.satisfies('+all'):
             all_components = get_all_components()
             regex = '(comp|openmp|intel-tbb|icc|ifort|psxe|icsxe-pset)'
             base_components = \
                 filter_pick(all_components, re.compile(regex).search)
-            regex = '(icsxe|imb|mpi|itac|intel-tc|clck)'
+            regex = '(icsxe|imb|mpi|itac|intel-ta|intel-tc|clck)'
             mpi_components = \
                 filter_pick(all_components, re.compile(regex).search)
             mkl_components = \
@@ -77,10 +92,10 @@ VTune Amplifier, and Inspector tools""")
             regex = '(gdb|vtune|inspector|advisor)'
             tool_components = \
                 filter_pick(all_components, re.compile(regex).search)
+            components = base_components
 
-        components = base_components
         if not spec.satisfies('+all'):
-            if spec.satisfies('+mpi') and 'cluster' in str(spec.version):
+            if spec.satisfies('+mpi'):
                 components += mpi_components
             if spec.satisfies('+mkl'):
                 components += mkl_components
@@ -89,16 +104,20 @@ VTune Amplifier, and Inspector tools""")
             if spec.satisfies('+ipp'):
                 components += ipp_components
             if spec.satisfies('+tools') and (spec.satisfies('@cluster') or
-               spec.satisfies('@professional')):
+                                             spec.satisfies('@professional')):
                 components += tool_components
 
-        self.intel_components = ';'.join(components)
+        if spec.satisfies('+all'):
+            self.intel_components = 'ALL'
+        else:
+            self.intel_components = ';'.join(components)
         IntelInstaller.install(self, spec, prefix)
 
-        absbindir = os.path.dirname(os.path.realpath(os.path.join(
-            self.prefix.bin, "icc")))
-        abslibdir = os.path.dirname(os.path.realpath(os.path.join
-                                    (self.prefix.lib, "intel64", "libimf.a")))
+        absbindir = os.path.dirname(
+            os.path.realpath(os.path.join(self.prefix.bin, "icc")))
+        abslibdir = os.path.dirname(
+            os.path.realpath(os.path.join(
+                self.prefix.lib, "intel64", "libimf.a")))
 
         os.symlink(self.global_license_file, os.path.join(absbindir,
                                                           "license.lic"))
@@ -116,22 +135,31 @@ VTune Amplifier, and Inspector tools""")
 
         if (spec.satisfies('+all') or spec.satisfies('+mpi')) and \
                 spec.satisfies('@cluster'):
-                os.symlink(self.global_license_file, os.path.join(
-                           self.prefix, "itac_latest", "license.lic"))
-                if spec.satisfies('~newdtags'):
-                    wrappers = ["mpif77", "mpif77", "mpif90", "mpif90",
-                                "mpigcc", "mpigcc", "mpigxx", "mpigxx",
-                                "mpiicc", "mpiicc", "mpiicpc", "mpiicpc",
-                                "mpiifort", "mpiifort"]
-                    wrapper_paths = []
-                    for root, dirs, files in os.walk(spec.prefix):
-                        for name in files:
-                            if name in wrappers:
-                                wrapper_paths.append(os.path.join(spec.prefix,
-                                                                  root, name))
-                    for wrapper in wrapper_paths:
-                        filter_file(r'-Xlinker --enable-new-dtags', r' ',
-                                    wrapper)
+            for ifile in os.listdir(os.path.join(self.prefix, "itac")):
+                if os.path.isdir(os.path.join(self.prefix, "itac", ifile)):
+                    os.symlink(self.global_license_file,
+                               os.path.join(self.prefix, "itac", ifile,
+                                            "license.lic"))
+                if os.path.isdir(os.path.join(self.prefix, "itac",
+                                              ifile, "intel64")):
+                    os.symlink(self.global_license_file,
+                               os.path.join(self.prefix, "itac",
+                                            ifile, "intel64",
+                                            "license.lic"))
+            if spec.satisfies('~newdtags'):
+                wrappers = ["mpif77", "mpif77", "mpif90", "mpif90",
+                            "mpigcc", "mpigcc", "mpigxx", "mpigxx",
+                            "mpiicc", "mpiicc", "mpiicpc", "mpiicpc",
+                            "mpiifort", "mpiifort"]
+                wrapper_paths = []
+                for root, dirs, files in os.walk(spec.prefix):
+                    for name in files:
+                        if name in wrappers:
+                            wrapper_paths.append(os.path.join(spec.prefix,
+                                                              root, name))
+                for wrapper in wrapper_paths:
+                    filter_file(r'-Xlinker --enable-new-dtags', r' ',
+                                wrapper)
 
         if spec.satisfies('+rpath'):
             for compiler_command in ["icc", "icpc", "ifort"]:
@@ -142,3 +170,130 @@ VTune Amplifier, and Inspector tools""")
 
         os.symlink(os.path.join(self.prefix.man, "common", "man1"),
                    os.path.join(self.prefix.man, "man1"))
+
+    def setup_dependent_package(self, module, dspec):
+        # For now use Single Dynamic Library:
+        # To set the threading layer at run time, use the
+        # mkl_set_threading_layer function or set MKL_THREADING_LAYER
+        # variable to one of the following values: INTEL, SEQUENTIAL, PGI.
+        # To set interface layer at run time, use the mkl_set_interface_layer
+        # function or set the MKL_INTERFACE_LAYER variable to LP64 or ILP64.
+
+        # Otherwise one would need to specify several libraries
+        # (e.g. mkl_intel_lp64;mkl_sequential;mkl_core), which reflect
+        # different interface and threading layers.
+
+        name = 'libmkl_rt.%s' % dso_suffix
+        libdir = find_library_path(name, self.prefix.lib64, self.prefix.lib)
+
+        self.spec.blas_shared_lib   = join_path(libdir, name)
+        self.spec.lapack_shared_lib = self.spec.blas_shared_lib
+
+    def setup_environment(self, spack_env, run_env):
+        # TODO: Determine variables needed for the professional edition.
+
+        major_ver = self.version[1]
+
+        # Remove paths that were guessed but are incorrect for this package.
+        run_env.remove_path('LIBRARY_PATH',
+                            join_path(self.prefix, 'lib'))
+        run_env.remove_path('LD_LIBRARY_PATH',
+                            join_path(self.prefix, 'lib'))
+        run_env.remove_path('CPATH',
+                            join_path(self.prefix, 'include'))
+
+        # Add the default set of variables
+        run_env.prepend_path('LIBRARY_PATH',
+                             join_path(self.prefix, 'lib', 'intel64'))
+        run_env.prepend_path('LD_LIBRARY_PATH',
+                             join_path(self.prefix, 'lib', 'intel64'))
+        run_env.prepend_path('LIBRARY_PATH',
+                             join_path(self.prefix, 'tbb', 'lib',
+                                       'intel64', 'gcc4.4'))
+        run_env.prepend_path('LD_LIBRARY_PATH',
+                             join_path(self.prefix, 'tbb', 'lib',
+                                       'intel64', 'gcc4.4'))
+        run_env.prepend_path('CPATH',
+                             join_path(self.prefix, 'tbb', 'include'))
+        run_env.prepend_path('MIC_LIBRARY_PATH',
+                             join_path(self.prefix, 'lib', 'mic'))
+        run_env.prepend_path('MIC_LD_LIBRARY_PATH',
+                             join_path(self.prefix, 'lib', 'mic'))
+        run_env.prepend_path('MIC_LIBRARY_PATH',
+                             join_path(self.prefix, 'tbb', 'lib', 'mic'))
+        run_env.prepend_path('MIC_LD_LIBRARY_PATH',
+                             join_path(self.prefix, 'tbb', 'lib', 'mic'))
+
+        if self.spec.satisfies('+all'):
+            run_env.prepend_path('LD_LIBRARY_PATH',
+                                 join_path(self.prefix,
+                                           'debugger_{0}'.format(major_ver),
+                                           'libipt', 'intel64', 'lib'))
+            run_env.set('GDBSERVER_MIC',
+                        join_path(self.prefix,
+                                  'debugger_{0}'.format(major_ver), 'gdb',
+                                  'targets', 'mic', 'bin', 'gdbserver'))
+            run_env.set('GDB_CROSS',
+                        join_path(self.prefix,
+                                  'debugger_{0}'.format(major_ver),
+                                  'gdb', 'intel64_mic', 'bin', 'gdb-mic'))
+            run_env.set('MPM_LAUNCHER',
+                        join_path(self.prefix,
+                                  'debugger_{0}'.format(major_ver), 'mpm',
+                                  'mic',
+                                  'bin', 'start_mpm.sh'))
+            run_env.set('INTEL_PYTHONHOME',
+                        join_path(self.prefix,
+                                  'debugger_{0}'.format(major_ver), 'python',
+                                  'intel64'))
+
+        if (self.spec.satisfies('+all') or self.spec.satisfies('+mpi')):
+            # Only I_MPI_ROOT is set here because setting the various PATH
+            # variables will potentially be in conflict with other MPI
+            # environment modules. The I_MPI_ROOT environment variable can be
+            # used as a base to set necessary PATH variables for using Intel
+            # MPI. It is also possible to set the variables in the modules.yaml
+            # file if Intel MPI is the dominant, or only, MPI on a system.
+            run_env.set('I_MPI_ROOT', join_path(self.prefix, 'impi'))
+
+        if self.spec.satisfies('+all') or self.spec.satisfies('+mkl'):
+            spack_env.set('MKLROOT', self.prefix)
+
+            run_env.prepend_path('LD_LIBRARY_PATH',
+                                 join_path(self.prefix, 'mkl', 'lib',
+                                           'intel64'))
+            run_env.prepend_path('LIBRARY_PATH',
+                                 join_path(self.prefix, 'mkl', 'lib',
+                                           'intel64'))
+            run_env.prepend_path('CPATH',
+                                 join_path(self.prefix, 'mkl', 'include'))
+            run_env.prepend_path('MIC_LD_LIBRARY_PATH',
+                                 join_path(self.prefix, 'mkl', 'lib', 'mic'))
+            run_env.set('MKLROOT', join_path(self.prefix, 'mkl'))
+
+        if self.spec.satisfies('+all') or self.spec.satisfies('+daal'):
+            run_env.prepend_path('LD_LIBRARY_PATH',
+                                 join_path(self.prefix, 'daal', 'lib',
+                                           'intel64_lin'))
+            run_env.prepend_path('LIBRARY_PATH',
+                                 join_path(self.prefix, 'daal', 'lib',
+                                           'intel64_lin'))
+            run_env.prepend_path('CPATH',
+                                 join_path(self.prefix, 'daal', 'include'))
+            run_env.prepend_path('CLASSPATH',
+                                 join_path(self.prefix, 'daal', 'lib',
+                                           'daal.jar'))
+            run_env.set('DAALROOT', join_path(self.prefix, 'daal'))
+
+        if self.spec.satisfies('+all') or self.spec.satisfies('+ipp'):
+            run_env.prepend_path('LD_LIBRARY_PATH',
+                                 join_path(self.prefix, 'ipp', 'lib',
+                                           'intel64'))
+            run_env.prepend_path('LIBRARY_PATH',
+                                 join_path(self.prefix, 'ipp', 'lib',
+                                           'intel64'))
+            run_env.prepend_path('CPATH',
+                                 join_path(self.prefix, 'ipp', 'include'))
+            run_env.prepend_path('MIC_LD_LIBRARY_PATH',
+                                 join_path(self.prefix, 'ipp', 'lib', 'mic'))
+            run_env.set('IPPROOT', join_path(self.prefix, 'ipp'))
diff --git a/var/spack/repos/builtin/packages/intel/package.py b/var/spack/repos/builtin/packages/intel/package.py
index 56d9fabddf..26134a12ae 100644
--- a/var/spack/repos/builtin/packages/intel/package.py
+++ b/var/spack/repos/builtin/packages/intel/package.py
@@ -49,13 +49,6 @@ class IntelInstaller(Package):
 
     def install(self, spec, prefix):
 
-        # Remove the installation DB, otherwise it will try to install into
-        # location of other Intel builds
-        if os.path.exists(os.path.join(os.environ["HOME"], "intel",
-                          "intel_sdp_products.db")):
-            os.remove(os.path.join(os.environ["HOME"], "intel",
-                      "intel_sdp_products.db"))
-
         if not hasattr(self, "intel_prefix"):
             self.intel_prefix = self.prefix
 
@@ -66,12 +59,14 @@ ACCEPT_EULA=accept
 PSET_MODE=install
 CONTINUE_WITH_INSTALLDIR_OVERWRITE=yes
 PSET_INSTALL_DIR=%s
+NONRPM_DB_DIR=%s
 ACTIVATION_LICENSE_FILE=%s
 ACTIVATION_TYPE=license_file
 PHONEHOME_SEND_USAGE_DATA=no
 CONTINUE_WITH_OPTIONAL_ERROR=yes
 COMPONENTS=%s
-""" % (self.intel_prefix, self.global_license_file, self.intel_components))
+""" % (self.intel_prefix, self.intel_prefix, self.global_license_file,
+                self.intel_components))
 
         install_script = Executable("./install.sh")
         install_script('--silent', silent_config_filename)
@@ -88,10 +83,10 @@ class Intel(IntelInstaller):
 
     # TODO: can also try the online installer (will download files on demand)
     version('16.0.2', '1133fb831312eb519f7da897fec223fa',
-        url="file://%s/parallel_studio_xe_2016_composer_edition_update2.tgz"  # NOQA: ignore=E501
+        url="file://%s/parallel_studio_xe_2016_composer_edition_update2.tgz"
         % os.getcwd())
     version('16.0.3', '3208eeabee951fc27579177b593cefe9',
-        url="file://%s/parallel_studio_xe_2016_composer_edition_update3.tgz"  # NOQA: ignore=E501
+        url="file://%s/parallel_studio_xe_2016_composer_edition_update3.tgz"
         % os.getcwd())
 
     variant('rpath', default=True, description="Add rpath to .cfg files")
@@ -111,8 +106,8 @@ class Intel(IntelInstaller):
             self.prefix.lib, "intel64", "libimf.a")))[0]
 
         # symlink or copy?
-        os.symlink(self.global_license_file, os.path.join(absbindir,
-                   "license.lic"))
+        os.symlink(self.global_license_file,
+                   os.path.join(absbindir, "license.lic"))
 
         if spec.satisfies('+rpath'):
             for compiler_command in ["icc", "icpc", "ifort"]:
@@ -123,3 +118,35 @@ class Intel(IntelInstaller):
 
         os.symlink(os.path.join(self.prefix.man, "common", "man1"),
                    os.path.join(self.prefix.man, "man1"))
+
+    def setup_environment(self, spack_env, run_env):
+
+        # Remove paths that were guessed but are incorrect for this package.
+        run_env.remove_path('LIBRARY_PATH',
+                            join_path(self.prefix, 'lib'))
+        run_env.remove_path('LD_LIBRARY_PATH',
+                            join_path(self.prefix, 'lib'))
+        run_env.remove_path('CPATH',
+                            join_path(self.prefix, 'include'))
+
+        # Add the default set of variables
+        run_env.prepend_path('LIBRARY_PATH',
+                             join_path(self.prefix, 'lib', 'intel64'))
+        run_env.prepend_path('LD_LIBRARY_PATH',
+                             join_path(self.prefix, 'lib', 'intel64'))
+        run_env.prepend_path('LIBRARY_PATH',
+                             join_path(self.prefix, 'tbb', 'lib',
+                                       'intel64', 'gcc4.4'))
+        run_env.prepend_path('LD_LIBRARY_PATH',
+                             join_path(self.prefix, 'tbb', 'lib',
+                                       'intel64', 'gcc4.4'))
+        run_env.prepend_path('CPATH',
+                             join_path(self.prefix, 'tbb', 'include'))
+        run_env.prepend_path('MIC_LIBRARY_PATH',
+                             join_path(self.prefix, 'lib', 'mic'))
+        run_env.prepend_path('MIC_LD_LIBRARY_PATH',
+                             join_path(self.prefix, 'lib', 'mic'))
+        run_env.prepend_path('MIC_LIBRARY_PATH',
+                             join_path(self.prefix, 'tbb', 'lib', 'mic'))
+        run_env.prepend_path('MIC_LD_LIBRARY_PATH',
+                             join_path(self.prefix, 'tbb', 'lib', 'mic'))
diff --git a/var/spack/repos/builtin/packages/intltool/package.py b/var/spack/repos/builtin/packages/intltool/package.py
index 48830c474a..e934734691 100644
--- a/var/spack/repos/builtin/packages/intltool/package.py
+++ b/var/spack/repos/builtin/packages/intltool/package.py
@@ -24,8 +24,12 @@
 ##############################################################################
 from spack import *
 
+
 class Intltool(Package):
-    """intltool is a set of tools to centralize translation of many different file formats using GNU gettext-compatible PO files."""
+    """intltool is a set of tools to centralize translation of many different
+       file formats using GNU gettext-compatible PO files.
+
+    """
     homepage  = 'https://freedesktop.org/wiki/Software/intltool/'
 
     version('0.51.0',    '12e517cac2b57a0121cda351570f1e63')
@@ -37,7 +41,7 @@ class Intltool(Package):
     def install(self, spec, prefix):
 
         # configure, build, install:
-        options = ['--prefix=%s' % prefix ]
+        options = ['--prefix=%s' % prefix]
         configure(*options)
         make()
         make('install')
diff --git a/var/spack/repos/builtin/packages/ior/package.py b/var/spack/repos/builtin/packages/ior/package.py
index 6aa72e5cc9..b8825c0fe4 100644
--- a/var/spack/repos/builtin/packages/ior/package.py
+++ b/var/spack/repos/builtin/packages/ior/package.py
@@ -25,6 +25,7 @@
 from spack import *
 import os
 
+
 class Ior(Package):
     """The IOR software is used for benchmarking parallel file systems
     using POSIX, MPI-IO, or HDF5 interfaces."""
@@ -41,7 +42,6 @@ class Ior(Package):
     depends_on('hdf5+mpi',   when='+hdf5')
     depends_on('netcdf+mpi', when='+ncmpi')
 
-
     def install(self, spec, prefix):
         os.system('./bootstrap')
 
diff --git a/var/spack/repos/builtin/packages/ipopt/package.py b/var/spack/repos/builtin/packages/ipopt/package.py
index 3bd21df89e..d5981e9975 100644
--- a/var/spack/repos/builtin/packages/ipopt/package.py
+++ b/var/spack/repos/builtin/packages/ipopt/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Ipopt(Package):
     """Ipopt (Interior Point OPTimizer, pronounced eye-pea-Opt) is a
        software package for large-scale nonlinear optimization."""
@@ -39,8 +40,8 @@ class Ipopt(Package):
     depends_on("blas")
     depends_on("lapack")
     depends_on("pkg-config", type='build')
-    depends_on("mumps+double~mpi") 
-    
+    depends_on("mumps+double~mpi")
+
     def install(self, spec, prefix):
         # Dependency directories
         blas_dir = spec['blas'].prefix
@@ -55,7 +56,7 @@ class Ipopt(Package):
         # By convention, spack links blas & lapack libs to libblas & liblapack
         blas_lib = "-L%s" % blas_dir.lib + " -lblas"
         lapack_lib = "-L%s" % lapack_dir.lib + " -llapack"
-        
+
         configure_args = [
             "--prefix=%s" % prefix,
             "--with-mumps-incdir=%s" % mumps_dir.include,
@@ -65,8 +66,8 @@ class Ipopt(Package):
             "--with-blas-lib=%s" % blas_lib,
             "--with-lapack-incdir=%s" % lapack_dir.include,
             "--with-lapack-lib=%s" % lapack_lib
-            ]
-        
+        ]
+
         configure(*configure_args)
 
         # IPOPT does not build correctly in parallel on OS X
diff --git a/var/spack/repos/builtin/packages/isl/package.py b/var/spack/repos/builtin/packages/isl/package.py
index f456f62225..259f4881f5 100644
--- a/var/spack/repos/builtin/packages/isl/package.py
+++ b/var/spack/repos/builtin/packages/isl/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Isl(Package):
     """isl is a thread-safe C library for manipulating sets and
     relations of integer points bounded by affine constraints."""
diff --git a/var/spack/repos/builtin/packages/jdk/package.py b/var/spack/repos/builtin/packages/jdk/package.py
index 2ec86f05e3..63bf6514cb 100644
--- a/var/spack/repos/builtin/packages/jdk/package.py
+++ b/var/spack/repos/builtin/packages/jdk/package.py
@@ -22,24 +22,25 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-#------------------------------------------------------------------------------
+#
 # Author: Justin Too <too1@llnl.gov>
-#------------------------------------------------------------------------------
-import distutils
-from distutils import dir_util
-from subprocess import call
+#
+import distutils.dir_util
 
 import spack
 from spack import *
 import llnl.util.tty as tty
 
+
 class Jdk(Package):
     """The Java Development Kit (JDK) released by Oracle Corporation
        in the form of a binary product aimed at Java developers."""
     homepage = "http://www.oracle.com/technetwork/java/javase/downloads/index.html"
 
     version('8u66-linux-x64', '88f31f3d642c3287134297b8c10e61bf',
-        url="http://download.oracle.com/otn-pub/java/jdk/8u66-b17/jdk-8u66-linux-x64.tar.gz")
+            url="http://download.oracle.com/otn-pub/java/jdk/8u66-b17/jdk-8u66-linux-x64.tar.gz")
+    version('8u92-linux-x64', '65a1cc17ea362453a6e0eb4f13be76e4',
+            url="http://download.oracle.com/otn-pub/java/jdk/8u92-b14/jdk-8u92-linux-x64.tar.gz")
 
     # Oracle requires that you accept their License Agreement in order
     # to access the Java packages in download.oracle.com. In order to
@@ -47,9 +48,9 @@ class Jdk(Package):
     # commandline options.
     #
     # See http://stackoverflow.com/questions/10268583/how-to-automate-download-and-installation-of-java-jdk-on-linux
-    curl_options=[
-        '-j', # junk cookies
-        '-H', # specify required License Agreement cookie
+    curl_options = [
+        '-j',  # junk cookies
+        '-H',  # specify required License Agreement cookie
         'Cookie: oraclelicense=accept-securebackup-cookie']
 
     def do_fetch(self, mirror_only=False):
@@ -65,6 +66,5 @@ class Jdk(Package):
         # Now perform the actual fetch
         super(Jdk, self).do_fetch(mirror_only)
 
-
     def install(self, spec, prefix):
         distutils.dir_util.copy_tree(".", prefix)
diff --git a/var/spack/repos/builtin/packages/jemalloc/package.py b/var/spack/repos/builtin/packages/jemalloc/package.py
index a67754a513..f5a983b7a9 100644
--- a/var/spack/repos/builtin/packages/jemalloc/package.py
+++ b/var/spack/repos/builtin/packages/jemalloc/package.py
@@ -24,8 +24,10 @@
 ##############################################################################
 from spack import *
 
+
 class Jemalloc(Package):
-    """jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and scalable concurrency support."""
+    """jemalloc is a general purpose malloc(3) implementation that emphasizes
+       fragmentation avoidance and scalable concurrency support."""
     homepage = "http://www.canonware.com/jemalloc/"
     url      = "https://github.com/jemalloc/jemalloc/releases/download/4.0.4/jemalloc-4.0.4.tar.bz2"
 
@@ -36,7 +38,7 @@ class Jemalloc(Package):
     variant('prof', default=False, description='Enable heap profiling')
 
     def install(self, spec, prefix):
-        configure_args = ['--prefix=%s' % prefix,]
+        configure_args = ['--prefix=%s' % prefix, ]
 
         if '+stats' in spec:
             configure_args.append('--enable-stats')
diff --git a/var/spack/repos/builtin/packages/jpeg/package.py b/var/spack/repos/builtin/packages/jpeg/package.py
index e4a9d8535b..594240d950 100644
--- a/var/spack/repos/builtin/packages/jpeg/package.py
+++ b/var/spack/repos/builtin/packages/jpeg/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Jpeg(Package):
     """libjpeg is a widely used free library with functions for handling the
     JPEG image data format. It implements a JPEG codec (encoding and decoding)
diff --git a/var/spack/repos/builtin/packages/judy/package.py b/var/spack/repos/builtin/packages/judy/package.py
index 8d47767ef0..8b8b261e53 100644
--- a/var/spack/repos/builtin/packages/judy/package.py
+++ b/var/spack/repos/builtin/packages/judy/package.py
@@ -24,8 +24,9 @@
 ##############################################################################
 from spack import *
 
+
 class Judy(Package):
-    """A general-purpose dynamic array, associative array and hash-trie - Judy"""
+    """Judy: General-purpose dynamic array, associative array and hash-trie."""
     homepage = "http://judy.sourceforge.net/"
     url      = "http://downloads.sourceforge.net/project/judy/judy/Judy-1.0.5/Judy-1.0.5.tar.gz"
 
diff --git a/var/spack/repos/builtin/packages/kdiff3/package.py b/var/spack/repos/builtin/packages/kdiff3/package.py
new file mode 100644
index 0000000000..48f4b9c379
--- /dev/null
+++ b/var/spack/repos/builtin/packages/kdiff3/package.py
@@ -0,0 +1,44 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Kdiff3(Package):
+    """Compare and merge 2 or 3 files or directories."""
+    homepage = "http://kdiff3.sourceforge.net/"
+    url      = "https://downloads.sourceforge.net/project/kdiff3/kdiff3/0.9.98/kdiff3-0.9.98.tar.gz"
+
+    version('0.9.98', 'b52f99f2cf2ea75ed5719315cbf77446')
+
+    depends_on("qt@5.2.0:")
+
+    def install(self, spec, prefix):
+        # make is done inside
+        configure('qt4')
+
+        # there is no make install, bummer...
+        mkdirp(self.prefix.bin)
+        install(join_path(self.stage.source_path, 'releaseQt', 'kdiff3'),
+                self.prefix.bin)
diff --git a/var/spack/repos/builtin/packages/kealib/package.py b/var/spack/repos/builtin/packages/kealib/package.py
index 7c73c4518b..5346fc8cb9 100644
--- a/var/spack/repos/builtin/packages/kealib/package.py
+++ b/var/spack/repos/builtin/packages/kealib/package.py
@@ -24,20 +24,21 @@
 ##############################################################################
 from spack import *
 
+
 class Kealib(Package):
     """An HDF5 Based Raster File Format
-    
+
     KEALib provides an implementation of the GDAL data model.
     The format supports raster attribute tables, image pyramids,
     meta-data and in-built statistics while also handling very
     large files and compression throughout.
-    
+
     Based on the HDF5 standard, it also provides a base from which
     other formats can be derived and is a good choice for long
     term data archiving. An independent software library (libkea)
     provides complete access to the KEA image format and a GDAL
     driver allowing KEA images to be used from any GDAL supported software.
-    
+
     Development work on this project has been funded by Landcare Research.
     """
     homepage = "http://kealib.org/"
@@ -51,7 +52,8 @@ class Kealib(Package):
         with working_dir('trunk', create=False):
             cmake_args = []
             cmake_args.append("-DCMAKE_INSTALL_PREFIX=%s" % prefix)
-            cmake_args.append("-DHDF5_INCLUDE_DIR=%s" % spec['hdf5'].prefix.include)
+            cmake_args.append("-DHDF5_INCLUDE_DIR=%s" %
+                              spec['hdf5'].prefix.include)
             cmake_args.append("-DHDF5_LIB_PATH=%s" % spec['hdf5'].prefix.lib)
             cmake('.', *cmake_args)
 
diff --git a/var/spack/repos/builtin/packages/kripke/package.py b/var/spack/repos/builtin/packages/kripke/package.py
index d405e9a51d..cf8d2b7e39 100644
--- a/var/spack/repos/builtin/packages/kripke/package.py
+++ b/var/spack/repos/builtin/packages/kripke/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Kripke(Package):
     """Kripke is a simple, scalable, 3D Sn deterministic particle
        transport proxy/mini app.
diff --git a/var/spack/repos/builtin/packages/launchmon/package.py b/var/spack/repos/builtin/packages/launchmon/package.py
index 8aa6d72727..d7c96a03d8 100644
--- a/var/spack/repos/builtin/packages/launchmon/package.py
+++ b/var/spack/repos/builtin/packages/launchmon/package.py
@@ -29,7 +29,7 @@ class Launchmon(Package):
     """Software infrastructure that enables HPC run-time tools to
        co-locate tool daemons with a parallel job."""
     homepage = "https://github.com/LLNL/LaunchMON"
-    url      = "https://github.com/LLNL/LaunchMON/releases/download/v1.0.2/launchmon-v1.0.2.tar.gz"  # NOQA: ignore=E501
+    url = "https://github.com/LLNL/LaunchMON/releases/download/v1.0.2/launchmon-v1.0.2.tar.gz"
 
     version('1.0.2', '8d6ba77a0ec2eff2fde2c5cc8fa7ff7a')
 
diff --git a/var/spack/repos/builtin/packages/lcms/package.py b/var/spack/repos/builtin/packages/lcms/package.py
index 434d8e6c98..4d3fc59568 100644
--- a/var/spack/repos/builtin/packages/lcms/package.py
+++ b/var/spack/repos/builtin/packages/lcms/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Lcms(Package):
     """Little cms is a color management library. Implements fast
        transforms between ICC profiles. It is focused on speed, and is
diff --git a/var/spack/repos/builtin/packages/leveldb/package.py b/var/spack/repos/builtin/packages/leveldb/package.py
index 408f1d31c1..f571baa1ce 100644
--- a/var/spack/repos/builtin/packages/leveldb/package.py
+++ b/var/spack/repos/builtin/packages/leveldb/package.py
@@ -22,10 +22,10 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import os
 import glob
 from spack import *
 
+
 class Leveldb(Package):
     """LevelDB is a fast key-value storage library written at Google
     that provides an ordered mapping from string keys to string values."""
diff --git a/var/spack/repos/builtin/packages/libNBC/package.py b/var/spack/repos/builtin/packages/libNBC/package.py
index ed1d0ce96f..414498a37a 100644
--- a/var/spack/repos/builtin/packages/libNBC/package.py
+++ b/var/spack/repos/builtin/packages/libNBC/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Libnbc(Package):
     """LibNBC is a prototypic implementation of a nonblocking
     interface for MPI collective operations. Based on ANSI C and
diff --git a/var/spack/repos/builtin/packages/libarchive/package.py b/var/spack/repos/builtin/packages/libarchive/package.py
index f11d732afa..0cf3932957 100644
--- a/var/spack/repos/builtin/packages/libarchive/package.py
+++ b/var/spack/repos/builtin/packages/libarchive/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Libarchive(Package):
     """libarchive: C library and command-line tools for reading and
        writing tar, cpio, zip, ISO, and other archive formats."""
diff --git a/var/spack/repos/builtin/packages/libatomic-ops/package.py b/var/spack/repos/builtin/packages/libatomic-ops/package.py
new file mode 100644
index 0000000000..0167fbcb33
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libatomic-ops/package.py
@@ -0,0 +1,42 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class LibatomicOps(Package):
+    """This package provides semi-portable access to hardware-provided
+    atomic memory update operations on a number architectures."""
+
+    homepage = "https://github.com/ivmai/libatomic_ops"
+    url      = "http://www.hboehm.info/gc/gc_source/libatomic_ops-7.4.4.tar.gz"
+
+    version('7.4.4', '426d804baae12c372967a6d183e25af2')
+
+    def install(self, spec, prefix):
+        configure('--prefix={0}'.format(prefix),
+                  '--enable-shared')
+
+        make()
+        make('install')
diff --git a/var/spack/repos/builtin/packages/libcerf/package.py b/var/spack/repos/builtin/packages/libcerf/package.py
index b30d76f4e9..7fb47f8dcd 100644
--- a/var/spack/repos/builtin/packages/libcerf/package.py
+++ b/var/spack/repos/builtin/packages/libcerf/package.py
@@ -27,9 +27,10 @@ from spack import *
 
 
 class Libcerf(Package):
-    """
-    A self-contained C library providing complex error functions, based on Faddeeva's plasma dispersion function
-    w(z). Also provides Dawson's integral and Voigt's convolution of a Gaussian and a Lorentzian
+    """A self-contained C library providing complex error functions, based
+       on Faddeeva's plasma dispersion function w(z). Also provides Dawson's
+       integral and Voigt's convolution of a Gaussian and a Lorentzian
+
     """
     homepage = "http://sourceforge.net/projects/libcerf"
     url      = "http://downloads.sourceforge.net/project/libcerf/libcerf-1.3.tgz"
diff --git a/var/spack/repos/builtin/packages/libcircle/package.py b/var/spack/repos/builtin/packages/libcircle/package.py
index 75fdb96125..971c29f5f1 100644
--- a/var/spack/repos/builtin/packages/libcircle/package.py
+++ b/var/spack/repos/builtin/packages/libcircle/package.py
@@ -22,9 +22,9 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import os
 from spack import *
 
+
 class Libcircle(Package):
     """libcircle provides an efficient distributed queue on a cluster,
        using self-stabilizing work stealing."""
@@ -32,7 +32,7 @@ class Libcircle(Package):
     homepage = "https://github.com/hpc/libcircle"
 
     version('0.2.1-rc.1', '2b1369a5736457239f908abf88143ec2',
-             url='https://github.com/hpc/libcircle/releases/download/0.2.1-rc.1/libcircle-0.2.1-rc.1.tar.gz')
+            url='https://github.com/hpc/libcircle/releases/download/0.2.1-rc.1/libcircle-0.2.1-rc.1.tar.gz')
 
     depends_on('mpi')
 
diff --git a/var/spack/repos/builtin/packages/libctl/package.py b/var/spack/repos/builtin/packages/libctl/package.py
new file mode 100644
index 0000000000..53d30ce5c3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libctl/package.py
@@ -0,0 +1,48 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Libctl(Package):
+    """libctl is a free Guile-based library implementing flexible
+    control files for scientific simulations."""
+
+    homepage = "http://ab-initio.mit.edu/wiki/index.php/Libctl"
+    url      = "http://ab-initio.mit.edu/libctl/libctl-3.2.2.tar.gz"
+
+    version('3.2.2', '5fd7634dc9ae8e7fa70a68473b9cbb68')
+
+    depends_on('guile')
+
+    def install(self, spec, prefix):
+        configure('--prefix={0}'.format(prefix),
+                  '--enable-shared',
+                  'GUILE={0}'.format(join_path(
+                      spec['guile'].prefix.bin, 'guile')),
+                  'GUILE_CONFIG={0}'.format(join_path(
+                      spec['guile'].prefix.bin, 'guile-config')))
+
+        make()
+        make('install')
diff --git a/var/spack/repos/builtin/packages/libdrm/package.py b/var/spack/repos/builtin/packages/libdrm/package.py
index b05412e588..543eab11b3 100644
--- a/var/spack/repos/builtin/packages/libdrm/package.py
+++ b/var/spack/repos/builtin/packages/libdrm/package.py
@@ -24,12 +24,13 @@
 ##############################################################################
 from spack import *
 
+
 class Libdrm(Package):
     """A userspace  library for  accessing the  DRM, direct
     rendering  manager, on  Linux,  BSD and  other  operating
     systems that support the  ioctl interface."""
 
-    homepage = "http://dri.freedesktop.org/libdrm/" # no real website...
+    homepage = "http://dri.freedesktop.org/libdrm/"  # no real website...
     url      = "http://dri.freedesktop.org/libdrm/libdrm-2.4.59.tar.gz"
 
     version('2.4.59', '105ac7af1afcd742d402ca7b4eb168b6')
diff --git a/var/spack/repos/builtin/packages/libedit/package.py b/var/spack/repos/builtin/packages/libedit/package.py
index 4366344679..235e7648bc 100644
--- a/var/spack/repos/builtin/packages/libedit/package.py
+++ b/var/spack/repos/builtin/packages/libedit/package.py
@@ -24,12 +24,14 @@
 ##############################################################################
 from spack import *
 
+
 class Libedit(Package):
     """An autotools compatible port of the NetBSD editline library"""
     homepage = "http://thrysoee.dk/editline/"
     url      = "http://thrysoee.dk/editline/libedit-20150325-3.1.tar.gz"
 
-    version('3.1', '43cdb5df3061d78b5e9d59109871b4f6', url="http://thrysoee.dk/editline/libedit-20150325-3.1.tar.gz")
+    version('3.1', '43cdb5df3061d78b5e9d59109871b4f6',
+            url="http://thrysoee.dk/editline/libedit-20150325-3.1.tar.gz")
 
     depends_on('ncurses')
 
diff --git a/var/spack/repos/builtin/packages/libelf/package.py b/var/spack/repos/builtin/packages/libelf/package.py
index 1e1deea818..3304d27bdb 100644
--- a/var/spack/repos/builtin/packages/libelf/package.py
+++ b/var/spack/repos/builtin/packages/libelf/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Libelf(Package):
     """libelf lets you read, modify or create ELF object files in an
        architecture-independent way. The library takes care of size
diff --git a/var/spack/repos/builtin/packages/libepoxy/package.py b/var/spack/repos/builtin/packages/libepoxy/package.py
new file mode 100644
index 0000000000..364ea1e30c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libepoxy/package.py
@@ -0,0 +1,39 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Libepoxy(Package):
+    """Epoxy is a library for handling OpenGL function pointer management for
+    you."""
+    homepage = "https://github.com/anholt/libepoxy"
+    url      = "https://github.com/anholt/libepoxy/releases/download/v1.3.1/libepoxy-1.3.1.tar.bz2"
+
+    version('1.3.1', '96f6620a9b005a503e7b44b0b528287d')
+
+    def install(self, spec, prefix):
+        configure('--prefix={0}'.format(prefix))
+        make()
+        make('install')
diff --git a/var/spack/repos/builtin/packages/libevent/package.py b/var/spack/repos/builtin/packages/libevent/package.py
index 3ae427a2eb..65b3a716c0 100644
--- a/var/spack/repos/builtin/packages/libevent/package.py
+++ b/var/spack/repos/builtin/packages/libevent/package.py
@@ -24,11 +24,13 @@
 ##############################################################################
 from spack import *
 
+
 class Libevent(Package):
     """The libevent API provides a mechanism to execute a callback function
-       when a specific event occurs on a file descriptor or after a timeout has been
-       reached. Furthermore, libevent also support callbacks due to signals or regular
-       timeouts.
+       when a specific event occurs on a file descriptor or after a
+       timeout has been reached. Furthermore, libevent also support
+       callbacks due to signals or regular timeouts.
+
     """
 
     homepage = "http://libevent.org"
@@ -46,7 +48,8 @@ class Libevent(Package):
     version('2.0.13', 'af786b4b3f790c9d3279792edf7867fc')
     version('2.0.12', '42986228baf95e325778ed328a93e070')
 
-    variant('openssl', default=True, description="Build with encryption enabled at the libevent level.")
+    variant('openssl', default=True,
+            description="Build with encryption enabled at the libevent level.")
     depends_on('openssl', when='+openssl')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/libffi/package.py b/var/spack/repos/builtin/packages/libffi/package.py
index 1d3c85c8e0..fa113ee86c 100644
--- a/var/spack/repos/builtin/packages/libffi/package.py
+++ b/var/spack/repos/builtin/packages/libffi/package.py
@@ -24,18 +24,21 @@
 ##############################################################################
 from spack import *
 
+
 class Libffi(Package):
     """The libffi library provides a portable, high level programming
     interface to various calling conventions. This allows a programmer
     to call any function specified by a call interface description at
     run time."""
     homepage = "https://sourceware.org/libffi/"
-    
-    version('3.2.1','83b89587607e3eb65c70d361f13bab43',url = "ftp://sourceware.org/pub/libffi/libffi-3.2.1.tar.gz")
-    #version('3.1', 'f5898b29bbfd70502831a212d9249d10',url = "ftp://sourceware.org/pub/libffi/libffi-3.1.tar.gz") # Has a bug $(lib64) instead of ${lib64} in libffi.pc
+
+    version('3.2.1', '83b89587607e3eb65c70d361f13bab43',
+            url="ftp://sourceware.org/pub/libffi/libffi-3.2.1.tar.gz")
+    # version('3.1', 'f5898b29bbfd70502831a212d9249d10',url =
+    # "ftp://sourceware.org/pub/libffi/libffi-3.1.tar.gz") # Has a bug
+    # $(lib64) instead of ${lib64} in libffi.pc
 
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
         make()
         make("install")
-
diff --git a/var/spack/repos/builtin/packages/libgcrypt/package.py b/var/spack/repos/builtin/packages/libgcrypt/package.py
index b1a316cc1b..b556def4d3 100644
--- a/var/spack/repos/builtin/packages/libgcrypt/package.py
+++ b/var/spack/repos/builtin/packages/libgcrypt/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Libgcrypt(Package):
     """Libgcrypt is a general purpose cryptographic library based on
        the code from GnuPG. It provides functions for all cryptographic
diff --git a/var/spack/repos/builtin/packages/libgd/package.py b/var/spack/repos/builtin/packages/libgd/package.py
index 938f4f6f3b..acfdebb972 100644
--- a/var/spack/repos/builtin/packages/libgd/package.py
+++ b/var/spack/repos/builtin/packages/libgd/package.py
@@ -27,11 +27,14 @@ from spack import *
 
 
 class Libgd(Package):
-    """
-    GD is an open source code library for the dynamic creation of images by programmers. GD is written in C, and
-    "wrappers" are available for Perl, PHP and other languages. GD creates PNG, JPEG, GIF, WebP, XPM, BMP images,
-    among other formats. GD is commonly used to generate charts, graphics, thumbnails, and most anything else, on the
-    fly. While not restricted to use on the web, the most common applications of GD involve website development.
+    """GD is an open source code library for the dynamic creation of images
+       by programmers. GD is written in C, and "wrappers" are available
+       for Perl, PHP and other languages. GD creates PNG, JPEG, GIF,
+       WebP, XPM, BMP images, among other formats. GD is commonly used to
+       generate charts, graphics, thumbnails, and most anything else, on
+       the fly. While not restricted to use on the web, the most common
+       applications of GD involve website development.
+
     """
 
     homepage = "https://github.com/libgd/libgd"
diff --git a/var/spack/repos/builtin/packages/libgpg-error/package.py b/var/spack/repos/builtin/packages/libgpg-error/package.py
index 3fe82a69e7..a0e2acd516 100644
--- a/var/spack/repos/builtin/packages/libgpg-error/package.py
+++ b/var/spack/repos/builtin/packages/libgpg-error/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class LibgpgError(Package):
     """Libgpg-error is a small library that defines common error
        values for all GnuPG components. Among these are GPG, GPGSM,
diff --git a/var/spack/repos/builtin/packages/libgtextutils/package.py b/var/spack/repos/builtin/packages/libgtextutils/package.py
new file mode 100644
index 0000000000..201e031869
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libgtextutils/package.py
@@ -0,0 +1,40 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Libgtextutils(Package):
+    """Gordon's Text utils Library."""
+
+    homepage = "https://github.com/agordon/libgtextutils"
+    url      = "https://github.com/agordon/libgtextutils/releases/download/0.7/libgtextutils-0.7.tar.gz"
+
+    version('0.7', '593c7c62e3c76ec49f5736eed4f96806')
+
+    def install(self, spec, prefix):
+        configure('--prefix={0}'.format(prefix))
+
+        make()
+        make('install')
diff --git a/var/spack/repos/builtin/packages/libhio/package.py b/var/spack/repos/builtin/packages/libhio/package.py
new file mode 100644
index 0000000000..17bd86d310
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libhio/package.py
@@ -0,0 +1,45 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Libhio(Package):
+    """
+    A library for writing to hierarchical data store systems.
+    """
+
+    homepage = "https://github.com/hpc/libhio/"
+    url      = "https://github.com/hpc/libhio/releases/download/hio.1.3.0.1/libhio-1.3.0.1.tar.gz"
+
+    version('1.3.0.1', 'c073541de8dd70aeb8878bd00d6d877f')
+
+    depends_on("libjson-c")
+    depends_on("bzip2")
+    depends_on("pkg-config", type="build")
+
+    def install(self, spec, prefix):
+        configure('--prefix=%s' % prefix)
+        make()
+        make("install")
diff --git a/var/spack/repos/builtin/packages/libiconv/package.py b/var/spack/repos/builtin/packages/libiconv/package.py
new file mode 100644
index 0000000000..f2eeb07b26
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libiconv/package.py
@@ -0,0 +1,43 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Libiconv(Package):
+    """GNU libiconv provides an implementation of the iconv() function
+    and the iconv program for character set conversion."""
+
+    homepage = "https://www.gnu.org/software/libiconv/"
+    url      = "http://ftp.gnu.org/pub/gnu/libiconv/libiconv-1.14.tar.gz"
+
+    version('1.14', 'e34509b1623cec449dfeb73d7ce9c6c6')
+
+    def install(self, spec, prefix):
+        configure('--prefix={0}'.format(prefix),
+                  '--enable-extra-encodings')
+
+        make()
+        make('check')
+        make('install')
diff --git a/var/spack/repos/builtin/packages/libjpeg-turbo/package.py b/var/spack/repos/builtin/packages/libjpeg-turbo/package.py
index d1239ba0d9..6252a88542 100644
--- a/var/spack/repos/builtin/packages/libjpeg-turbo/package.py
+++ b/var/spack/repos/builtin/packages/libjpeg-turbo/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class LibjpegTurbo(Package):
     """libjpeg-turbo is a fork of the original IJG libjpeg which uses
        SIMD to accelerate baseline JPEG compression and
diff --git a/var/spack/repos/builtin/packages/libmng/package.py b/var/spack/repos/builtin/packages/libmng/package.py
index dd0903c4bd..a77aada79c 100644
--- a/var/spack/repos/builtin/packages/libmng/package.py
+++ b/var/spack/repos/builtin/packages/libmng/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Libmng(Package):
     """libmng -THE reference library for reading, displaying, writing
        and examining Multiple-Image Network Graphics.  MNG is the animation
@@ -39,7 +40,8 @@ class Libmng(Package):
 
     def patch(self):
         # jpeg requires stdio to beincluded before its headrs.
-        filter_file(r'^(\#include \<jpeglib\.h\>)', '#include<stdio.h>\n\\1', 'libmng_types.h')
+        filter_file(r'^(\#include \<jpeglib\.h\>)',
+                    '#include<stdio.h>\n\\1', 'libmng_types.h')
 
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
diff --git a/var/spack/repos/builtin/packages/libmonitor/package.py b/var/spack/repos/builtin/packages/libmonitor/package.py
index 883d8af405..f680baa265 100644
--- a/var/spack/repos/builtin/packages/libmonitor/package.py
+++ b/var/spack/repos/builtin/packages/libmonitor/package.py
@@ -24,19 +24,19 @@
 ##############################################################################
 from spack import *
 
+
 class Libmonitor(Package):
     """Libmonitor is a library for process and thread control."""
-    homepage = "http://hpctoolkit.org"
-
-    version('20130218', svn='http://libmonitor.googlecode.com/svn/trunk/', revision=146)
-    variant('krellpatch', default=False, description="build with openspeedshop based patch.")
-
+    homepage = "https://github.com/HPCToolkit/libmonitor"
+    version('20130218', git='https://github.com/HPCToolkit/libmonitor.git',
+            commit='4f2311e')
+    variant('krellpatch', default=False,
+            description="build with openspeedshop based patch.")
 
     patch('libmonitorkrell-0000.patch', when='@20130218+krellpatch')
     patch('libmonitorkrell-0001.patch', when='@20130218+krellpatch')
     patch('libmonitorkrell-0002.patch', when='@20130218+krellpatch')
 
-
     def install(self, spec, prefix):
         configure("--prefix=" + prefix)
         make()
diff --git a/var/spack/repos/builtin/packages/libpciaccess/package.py b/var/spack/repos/builtin/packages/libpciaccess/package.py
index 91cef95cec..a65b81b69b 100644
--- a/var/spack/repos/builtin/packages/libpciaccess/package.py
+++ b/var/spack/repos/builtin/packages/libpciaccess/package.py
@@ -23,7 +23,7 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
-import os.path
+
 
 class Libpciaccess(Package):
     """Generic PCI access library."""
diff --git a/var/spack/repos/builtin/packages/libpng/package.py b/var/spack/repos/builtin/packages/libpng/package.py
index 951b91eabd..1afe4911e6 100644
--- a/var/spack/repos/builtin/packages/libpng/package.py
+++ b/var/spack/repos/builtin/packages/libpng/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Libpng(Package):
     """libpng graphics file format"""
     homepage = "http://www.libpng.org/pub/png/libpng.html"
diff --git a/var/spack/repos/builtin/packages/libpthread-stubs/package.py b/var/spack/repos/builtin/packages/libpthread-stubs/package.py
index 4bcca43c24..ea36758a83 100644
--- a/var/spack/repos/builtin/packages/libpthread-stubs/package.py
+++ b/var/spack/repos/builtin/packages/libpthread-stubs/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class LibpthreadStubs(Package):
     """The libpthread-stubs package provides weak aliases for pthread
        functions not provided in libc or otherwise available by
diff --git a/var/spack/repos/builtin/packages/libsigsegv/package.py b/var/spack/repos/builtin/packages/libsigsegv/package.py
index 14acdcbcd2..715d24bcf7 100644
--- a/var/spack/repos/builtin/packages/libsigsegv/package.py
+++ b/var/spack/repos/builtin/packages/libsigsegv/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Libsigsegv(Package):
     """GNU libsigsegv is a library for handling page faults in user mode."""
     homepage = "https://www.gnu.org/software/libsigsegv/"
diff --git a/var/spack/repos/builtin/packages/libsodium/package.py b/var/spack/repos/builtin/packages/libsodium/package.py
index 831a75e659..1c930e21dd 100644
--- a/var/spack/repos/builtin/packages/libsodium/package.py
+++ b/var/spack/repos/builtin/packages/libsodium/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Libsodium(Package):
     """Sodium is a modern, easy-to-use software library for encryption,
     decryption, signatures, password hashing and more."""
diff --git a/var/spack/repos/builtin/packages/libtermkey/package.py b/var/spack/repos/builtin/packages/libtermkey/package.py
index c7db959a40..64688505c4 100644
--- a/var/spack/repos/builtin/packages/libtermkey/package.py
+++ b/var/spack/repos/builtin/packages/libtermkey/package.py
@@ -24,17 +24,17 @@
 ##############################################################################
 from spack import *
 
+
 class Libtermkey(Package):
     """Easy keyboard entry processing for terminal programs"""
     homepage = "http://www.leonerd.org.uk/code/libtermkey/"
     url      = "http://www.leonerd.org.uk/code/libtermkey/libtermkey-0.18.tar.gz"
 
-    version('0.18' , '3be2e3e5a851a49cc5e8567ac108b520')
-    version('0.17' , '20edb99e0d95ec1690fe90e6a555ae6d')
-    version('0.16' , '7a24b675aaeb142d30db28e7554987d4')
+    version('0.18', '3be2e3e5a851a49cc5e8567ac108b520')
+    version('0.17', '20edb99e0d95ec1690fe90e6a555ae6d')
+    version('0.16', '7a24b675aaeb142d30db28e7554987d4')
     version('0.15b', '27689756e6c86c56ae454f2ac259bc3d')
-    version('0.14' , 'e08ce30f440f9715c459060e0e048978')
-
+    version('0.14', 'e08ce30f440f9715c459060e0e048978')
 
     def install(self, spec, prefix):
         make()
diff --git a/var/spack/repos/builtin/packages/libtiff/package.py b/var/spack/repos/builtin/packages/libtiff/package.py
index 4b03e7997b..cef9fcaae5 100644
--- a/var/spack/repos/builtin/packages/libtiff/package.py
+++ b/var/spack/repos/builtin/packages/libtiff/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Libtiff(Package):
     """libtiff graphics format library"""
     homepage = "http://www.remotesensing.org/libtiff/"
diff --git a/var/spack/repos/builtin/packages/libunistring/package.py b/var/spack/repos/builtin/packages/libunistring/package.py
new file mode 100644
index 0000000000..5b8837e72b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libunistring/package.py
@@ -0,0 +1,42 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Libunistring(Package):
+    """This library provides functions for manipulating Unicode strings
+    and for manipulating C strings according to the Unicode standard."""
+
+    homepage = "https://www.gnu.org/software/libunistring/"
+    url      = "http://ftp.gnu.org/gnu/libunistring/libunistring-0.9.6.tar.xz"
+
+    version('0.9.6', 'cb09c398020c27edac10ca590e9e9ef3')
+
+    def install(self, spec, prefix):
+        configure('--prefix={0}'.format(prefix))
+
+        make()
+        # make('check')  # test-verify fails for me, contacted developers
+        make('install')
diff --git a/var/spack/repos/builtin/packages/libunwind/package.py b/var/spack/repos/builtin/packages/libunwind/package.py
index 980b765c02..63ab4aec59 100644
--- a/var/spack/repos/builtin/packages/libunwind/package.py
+++ b/var/spack/repos/builtin/packages/libunwind/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Libunwind(Package):
     """A portable and efficient C programming interface (API) to determine
        the call-chain of a program."""
diff --git a/var/spack/repos/builtin/packages/libuuid/package.py b/var/spack/repos/builtin/packages/libuuid/package.py
index 0dd32ec77d..553f0dddb8 100644
--- a/var/spack/repos/builtin/packages/libuuid/package.py
+++ b/var/spack/repos/builtin/packages/libuuid/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Libuuid(Package):
     """Portable uuid C library"""
     # FIXME: add a proper url for your package's homepage here.
diff --git a/var/spack/repos/builtin/packages/libuv/package.py b/var/spack/repos/builtin/packages/libuv/package.py
index 0d29270b38..dae10809f2 100644
--- a/var/spack/repos/builtin/packages/libuv/package.py
+++ b/var/spack/repos/builtin/packages/libuv/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Libuv(Package):
     """Multi-platform library with a focus on asynchronous IO"""
     homepage = "http://libuv.org"
diff --git a/var/spack/repos/builtin/packages/libvterm/package.py b/var/spack/repos/builtin/packages/libvterm/package.py
index e57af273ad..2e1ef99b98 100644
--- a/var/spack/repos/builtin/packages/libvterm/package.py
+++ b/var/spack/repos/builtin/packages/libvterm/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Libvterm(Package):
     """An abstract library implementation of a terminal emulator"""
     homepage = "http://www.leonerd.org.uk/code/libvterm/"
diff --git a/var/spack/repos/builtin/packages/libxau/package.py b/var/spack/repos/builtin/packages/libxau/package.py
index 55816ecdbd..b9215bc601 100644
--- a/var/spack/repos/builtin/packages/libxau/package.py
+++ b/var/spack/repos/builtin/packages/libxau/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Libxau(Package):
     """The libXau package contains a library implementing the X11
        Authorization Protocol. This is useful for restricting client
@@ -34,11 +35,10 @@ class Libxau(Package):
     version('1.0.8', '685f8abbffa6d145c0f930f00703b21b')
 
     depends_on('xproto')
+    depends_on('pkg-config', type='build')
 
     def install(self, spec, prefix):
-        # FIXME: Modify the configure line to suit your build system here.
         configure('--prefix=%s' % prefix)
 
-        # FIXME: Add logic to build and install here
         make()
         make("install")
diff --git a/var/spack/repos/builtin/packages/libxc/package.py b/var/spack/repos/builtin/packages/libxc/package.py
index 87437373d6..9ea4d1c326 100644
--- a/var/spack/repos/builtin/packages/libxc/package.py
+++ b/var/spack/repos/builtin/packages/libxc/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Libxc(Package):
     """Libxc is a library of exchange-correlation functionals for
     density-functional theory."""
@@ -33,7 +34,6 @@ class Libxc(Package):
 
     version('2.2.2', 'd9f90a0d6e36df6c1312b6422280f2ec')
 
-
     def install(self, spec, prefix):
         configure('--prefix=%s' % prefix,
                   '--enable-shared')
diff --git a/var/spack/repos/builtin/packages/libxcb/package.py b/var/spack/repos/builtin/packages/libxcb/package.py
index 586eb970d8..82ddb2742e 100644
--- a/var/spack/repos/builtin/packages/libxcb/package.py
+++ b/var/spack/repos/builtin/packages/libxcb/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Libxcb(Package):
     """The X protocol C-language Binding (XCB) is a replacement
     for Xlib featuring a small footprint, latency hiding, direct
@@ -43,11 +44,14 @@ class Libxcb(Package):
     depends_on('libxau')
 
     def patch(self):
-        filter_file('typedef struct xcb_auth_info_t {', 'typedef struct {', 'src/xcb.h')
-
+        filter_file(
+            'typedef struct xcb_auth_info_t {',
+            'typedef struct {',
+            'src/xcb.h')
 
     def install(self, spec, prefix):
-        env['PKG_CONFIG_PATH'] = env['PKG_CONFIG_PATH'] + ':/usr/lib64/pkgconfig'
+        env['PKG_CONFIG_PATH'] = env[
+            'PKG_CONFIG_PATH'] + ':/usr/lib64/pkgconfig'
         configure("--prefix=%s" % prefix)
 
         make()
diff --git a/var/spack/repos/builtin/packages/libxml2/package.py b/var/spack/repos/builtin/packages/libxml2/package.py
index a6dabd2c05..0f4810fa8a 100644
--- a/var/spack/repos/builtin/packages/libxml2/package.py
+++ b/var/spack/repos/builtin/packages/libxml2/package.py
@@ -36,7 +36,9 @@ class Libxml2(Package):
 
     variant('python', default=False, description='Enable Python support')
 
-    extends('python', when='+python', ignore=r'(bin.*$)|(include.*$)|(share.*$)|(lib/libxml2.*$)|(lib/xml2.*$)|(lib/cmake.*$)')
+    extends('python', when='+python',
+            ignore=r'(bin.*$)|(include.*$)|(share.*$)|(lib/libxml2.*$)|'
+            '(lib/xml2.*$)|(lib/cmake.*$)')
     depends_on('zlib')
     depends_on('xz')
 
diff --git a/var/spack/repos/builtin/packages/libxshmfence/package.py b/var/spack/repos/builtin/packages/libxshmfence/package.py
index 6d63ea6426..fe5d5667e9 100644
--- a/var/spack/repos/builtin/packages/libxshmfence/package.py
+++ b/var/spack/repos/builtin/packages/libxshmfence/package.py
@@ -24,11 +24,12 @@
 ##############################################################################
 from spack import *
 
+
 class Libxshmfence(Package):
     """This is a tiny library that exposes a event API on top of Linux
     futexes."""
 
-    homepage = "http://keithp.com/blogs/dri3_extension/" # not really...
+    homepage = "http://keithp.com/blogs/dri3_extension/"  # not really...
     url      = "http://xorg.freedesktop.org/archive/individual/lib/libxshmfence-1.2.tar.gz"
 
     version('1.2', 'f0b30c0fc568b22ec524859ee28556f1')
diff --git a/var/spack/repos/builtin/packages/libxslt/package.py b/var/spack/repos/builtin/packages/libxslt/package.py
index c6c439ad09..47d1c170c6 100644
--- a/var/spack/repos/builtin/packages/libxslt/package.py
+++ b/var/spack/repos/builtin/packages/libxslt/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Libxslt(Package):
     """Libxslt is the XSLT C library developed for the GNOME
        project. XSLT itself is a an XML language to define
diff --git a/var/spack/repos/builtin/packages/libxsmm/package.py b/var/spack/repos/builtin/packages/libxsmm/package.py
new file mode 100644
index 0000000000..a736490600
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libxsmm/package.py
@@ -0,0 +1,66 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Libxsmm(Package):
+    '''LIBXSMM is a library for small dense and small sparse matrix-matrix
+    multiplications targeting Intel Architecture (x86).'''
+
+    homepage = 'https://github.com/hfp/libxsmm'
+    url      = 'https://github.com/hfp/libxsmm/archive/1.4.3.tar.gz'
+
+    version('1.4.3', '9839bf0fb8be7badf1e97ce4c817149b')
+    version('1.4.2', 'ea025761437f3b5c936821b9ca21ec31')
+    version('1.4.1', '71648500ea4510529845d329091917df')
+    version('1.4',   'b42f91bf5285e7ad0463446e55ebdc2b')
+
+    def patch(self):
+        kwargs = {'ignore_absent': False, 'backup': False, 'string': True}
+        makefile = FileFilter('Makefile.inc')
+
+        # Spack sets CC, CXX, and FC to point to the compiler wrappers
+        # Don't let Makefile.inc overwrite these
+        makefile.filter('CC = icc',         'CC ?= icc', **kwargs)
+        makefile.filter('CC = gcc',         'CC ?= gcc', **kwargs)
+        makefile.filter('CXX = icpc',       'CXX ?= icpc', **kwargs)
+        makefile.filter('CXX = g++',        'CXX ?= g++', **kwargs)
+        makefile.filter('FC = ifort',       'FC ?= ifort', **kwargs)
+        makefile.filter('FC = gfortran',    'FC ?= gfortran', **kwargs)
+
+    def manual_install(self, prefix):
+        install_tree('include', prefix.include)
+        install_tree('lib', prefix.lib)
+        install_tree('documentation', prefix.share + '/libxsmm/doc')
+
+    def install(self, spec, prefix):
+        make_args = [
+            'ROW_MAJOR=0',
+            'INDICES_M={0}'.format(' '.join(str(i) for i in range(1, 25))),
+            'INDICES_N={0}'.format(' '.join(str(i) for i in range(1, 25))),
+            'INDICES_K={0}'.format(' '.join(str(i) for i in range(1, 25)))
+        ]
+        make(*make_args)
+        self.manual_install(prefix)
diff --git a/var/spack/repos/builtin/packages/llvm-lld/package.py b/var/spack/repos/builtin/packages/llvm-lld/package.py
index 127fe1204d..1dcf88e3c0 100644
--- a/var/spack/repos/builtin/packages/llvm-lld/package.py
+++ b/var/spack/repos/builtin/packages/llvm-lld/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class LlvmLld(Package):
     """lld - The LLVM Linker
        lld is a new set of modular code for creating linker tools."""
diff --git a/var/spack/repos/builtin/packages/llvm/package.py b/var/spack/repos/builtin/packages/llvm/package.py
index e79c123a7e..61ea8daac4 100644
--- a/var/spack/repos/builtin/packages/llvm/package.py
+++ b/var/spack/repos/builtin/packages/llvm/package.py
@@ -23,32 +23,51 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
-import os, glob
+import os
 
 
 class Llvm(Package):
     """The LLVM Project is a collection of modular and reusable compiler and
-       toolchain technologies. Despite its name, LLVM has little to do with
-       traditional virtual machines, though it does provide helpful libraries
-       that can be used to build them. The name "LLVM" itself is not an acronym;
-       it is the full name of the project.
+       toolchain technologies. Despite its name, LLVM has little to do
+       with traditional virtual machines, though it does provide helpful
+       libraries that can be used to build them. The name "LLVM" itself
+       is not an acronym; it is the full name of the project.
+
     """
     homepage = 'http://llvm.org/'
     url = 'http://llvm.org/releases/3.7.1/llvm-3.7.1.src.tar.xz'
 
-    version('3.0', 'a8e5f5f1c1adebae7b4a654c376a6005', url='http://llvm.org/releases/3.0/llvm-3.0.tar.gz') # currently required by mesa package
+    # currently required by mesa package
+    version('3.0', 'a8e5f5f1c1adebae7b4a654c376a6005',
+            url='http://llvm.org/releases/3.0/llvm-3.0.tar.gz')
 
-    variant('debug', default=False, description="Build a debug version of LLVM, this increases binary size by an order of magnitude, make sure you have 20-30gb of space available to build this")
-    variant('clang', default=True, description="Build the LLVM C/C++/Objective-C compiler frontend")
+    variant('debug', default=False,
+            description="Build a debug version of LLVM, this increases "
+            "binary size by an order of magnitude, make sure you have "
+            "20-30gb of space available to build this")
+    variant('clang', default=True,
+            description="Build the LLVM C/C++/Objective-C compiler frontend")
     variant('lldb', default=True, description="Build the LLVM debugger")
-    variant('internal_unwind', default=True, description="Build the libcxxabi libunwind")
-    variant('polly', default=True, description="Build the LLVM polyhedral optimization plugin, only builds for 3.7.0+")
-    variant('libcxx', default=True, description="Build the LLVM C++ standard library")
-    variant('compiler-rt', default=True, description="Build the LLVM compiler runtime, including sanitizers")
-    variant('gold', default=True, description="Add support for LTO with the gold linker plugin")
-    variant('shared_libs', default=False, description="Build all components as shared libraries, faster, less memory to build, less stable")
-    variant('link_dylib', default=False, description="Build and link the libLLVM shared library rather than static")
-    variant('all_targets', default=True, description="Build all supported targets, default targets <current arch>,NVPTX,AMDGPU,CppBackend")
+    variant('internal_unwind', default=True,
+            description="Build the libcxxabi libunwind")
+    variant('polly', default=True,
+            description="Build the LLVM polyhedral optimization plugin, "
+            "only builds for 3.7.0+")
+    variant('libcxx', default=True,
+            description="Build the LLVM C++ standard library")
+    variant('compiler-rt', default=True,
+            description="Build LLVM compiler runtime, including sanitizers")
+    variant('gold', default=True,
+            description="Add support for LTO with the gold linker plugin")
+    variant('shared_libs', default=False,
+            description="Build all components as shared libraries, faster, "
+            "less memory to build, less stable")
+    variant('link_dylib', default=False,
+            description="Build and link the libLLVM shared library rather "
+            "than static")
+    variant('all_targets', default=True,
+            description="Build all supported targets, default targets "
+            "<current arch>,NVPTX,AMDGPU,CppBackend")
 
     # Build dependency
     depends_on('cmake@2.8.12.2:', type='build')
@@ -68,147 +87,147 @@ class Llvm(Package):
     depends_on('gmp', when='@:3.6.999 +polly')
     depends_on('isl', when='@:3.6.999 +polly')
 
-    base_url =  'http://llvm.org/releases/%%(version)s/%(pkg)s-%%(version)s.src.tar.xz'
-    llvm_url = base_url % { 'pkg' : 'llvm'}
+    base_url = 'http://llvm.org/releases/%%(version)s/%(pkg)s-%%(version)s.src.tar.xz'
+    llvm_url = base_url % {'pkg': 'llvm'}
 
     resources = {
-                    'compiler-rt' : {
-                        'url' : base_url % { 'pkg' : 'compiler-rt'},
-                        'destination' : 'projects',
-                        'placement' : 'compiler-rt',
-                    },
-                    'openmp' : {
-                        'url' : base_url % { 'pkg' : 'openmp'},
-                        'destination' : 'projects',
-                        'placement' : 'openmp',
-                    },
-                    'libcxx' : {
-                        'url' : base_url % { 'pkg' : 'libcxx'},
-                        'destination' : 'projects',
-                        'placement' : 'libcxx',
-                    },
-                    'libcxxabi' : {
-                        'url' :  base_url % { 'pkg' : 'libcxxabi'},
-                        'destination' : 'projects',
-                        'placement' : 'libcxxabi',
-                    },
-                    'clang' : {
-                        'url' :  base_url % { 'pkg' : 'cfe'},
-                        'destination' : 'tools',
-                        'placement' : 'clang',
-                    },
-                    'clang-tools-extra' : {
-                        'url' :  base_url % { 'pkg' : 'clang-tools-extra'},
-                        'destination' : 'tools/clang/tools',
-                        'placement' : 'extra',
-                    },
-                    'lldb' : {
-                        'url' :  base_url % { 'pkg' : 'lldb'},
-                        'destination' : 'tools',
-                        'placement' : 'lldb',
-                    },
-                    'polly' : {
-                        'url' :  base_url % { 'pkg' : 'polly'},
-                        'destination' : 'tools',
-                        'placement' : 'polly',
-                    },
-                    'llvm-libunwind' : {
-                        'url' :  base_url % { 'pkg' : 'libunwind'},
-                        'destination' : 'projects',
-                        'placement' : 'libunwind',
-                    },
-                }
+        'compiler-rt': {
+            'url': base_url % {'pkg': 'compiler-rt'},
+            'destination': 'projects',
+            'placement': 'compiler-rt',
+        },
+        'openmp': {
+            'url': base_url % {'pkg': 'openmp'},
+            'destination': 'projects',
+            'placement': 'openmp',
+        },
+        'libcxx': {
+            'url': base_url % {'pkg': 'libcxx'},
+            'destination': 'projects',
+            'placement': 'libcxx',
+        },
+        'libcxxabi': {
+            'url':  base_url % {'pkg': 'libcxxabi'},
+            'destination': 'projects',
+            'placement': 'libcxxabi',
+        },
+        'clang': {
+            'url':  base_url % {'pkg': 'cfe'},
+            'destination': 'tools',
+            'placement': 'clang',
+        },
+        'clang-tools-extra': {
+            'url':  base_url % {'pkg': 'clang-tools-extra'},
+            'destination': 'tools/clang/tools',
+            'placement': 'extra',
+        },
+        'lldb': {
+            'url':  base_url % {'pkg': 'lldb'},
+            'destination': 'tools',
+            'placement': 'lldb',
+        },
+        'polly': {
+            'url':  base_url % {'pkg': 'polly'},
+            'destination': 'tools',
+            'placement': 'polly',
+        },
+        'llvm-libunwind': {
+            'url':  base_url % {'pkg': 'libunwind'},
+            'destination': 'projects',
+            'placement': 'libunwind',
+        },
+    }
     releases = [
-                  {
-                    'version' : 'trunk',
-                    'repo' : 'http://llvm.org/svn/llvm-project/llvm/trunk',
-                    'resources' : {
-                        'compiler-rt' : 'http://llvm.org/svn/llvm-project/compiler-rt/trunk',
-                        'openmp' : 'http://llvm.org/svn/llvm-project/openmp/trunk',
-                        'polly' : 'http://llvm.org/svn/llvm-project/polly/trunk',
-                        'libcxx' : 'http://llvm.org/svn/llvm-project/libcxx/trunk',
-                        'libcxxabi' : 'http://llvm.org/svn/llvm-project/libcxxabi/trunk',
-                        'clang' : 'http://llvm.org/svn/llvm-project/cfe/trunk',
-                        'clang-tools-extra' : 'http://llvm.org/svn/llvm-project/clang-tools-extra/trunk',
-                        'lldb' : 'http://llvm.org/svn/llvm-project/lldb/trunk',
-                        'llvm-libunwind' : 'http://llvm.org/svn/llvm-project/libunwind/trunk',
-                        }
-                  },
-                  {
-                    'version' : '3.8.0',
-                    'md5':'07a7a74f3c6bd65de4702bf941b511a0',
-                    'resources' : {
-                        'compiler-rt' : 'd6fcbe14352ffb708e4d1ac2e48bb025',
-                        'openmp' : '8fd7cc35d48051613cf1e750e9f22e40',
-                        'polly' : '1b3b20f52d34a4024e21a4ea7112caa7',
-                        'libcxx' : 'd6e0bdbbee39f7907ad74fd56d03b88a',
-                        'libcxxabi' : 'bbe6b4d72c7c5978550d370af529bcf7',
-                        'clang' : 'cc99e7019bb74e6459e80863606250c5',
-                        'clang-tools-extra' : 'c2344f50e0eea0b402f0092a80ddc036',
-                        'lldb' : 'a5da35ed9cc8c8817ee854e3dbfba00e',
-                        'llvm-libunwind' : '162ade468607f153cca12be90b5194fa',
-                        }
-                  },
-                  {
-                    'version' : '3.7.1',
-                    'md5':'bf8b3a2c79e61212c5409041dfdbd319',
-                    'resources' : {
-                        'compiler-rt' : '1c6975daf30bb3b0473b53c3a1a6ff01',
-                        'openmp' : 'b4ad08cda4e5c22e42b66062b140438e',
-                        'polly' : '3a2a7367002740881637f4d47bca4dc3',
-                        'libcxx' : 'f9c43fa552a10e14ff53b94d04bea140',
-                        'libcxxabi' : '52d925afac9f97e9dcac90745255c169',
-                        'clang' : '0acd026b5529164197563d135a8fd83e',
-                        'clang-tools-extra' : '5d49ff745037f061a7c86aeb6a24c3d2',
-                        'lldb' : 'a106d8a0d21fc84d76953822fbaf3398',
-                        'llvm-libunwind' : '814bd52c9247c5d04629658fbcb3ab8c',
-                        }
-                  },
-                  {
-                    'version' : '3.7.0',
-                    'md5':'b98b9495e5655a672d6cb83e1a180f8e',
-                    'resources' : {
-                        'compiler-rt' : '383c10affd513026f08936b5525523f5',
-                        'openmp' : 'f482c86fdead50ba246a1a2b0bbf206f',
-                        'polly' : '32f93ffc9cc7e042df22089761558f8b',
-                        'libcxx' : '46aa5175cbe1ad42d6e9c995968e56dd',
-                        'libcxxabi' : '5aa769e2fca79fa5335cfae8f6258772',
-                        'clang' : '8f9d27335e7331cf0a4711e952f21f01',
-                        'clang-tools-extra' : 'd5a87dacb65d981a427a536f6964642e',
-                        'lldb' : 'e5931740400d1dc3e7db4c7ba2ceff68',
-                        'llvm-libunwind' : '9a75392eb7eb8ed5c0840007e212baf5',
-                        }
-                  },
-                  {
-                    'version' : '3.6.2',
-                    'md5':'0c1ee3597d75280dee603bae9cbf5cc2',
-                    'resources' : {
-                        'compiler-rt' : 'e3bc4eb7ba8c39a6fe90d6c988927f3c',
-                        'openmp' : '65dd5863b9b270960a96817e9152b123',
-                        'libcxx' : '22214c90697636ef960a49aef7c1823a',
-                        'libcxxabi' : '17518e361e4e228f193dd91e8ef54ba2',
-                        'clang' : 'ff862793682f714bb7862325b9c06e20',
-                        'clang-tools-extra' : '3ebc1dc41659fcec3db1b47d81575e06',
-                        'lldb' : '51e5eb552f777b950bb0ff326e60d5f0',
-                        }
-                  },
-                  {
-                    'version' : '3.5.1',
-                    'md5':'2d3d8004f38852aa679e5945b8ce0b14',
-                    'resources' : {
-                        'compiler-rt' : 'd626cfb8a9712cb92b820798ab5bc1f8',
-                        'openmp' : '121ddb10167d7fc38b1f7e4b029cf059',
-                        'libcxx' : '406f09b1dab529f3f7879f4d548329d2',
-                        'libcxxabi' : 'b22c707e8d474a99865ad3c521c3d464',
-                        'clang' : '93f9532f8f7e6f1d8e5c1116907051cb',
-                        'clang-tools-extra' : 'f13f31ed3038acadc6fa63fef812a246',
-                        'lldb' : 'cc5ea8a414c62c33e760517f8929a204',
-                        }
-                  },
-               ]
+        {
+            'version': 'trunk',
+            'repo': 'http://llvm.org/svn/llvm-project/llvm/trunk',
+                    'resources': {
+                        'compiler-rt': 'http://llvm.org/svn/llvm-project/compiler-rt/trunk',
+                        'openmp': 'http://llvm.org/svn/llvm-project/openmp/trunk',
+                        'polly': 'http://llvm.org/svn/llvm-project/polly/trunk',
+                        'libcxx': 'http://llvm.org/svn/llvm-project/libcxx/trunk',
+                        'libcxxabi': 'http://llvm.org/svn/llvm-project/libcxxabi/trunk',
+                        'clang': 'http://llvm.org/svn/llvm-project/cfe/trunk',
+                        'clang-tools-extra': 'http://llvm.org/svn/llvm-project/clang-tools-extra/trunk',
+                        'lldb': 'http://llvm.org/svn/llvm-project/lldb/trunk',
+                        'llvm-libunwind': 'http://llvm.org/svn/llvm-project/libunwind/trunk',
+                    }
+        },
+        {
+            'version': '3.8.0',
+            'md5': '07a7a74f3c6bd65de4702bf941b511a0',
+            'resources': {
+                'compiler-rt': 'd6fcbe14352ffb708e4d1ac2e48bb025',
+                'openmp': '8fd7cc35d48051613cf1e750e9f22e40',
+                'polly': '1b3b20f52d34a4024e21a4ea7112caa7',
+                'libcxx': 'd6e0bdbbee39f7907ad74fd56d03b88a',
+                'libcxxabi': 'bbe6b4d72c7c5978550d370af529bcf7',
+                'clang': 'cc99e7019bb74e6459e80863606250c5',
+                'clang-tools-extra': 'c2344f50e0eea0b402f0092a80ddc036',
+                'lldb': 'a5da35ed9cc8c8817ee854e3dbfba00e',
+                        'llvm-libunwind': '162ade468607f153cca12be90b5194fa',
+            }
+        },
+        {
+            'version': '3.7.1',
+            'md5': 'bf8b3a2c79e61212c5409041dfdbd319',
+            'resources': {
+                'compiler-rt': '1c6975daf30bb3b0473b53c3a1a6ff01',
+                'openmp': 'b4ad08cda4e5c22e42b66062b140438e',
+                'polly': '3a2a7367002740881637f4d47bca4dc3',
+                'libcxx': 'f9c43fa552a10e14ff53b94d04bea140',
+                'libcxxabi': '52d925afac9f97e9dcac90745255c169',
+                'clang': '0acd026b5529164197563d135a8fd83e',
+                'clang-tools-extra': '5d49ff745037f061a7c86aeb6a24c3d2',
+                'lldb': 'a106d8a0d21fc84d76953822fbaf3398',
+                        'llvm-libunwind': '814bd52c9247c5d04629658fbcb3ab8c',
+            }
+        },
+        {
+            'version': '3.7.0',
+            'md5': 'b98b9495e5655a672d6cb83e1a180f8e',
+            'resources': {
+                'compiler-rt': '383c10affd513026f08936b5525523f5',
+                'openmp': 'f482c86fdead50ba246a1a2b0bbf206f',
+                'polly': '32f93ffc9cc7e042df22089761558f8b',
+                'libcxx': '46aa5175cbe1ad42d6e9c995968e56dd',
+                'libcxxabi': '5aa769e2fca79fa5335cfae8f6258772',
+                'clang': '8f9d27335e7331cf0a4711e952f21f01',
+                'clang-tools-extra': 'd5a87dacb65d981a427a536f6964642e',
+                'lldb': 'e5931740400d1dc3e7db4c7ba2ceff68',
+                        'llvm-libunwind': '9a75392eb7eb8ed5c0840007e212baf5',
+            }
+        },
+        {
+            'version': '3.6.2',
+            'md5': '0c1ee3597d75280dee603bae9cbf5cc2',
+            'resources': {
+                'compiler-rt': 'e3bc4eb7ba8c39a6fe90d6c988927f3c',
+                'openmp': '65dd5863b9b270960a96817e9152b123',
+                'libcxx': '22214c90697636ef960a49aef7c1823a',
+                'libcxxabi': '17518e361e4e228f193dd91e8ef54ba2',
+                'clang': 'ff862793682f714bb7862325b9c06e20',
+                'clang-tools-extra': '3ebc1dc41659fcec3db1b47d81575e06',
+                'lldb': '51e5eb552f777b950bb0ff326e60d5f0',
+            }
+        },
+        {
+            'version': '3.5.1',
+            'md5': '2d3d8004f38852aa679e5945b8ce0b14',
+            'resources': {
+                'compiler-rt': 'd626cfb8a9712cb92b820798ab5bc1f8',
+                'openmp': '121ddb10167d7fc38b1f7e4b029cf059',
+                'libcxx': '406f09b1dab529f3f7879f4d548329d2',
+                'libcxxabi': 'b22c707e8d474a99865ad3c521c3d464',
+                'clang': '93f9532f8f7e6f1d8e5c1116907051cb',
+                'clang-tools-extra': 'f13f31ed3038acadc6fa63fef812a246',
+                'lldb': 'cc5ea8a414c62c33e760517f8929a204',
+            }
+        },
+    ]
 
     for release in releases:
-        if release['version'] == 'trunk' :
+        if release['version'] == 'trunk':
             version(release['version'], svn=release['repo'])
 
             for name, repo in release['resources'].items():
@@ -230,18 +249,19 @@ class Llvm(Package):
 
     def install(self, spec, prefix):
         env['CXXFLAGS'] = self.compiler.cxx11_flag
-        cmake_args = [ arg for arg in std_cmake_args if 'BUILD_TYPE' not in arg ]
+        cmake_args = [arg for arg in std_cmake_args if 'BUILD_TYPE' not in arg]
 
         build_type = 'RelWithDebInfo' if '+debug' in spec else 'Release'
         cmake_args.extend([
-                '..',
-                '-DCMAKE_BUILD_TYPE=' + build_type,
-                '-DLLVM_REQUIRES_RTTI:BOOL=ON',
-                '-DCLANG_DEFAULT_OPENMP_RUNTIME:STRING=libomp',
-                '-DPYTHON_EXECUTABLE:PATH=%s/bin/python' % spec['python'].prefix ])
+            '..',
+            '-DCMAKE_BUILD_TYPE=' + build_type,
+            '-DLLVM_REQUIRES_RTTI:BOOL=ON',
+            '-DCLANG_DEFAULT_OPENMP_RUNTIME:STRING=libomp',
+            '-DPYTHON_EXECUTABLE:PATH=%s/bin/python' % spec['python'].prefix])
 
         if '+gold' in spec:
-            cmake_args.append('-DLLVM_BINUTILS_INCDIR=' + os.path.join( spec['binutils'].prefix, 'include'))
+            cmake_args.append('-DLLVM_BINUTILS_INCDIR=' +
+                              os.path.join(spec['binutils'].prefix, 'include'))
         if '+polly' in spec:
             cmake_args.append('-DLINK_POLLY_INTO_TOOLS:Bool=ON')
         else:
@@ -265,7 +285,7 @@ class Llvm(Package):
         if '+link_dylib' in spec:
             cmake_args.append('-DLLVM_LINK_LLVM_DYLIB:Bool=ON')
 
-        if '+all_targets' not in spec: # all is default on cmake
+        if '+all_targets' not in spec:  # all is default on cmake
             targets = ['CppBackend', 'NVPTX', 'AMDGPU']
             if 'x86' in spec.architecture.target.lower():
                 targets.append('X86')
@@ -279,13 +299,16 @@ class Llvm(Package):
                   'power' in spec.architecture.target.lower()):
                 targets.append('PowerPC')
 
-            cmake_args.append('-DLLVM_TARGETS_TO_BUILD:Bool=' + ';'.join(targets))
+            cmake_args.append(
+                '-DLLVM_TARGETS_TO_BUILD:Bool=' + ';'.join(targets))
 
-        if  '+clang' not in spec:
+        if '+clang' not in spec:
             if '+clang_extra' in spec:
-                raise SpackException('The clang_extra variant requires the clang variant to be selected')
+                raise SpackException(
+                    'The clang_extra variant requires the `+clang` variant.')
             if '+lldb' in spec:
-                raise SpackException('The lldb variant requires the clang variant to be selected')
+                raise SpackException(
+                    'The lldb variant requires the `+clang` variant')
 
         with working_dir('spack-build', create=True):
             cmake(*cmake_args)
diff --git a/var/spack/repos/builtin/packages/lmdb/package.py b/var/spack/repos/builtin/packages/lmdb/package.py
index 79c020b2df..8c6c23d8dc 100644
--- a/var/spack/repos/builtin/packages/lmdb/package.py
+++ b/var/spack/repos/builtin/packages/lmdb/package.py
@@ -25,12 +25,12 @@
 import os
 from spack import *
 
+
 class Lmdb(Package):
     """Read-only mirror of official repo on openldap.org. Issues and
     pull requests here are ignored. Use OpenLDAP ITS for issues.
     http://www.openldap.org/software/repo.html"""
 
-
     homepage = "http://www.openldap.org/software/repo.html"
     url      = "https://github.com/LMDB/lmdb/archive/LMDB_0.9.16.tar.gz"
 
diff --git a/var/spack/repos/builtin/packages/lmod/fix_tclsh_paths.patch b/var/spack/repos/builtin/packages/lmod/fix_tclsh_paths.patch
new file mode 100644
index 0000000000..70f0d47925
--- /dev/null
+++ b/var/spack/repos/builtin/packages/lmod/fix_tclsh_paths.patch
@@ -0,0 +1,10 @@
+--- a/Makefile.in	2016-07-21 13:03:27.861000000 -0400
++++ b/Makefile.in	2016-07-21 13:03:58.416000000 -0400
+@@ -197,6 +197,7 @@
+ 	        -e 's|@colorize@|$(COLORIZE)|g'                       	   	  \
+ 	        -e 's|@duplicate_paths@|$(DUPLICATE_PATHS)|g'      	   	  \
+ 	        -e 's|@allow_tcl_mfiles@|$(ALLOW_TCL_MFILES)|g'      	   	  \
++	        -e 's|@path_to_tclsh@|$(PATH_TO_TCLSH)|g'	      	   	  \
+ 	        -e 's|@mpath_avail@|$(MPATH_AVAIL)|g'            	   	  \
+ 	        -e 's|@short_time@|$(SHORT_TIME)|g'                   	   	  \
+ 	        -e 's|@cacheDirs@|$(SPIDER_CACHE_DIRS)|g'             	   	  \
diff --git a/var/spack/repos/builtin/packages/lmod/package.py b/var/spack/repos/builtin/packages/lmod/package.py
index efa235f646..69965bc423 100644
--- a/var/spack/repos/builtin/packages/lmod/package.py
+++ b/var/spack/repos/builtin/packages/lmod/package.py
@@ -23,6 +23,7 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
+from glob import glob
 
 
 class Lmod(Package):
@@ -34,9 +35,10 @@ class Lmod(Package):
     variable. Modulefiles for Library packages provide environment variables
     that specify where the library and header files can be found.
     """
-    homepage = 'https://www.tacc.utexas.edu/research-development/tacc-projects/lmod'  # NOQA: ignore=E501
+    homepage = 'https://www.tacc.utexas.edu/research-development/tacc-projects/lmod'
     url = 'https://github.com/TACC/Lmod/archive/6.4.1.tar.gz'
 
+    version('6.4.5', '14f6c58dbc0a5a75574d795eac2c1e3c')
     version('6.4.1', '7978ba777c8aa41a4d8c05fec5f780f4')
     version('6.3.7', '0fa4d5a24c41cae03776f781aa2dedc1')
     version('6.0.1', '91abf52fe5033bd419ffe2842ebe7af9')
@@ -44,6 +46,7 @@ class Lmod(Package):
     depends_on('lua@5.2:')
     depends_on('lua-luaposix', type=nolink)
     depends_on('lua-luafilesystem', type=nolink)
+    depends_on('tcl', type=nolink)
 
     parallel = False
 
@@ -53,6 +56,17 @@ class Lmod(Package):
         spack_env.append_path('LUA_PATH', stage_lua_path.format(
             version=self.version), separator=';')
 
+    patch('fix_tclsh_paths.patch', when='@:6.4.3')
+
+    def patch(self):
+        """The tcl scripts should use the tclsh that was discovered
+           by the configure script.  Touch up their #! lines so that the
+           sed in the Makefile's install step has something to work on.
+           Requires the change in the associated patch file.fg"""
+        if self.spec.version <= Version('6.4.3'):
+            for tclscript in glob('src/*.tcl'):
+                filter_file(r'^#!.*tclsh', '#!@path_to_tclsh@', tclscript)
+
     def install(self, spec, prefix):
         configure('--prefix=%s' % prefix)
         make('install')
diff --git a/var/spack/repos/builtin/packages/lwgrp/package.py b/var/spack/repos/builtin/packages/lwgrp/package.py
index 471098c873..9322d69b9b 100644
--- a/var/spack/repos/builtin/packages/lwgrp/package.py
+++ b/var/spack/repos/builtin/packages/lwgrp/package.py
@@ -22,9 +22,9 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import os
 from spack import *
 
+
 class Lwgrp(Package):
     """Thie light-weight group library provides process group
        representations using O(log N) space and time."""
diff --git a/var/spack/repos/builtin/packages/lwm2/package.py b/var/spack/repos/builtin/packages/lwm2/package.py
index 340474b47e..063204b84a 100644
--- a/var/spack/repos/builtin/packages/lwm2/package.py
+++ b/var/spack/repos/builtin/packages/lwm2/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Lwm2(Package):
     """LWM2: Light Weight Measurement Module.  This is a PMPI module
        that can collect a number of time-sliced MPI and POSIX I/O
diff --git a/var/spack/repos/builtin/packages/m4/package.py b/var/spack/repos/builtin/packages/m4/package.py
index dcb306dcd3..b3bb5e61ce 100644
--- a/var/spack/repos/builtin/packages/m4/package.py
+++ b/var/spack/repos/builtin/packages/m4/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class M4(Package):
     """GNU M4 is an implementation of the traditional Unix macro processor."""
     homepage = "https://www.gnu.org/software/m4/m4.html"
@@ -33,14 +34,16 @@ class M4(Package):
 
     patch('pgi.patch', when='@1.4.17')
 
-    variant('sigsegv', default=True, description="Build the libsigsegv dependency")
+    variant('sigsegv', default=True,
+            description="Build the libsigsegv dependency")
 
     depends_on('libsigsegv', when='+sigsegv')
 
     def install(self, spec, prefix):
         configure_args = []
         if 'libsigsegv' in spec:
-            configure_args.append('--with-libsigsegv-prefix=%s' % spec['libsigsegv'].prefix)
+            configure_args.append('--with-libsigsegv-prefix=%s' %
+                                  spec['libsigsegv'].prefix)
         else:
             configure_args.append('--without-libsigsegv-prefix')
 
diff --git a/var/spack/repos/builtin/packages/mafft/package.py b/var/spack/repos/builtin/packages/mafft/package.py
new file mode 100644
index 0000000000..131b8c58f9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mafft/package.py
@@ -0,0 +1,42 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Mafft(Package):
+    """MAFFT is a multiple sequence alignment program for unix-like
+       operating systems.  It offers a range of multiple alignment
+       methods, L-INS-i (accurate; for alignment of <~200 sequences),
+       FFT-NS-2 (fast; for alignment of <~30,000 sequences), etc."""
+
+    homepage = "http://mafft.cbrc.jp/alignment/software/index.html"
+    url      = "http://mafft.cbrc.jp/alignment/software/mafft-7.221-with-extensions-src.tgz"
+
+    version('7.221', 'b1aad911e51024d631722a2e061ba215')
+
+    def install(self, spec, prefix):
+        with working_dir('core'):
+            make('PREFIX=%s' % prefix)
+            make('PREFIX=%s' % prefix, 'install')
diff --git a/var/spack/repos/builtin/packages/mbedtls/package.py b/var/spack/repos/builtin/packages/mbedtls/package.py
index 13c0ce768f..e1a42c0d9a 100644
--- a/var/spack/repos/builtin/packages/mbedtls/package.py
+++ b/var/spack/repos/builtin/packages/mbedtls/package.py
@@ -24,17 +24,21 @@
 ##############################################################################
 from spack import *
 
+
 class Mbedtls(Package):
-    """
-    mbed TLS (formerly known as PolarSSL) makes it trivially easy for developers to include cryptographic and SSL/TLS capabilities in their (embedded) products, facilitating this functionality with a minimal coding footprint.
+    """mbed TLS (formerly known as PolarSSL) makes it trivially easy for
+       developers to include cryptographic and SSL/TLS capabilities in
+       their (embedded) products, facilitating this functionality with a
+       minimal coding footprint.
+
     """
     homepage = "https://tls.mbed.org"
     url      = "https://github.com/ARMmbed/mbedtls/archive/mbedtls-2.2.1.tar.gz"
 
-    version('2.2.1' , '73a38f96898d6d03e32f55dd9f9a67be')
-    version('2.2.0' , 'eaf4586c1ef93ae872e606b6c1203942')
-    version('2.1.4' , '40cdf67b6c6d92c9cbcfd552d39ea3ae')
-    version('2.1.3' , '7eb4cf1dfa68578a2c8dbd0b6fa752dd')
+    version('2.2.1', '73a38f96898d6d03e32f55dd9f9a67be')
+    version('2.2.0', 'eaf4586c1ef93ae872e606b6c1203942')
+    version('2.1.4', '40cdf67b6c6d92c9cbcfd552d39ea3ae')
+    version('2.1.3', '7eb4cf1dfa68578a2c8dbd0b6fa752dd')
     version('1.3.16', '4144d7320c691f721aeb9e67a1bc38e0')
 
     depends_on('cmake', type='build')
diff --git a/var/spack/repos/builtin/packages/meep/package.py b/var/spack/repos/builtin/packages/meep/package.py
new file mode 100644
index 0000000000..2c1018e711
--- /dev/null
+++ b/var/spack/repos/builtin/packages/meep/package.py
@@ -0,0 +1,109 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Meep(Package):
+    """Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation
+    software package developed at MIT to model electromagnetic systems."""
+
+    homepage = "http://ab-initio.mit.edu/wiki/index.php/Meep"
+
+    version('1.3',   '18a5b9e18008627a0411087e0bb60db5')
+    version('1.2.1', '9be2e743c3a832ae922de9d955d016c5')
+    version('1.1.1', '415e0cd312b6caa22b5dd612490e1ccf')
+
+    variant('blas',    default=True, description='Enable BLAS support')
+    variant('lapack',  default=True, description='Enable LAPACK support')
+    variant('harminv', default=True, description='Enable Harminv support')
+    variant('guile',   default=True, description='Enable Guilde support')
+    variant('libctl',  default=True, description='Enable libctl support')
+    variant('mpi',     default=True, description='Enable MPI support')
+    variant('hdf5',    default=True, description='Enable HDF5 support')
+    variant('gsl',     default=True, description='Enable GSL support')
+
+    depends_on('blas',        when='+blas')
+    depends_on('lapack',      when='+lapack')
+    depends_on('harminv',     when='+harminv')
+    depends_on('guile',       when='+guile')
+    depends_on('libctl@3.2:', when='+libctl')
+    depends_on('mpi',         when='+mpi')
+    depends_on('hdf5~mpi',    when='+hdf5~mpi')
+    depends_on('hdf5+mpi',    when='+hdf5+mpi')
+    depends_on('gsl',         when='+gsl')
+
+    def url_for_version(self, version):
+        base_url = "http://ab-initio.mit.edu/meep"
+        if version > Version('1.1.1'):
+            return "{0}/meep-{1}.tar.gz".format(base_url, version)
+        else:
+            return "{0}/old/meep-{1}.tar.gz".format(base_url, version)
+
+    def install(self, spec, prefix):
+        config_args = [
+            '--prefix={0}'.format(prefix),
+            '--enable-shared'
+        ]
+
+        if '+blas' in spec:
+            config_args.append('--with-blas={0}'.format(
+                spec['blas'].prefix.lib))
+        else:
+            config_args.append('--without-blas')
+
+        if '+lapack' in spec:
+            config_args.append('--with-lapack={0}'.format(
+                spec['lapack'].prefix.lib))
+        else:
+            config_args.append('--without-lapack')
+
+        if '+libctl' in spec:
+            config_args.append('--with-libctl={0}'.format(
+                join_path(spec['libctl'].prefix.share, 'libctl')))
+        else:
+            config_args.append('--without-libctl')
+
+        if '+mpi' in spec:
+            config_args.append('--with-mpi')
+        else:
+            config_args.append('--without-mpi')
+
+        if '+hdf5' in spec:
+            config_args.append('--with-hdf5')
+        else:
+            config_args.append('--without-hdf5')
+
+        configure(*config_args)
+
+        make()
+
+        # aniso_disp test fails unless installed with harminv
+        # near2far test fails unless installed with gsl
+        if self.run_tests and '+harminv' in spec and '+gsl' in spec:
+            # Most tests fail when run in parallel
+            # 2D_convergence tests still fails to converge for unknown reasons
+            make('check', parallel=False)
+
+        make('install')
diff --git a/var/spack/repos/builtin/packages/memaxes/package.py b/var/spack/repos/builtin/packages/memaxes/package.py
index 31672abaec..ffad167788 100644
--- a/var/spack/repos/builtin/packages/memaxes/package.py
+++ b/var/spack/repos/builtin/packages/memaxes/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Memaxes(Package):
     """MemAxes is a visualizer for sampled memory trace data."""
 
diff --git a/var/spack/repos/builtin/packages/mesa/package.py b/var/spack/repos/builtin/packages/mesa/package.py
index 3bad17b5cb..299b9a9267 100644
--- a/var/spack/repos/builtin/packages/mesa/package.py
+++ b/var/spack/repos/builtin/packages/mesa/package.py
@@ -24,13 +24,13 @@
 ##############################################################################
 from spack import *
 
+
 class Mesa(Package):
     """Mesa is an open-source implementation of the OpenGL
     specification - a system for rendering interactive 3D graphics."""
 
     homepage = "http://www.mesa3d.org"
     url      = "ftp://ftp.freedesktop.org/pub/mesa/older-versions/8.x/8.0.5/MesaLib-8.0.5.tar.gz"
-    # url      = "ftp://ftp.freedesktop.org/pub/mesa/10.4.4/MesaLib-10.4.4.tar.gz"
 
     # version('10.4.4', '8d863a3c209bf5116b2babfccccc68ce')
     version('8.0.5', 'cda5d101f43b8784fa60bdeaca4056f2')
@@ -50,7 +50,6 @@ class Mesa(Package):
     # depends_on("libxcb")
     # depends_on("libxshmfence")
 
-
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
 
diff --git a/var/spack/repos/builtin/packages/metis/package.py b/var/spack/repos/builtin/packages/metis/package.py
index 2180f2cce2..9f8ed5c9e8 100644
--- a/var/spack/repos/builtin/packages/metis/package.py
+++ b/var/spack/repos/builtin/packages/metis/package.py
@@ -43,12 +43,16 @@ class Metis(Package):
     version('5.0.2', 'acb521a4e8c2e6dd559a7f9abd0468c5')
     version('4.0.3', 'd3848b454532ef18dc83e4fb160d1e10')
 
-    variant('shared', default=True, description='Enables the build of shared libraries')
-    variant('debug', default=False, description='Builds the library in debug mode')
+    variant('shared', default=True,
+            description='Enables the build of shared libraries')
+    variant('debug', default=False,
+            description='Builds the library in debug mode')
     variant('gdb', default=False, description='Enables gdb support')
 
-    variant('idx64', default=False, description='Use int64_t as default index type')
-    variant('real64', default=False, description='Use double precision floating point types')
+    variant('idx64', default=False,
+            description='Use int64_t as default index type')
+    variant('real64', default=False,
+            description='Use double precision floating point types')
 
     depends_on('cmake@2.8:', when='@5:', type='build')
 
diff --git a/var/spack/repos/builtin/packages/mfem/package.py b/var/spack/repos/builtin/packages/mfem/package.py
index e7a1d96388..fd91f705eb 100644
--- a/var/spack/repos/builtin/packages/mfem/package.py
+++ b/var/spack/repos/builtin/packages/mfem/package.py
@@ -23,7 +23,9 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
-import glob, string
+import glob
+import string
+
 
 class Mfem(Package):
     """Free, lightweight, scalable C++ library for finite element methods."""
@@ -31,10 +33,12 @@ class Mfem(Package):
     homepage = 'http://www.mfem.org'
     url      = 'https://github.com/mfem/mfem'
 
-    version('3.2', '2938c3deed4ec4f7fd5b5f5cfe656845282e86e2dcd477d292390058b7b94340',
+    version('3.2',
+            '2938c3deed4ec4f7fd5b5f5cfe656845282e86e2dcd477d292390058b7b94340',
             url='http://goo.gl/Y9T75B', expand=False, preferred=True)
 
-    version('3.1', '841ea5cf58de6fae4de0f553b0e01ebaab9cd9c67fa821e8a715666ecf18fc57',
+    version('3.1',
+            '841ea5cf58de6fae4de0f553b0e01ebaab9cd9c67fa821e8a715666ecf18fc57',
             url='http://goo.gl/xrScXn', expand=False)
 #    version('3.1', git='https://github.com/mfem/mfem.git',
 #            commit='dbae60fe32e071989b52efaaf59d7d0eb2a3b574')
@@ -71,8 +75,9 @@ class Mfem(Package):
         if '+suite-sparse' in spec and ('+metis' not in spec or
                                         '+lapack' not in spec):
             raise InstallError('mfem+suite-sparse must be built with ' +
-            '+metis and +lapack!')
-        if 'metis@5:' in spec and '%clang' in spec and ('^cmake %gcc' not in spec):
+                               '+metis and +lapack!')
+        if 'metis@5:' in spec and '%clang' in spec and (
+                '^cmake %gcc' not in spec):
             raise InstallError('To work around CMake bug with clang, must ' +
                                'build mfem with mfem[+variants] %clang ' +
                                '^cmake %gcc to force CMake to build with gcc')
@@ -86,15 +91,17 @@ class Mfem(Package):
         if '+lapack' in spec:
             lapack_lib = '-L{0} -llapack -L{1} -lblas'.format(
                 spec['lapack'].prefix.lib, spec['blas'].prefix.lib)
-            options.extend(['MFEM_USE_LAPACK=YES',
-                            'LAPACK_OPT=-I%s' % spec['lapack'].prefix.include,
-                            'LAPACK_LIB=%s' % lapack_lib])
+            options.extend([
+                'MFEM_USE_LAPACK=YES',
+                'LAPACK_OPT=-I%s' % spec['lapack'].prefix.include,
+                'LAPACK_LIB=%s' % lapack_lib])
 
         if '+hypre' in spec:
-            options.extend(['HYPRE_DIR=%s' % spec['hypre'].prefix,
-                            'HYPRE_OPT=-I%s' % spec['hypre'].prefix.include,
-                            'HYPRE_LIB=-L%s' % spec['hypre'].prefix.lib +
-                            ' -lHYPRE'])
+            options.extend([
+                'HYPRE_DIR=%s' % spec['hypre'].prefix,
+                'HYPRE_OPT=-I%s' % spec['hypre'].prefix.include,
+                'HYPRE_LIB=-L%s' % spec['hypre'].prefix.lib +
+                ' -lHYPRE'])
 
         if '+metis' in spec:
             metis_lib = '-L%s -lmetis' % spec['metis'].prefix.lib
@@ -102,22 +109,26 @@ class Mfem(Package):
                 metis_str = 'MFEM_USE_METIS_5=YES'
             else:
                 metis_str = 'MFEM_USE_METIS_5=NO'
-            options.extend([metis_str,
-                            'METIS_DIR=%s' % spec['metis'].prefix,
-                            'METIS_OPT=-I%s' % spec['metis'].prefix.include,
-                            'METIS_LIB=%s' % metis_lib])
+            options.extend([
+                metis_str,
+                'METIS_DIR=%s' % spec['metis'].prefix,
+                'METIS_OPT=-I%s' % spec['metis'].prefix.include,
+                'METIS_LIB=%s' % metis_lib])
 
-        if '+mpi' in spec: options.extend(['MFEM_USE_MPI=YES'])
+        if '+mpi' in spec:
+            options.extend(['MFEM_USE_MPI=YES'])
 
         if '+suite-sparse' in spec:
             ssp = spec['suite-sparse'].prefix
             ss_lib = '-L%s' % ssp.lib
             ss_lib += (' -lumfpack -lcholmod -lcolamd -lamd -lcamd' +
-                        ' -lccolamd -lsuitesparseconfig')
+                       ' -lccolamd -lsuitesparseconfig')
 
             no_librt_archs = ['darwin-i686', 'darwin-x86_64']
-            no_rt = any(map(lambda a: spec.satisfies('='+a), no_librt_archs))
-            if not no_rt: ss_lib += ' -lrt'
+            no_rt = any(map(lambda a: spec.satisfies('=' + a),
+                            no_librt_archs))
+            if not no_rt:
+                ss_lib += ' -lrt'
             ss_lib += (' ' + metis_lib + ' ' + lapack_lib)
 
             options.extend(['MFEM_USE_SUITESPARSE=YES',
@@ -125,10 +136,11 @@ class Mfem(Package):
                             'SUITESPARSE_OPT=-I%s' % ssp.include,
                             'SUITESPARSE_LIB=%s' % ss_lib])
 
-        if '+debug' in spec: options.extend(['MFEM_DEBUG=YES'])
+        if '+debug' in spec:
+            options.extend(['MFEM_DEBUG=YES'])
 
         # Dirty hack to cope with URL redirect
-        tgz_file = string.split(self.url,'/')[-1]
+        tgz_file = string.split(self.url, '/')[-1]
         tar = which('tar')
         tar('xzvf', tgz_file)
         cd(glob.glob('mfem*')[0])
@@ -138,12 +150,12 @@ class Mfem(Package):
         make('all')
 
         # Run a small test before installation
-        args = ['-m', join_path('data','star.mesh'), '--no-visualization']
+        args = ['-m', join_path('data', 'star.mesh'), '--no-visualization']
         if '+mpi' in spec:
             Executable(join_path(spec['mpi'].prefix.bin,
                                  'mpirun'))('-np',
                                             '4',
-                                            join_path('examples','ex1p'),
+                                            join_path('examples', 'ex1p'),
                                             *args)
         else:
             Executable(join_path('examples', 'ex1'))(*args)
diff --git a/var/spack/repos/builtin/packages/mkl/package.py b/var/spack/repos/builtin/packages/mkl/package.py
index 6ea64f5313..71a233ff3e 100644
--- a/var/spack/repos/builtin/packages/mkl/package.py
+++ b/var/spack/repos/builtin/packages/mkl/package.py
@@ -12,9 +12,9 @@ class Mkl(IntelInstaller):
     mirror, see http://software.llnl.gov/spack/mirrors.html.
 
     To set the threading layer at run time set MKL_THREADING_LAYER
-    variable to one of the following values: INTEL, SEQUENTIAL, PGI.
+    variable to one of the following values: INTEL (default), SEQUENTIAL, PGI.
     To set interface layer at run time, use set the MKL_INTERFACE_LAYER
-    variable to LP64 or ILP64.
+    variable to LP64 (default) or ILP64.
     """
 
     homepage = "https://software.intel.com/en-us/intel-mkl"
@@ -38,6 +38,13 @@ class Mkl(IntelInstaller):
         for f in os.listdir(mkl_dir):
             os.symlink(os.path.join(mkl_dir, f), os.path.join(self.prefix, f))
 
+        # Unfortunately MKL libs are natively distrubted in prefix/lib/intel64.
+        # To make MKL play nice with Spack, symlink all files to prefix/lib:
+        mkl_lib_dir = os.path.join(prefix, "lib", "intel64")
+        for f in os.listdir(mkl_lib_dir):
+            os.symlink(os.path.join(mkl_lib_dir, f),
+                       os.path.join(self.prefix, "lib", f))
+
     def setup_dependent_package(self, module, dspec):
         # For now use Single Dynamic Library:
         # To set the threading layer at run time, use the
@@ -53,6 +60,7 @@ class Mkl(IntelInstaller):
         name = 'libmkl_rt.%s' % dso_suffix
         libdir = find_library_path(name, self.prefix.lib64, self.prefix.lib)
 
+        # Now set blas/lapack libs:
         self.spec.blas_shared_lib   = join_path(libdir, name)
         self.spec.lapack_shared_lib = self.spec.blas_shared_lib
 
diff --git a/var/spack/repos/builtin/packages/mpc/package.py b/var/spack/repos/builtin/packages/mpc/package.py
index 92eb976f8b..71cacd5dfe 100644
--- a/var/spack/repos/builtin/packages/mpc/package.py
+++ b/var/spack/repos/builtin/packages/mpc/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Mpc(Package):
     """Gnu Mpc is a C library for the arithmetic of complex numbers
        with arbitrarily high precision and correct rounding of the
diff --git a/var/spack/repos/builtin/packages/mpe2/package.py b/var/spack/repos/builtin/packages/mpe2/package.py
index f69ea2d65b..a129d59949 100644
--- a/var/spack/repos/builtin/packages/mpe2/package.py
+++ b/var/spack/repos/builtin/packages/mpe2/package.py
@@ -24,8 +24,9 @@
 ##############################################################################
 from spack import *
 
+
 class Mpe2(Package):
-    """Message Passing Extensions (MPE) -- Parallel, shared X window graphics"""
+    """Message Passing Extensions (MPE): Parallel, shared X window graphics"""
 
     homepage = "http://www.mcs.anl.gov/research/projects/perfvis/software/MPE/"
     url      = "ftp://ftp.mcs.anl.gov/pub/mpi/mpe/mpe2-1.3.0.tar.gz"
diff --git a/var/spack/repos/builtin/packages/mpfr/package.py b/var/spack/repos/builtin/packages/mpfr/package.py
index ed3926a8ab..5777cd1926 100644
--- a/var/spack/repos/builtin/packages/mpfr/package.py
+++ b/var/spack/repos/builtin/packages/mpfr/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Mpfr(Package):
     """The MPFR library is a C library for multiple-precision
        floating-point computations with correct rounding."""
diff --git a/var/spack/repos/builtin/packages/mpibash/package.py b/var/spack/repos/builtin/packages/mpibash/package.py
index e659663d90..f3feaaaa42 100644
--- a/var/spack/repos/builtin/packages/mpibash/package.py
+++ b/var/spack/repos/builtin/packages/mpibash/package.py
@@ -22,9 +22,9 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import os
 from spack import *
 
+
 class Mpibash(Package):
     """Parallel scripting right from the Bourne-Again Shell (Bash)"""
     homepage = "http://www.ccs3.lanl.gov/~pakin/software/mpibash-4.3.html"
diff --git a/var/spack/repos/builtin/packages/mpileaks/package.py b/var/spack/repos/builtin/packages/mpileaks/package.py
index 51bc66a0eb..ec4e9b30cc 100644
--- a/var/spack/repos/builtin/packages/mpileaks/package.py
+++ b/var/spack/repos/builtin/packages/mpileaks/package.py
@@ -24,8 +24,10 @@
 ##############################################################################
 from spack import *
 
+
 class Mpileaks(Package):
-    """Tool to detect and report leaked MPI objects like MPI_Requests and MPI_Datatypes."""
+    """Tool to detect and report leaked MPI objects like MPI_Requests and
+       MPI_Datatypes."""
 
     homepage = "https://github.com/hpc/mpileaks"
     url      = "https://github.com/hpc/mpileaks/releases/download/v1.0/mpileaks-1.0.tar.gz"
diff --git a/var/spack/repos/builtin/packages/mrnet/package.py b/var/spack/repos/builtin/packages/mrnet/package.py
index 3380c7f823..490e99dd83 100644
--- a/var/spack/repos/builtin/packages/mrnet/package.py
+++ b/var/spack/repos/builtin/packages/mrnet/package.py
@@ -24,34 +24,40 @@
 ##############################################################################
 from spack import *
 
+
 class Mrnet(Package):
     """The MRNet Multi-Cast Reduction Network."""
     homepage = "http://paradyn.org/mrnet"
     url      = "ftp://ftp.cs.wisc.edu/paradyn/mrnet/mrnet_5.0.1.tar.gz"
     list_url = "http://ftp.cs.wisc.edu/paradyn/mrnet"
 
-    version('5.0.1-2', git='https://github.com/dyninst/mrnet.git', commit='20b1eacfc6d680d9f6472146d2dfaa0f900cc2e9')
+    version('5.0.1-2', git='https://github.com/dyninst/mrnet.git',
+            commit='20b1eacfc6d680d9f6472146d2dfaa0f900cc2e9')
     version('5.0.1', '17f65738cf1b9f9b95647ff85f69ecdd')
     version('4.1.0', '5a248298b395b329e2371bf25366115c')
     version('4.0.0', 'd00301c078cba57ef68613be32ceea2f')
 
-    # Add a patch that brings mrnet-5.0.1 up to date with the current development tree
-    # The development tree contains fixes needed for the krell based tools
-    variant('krellpatch', default=False, description="Build MRNet with krell openspeedshop based patch.")
+    # Add a patch that brings mrnet-5.0.1 up to date with the current
+    # development tree The development tree contains fixes needed for the
+    # krell based tools
+    variant('krellpatch', default=False,
+            description="Build MRNet with krell openspeedshop based patch.")
     patch('krell-5.0.1.patch', when='@5.0.1+krellpatch')
 
-    variant('lwthreads', default=False, description="Also build the MRNet LW threadsafe libraries")
+    variant('lwthreads', default=False,
+            description="Also build the MRNet LW threadsafe libraries")
     parallel = False
 
     depends_on("boost")
 
     def install(self, spec, prefix):
-        # Build the MRNet LW thread safe libraries when the krelloptions variant is present
+        # Build the MRNet LW thread safe libraries when the krelloptions
+        # variant is present
         if '+lwthreads' in spec:
-           configure("--prefix=%s" %prefix, "--enable-shared", "--enable-ltwt-threadsafe")
+            configure("--prefix=%s" % prefix, "--enable-shared",
+                      "--enable-ltwt-threadsafe")
         else:
-           configure("--prefix=%s" %prefix, "--enable-shared")
+            configure("--prefix=%s" % prefix, "--enable-shared")
 
         make()
         make("install")
-
diff --git a/var/spack/repos/builtin/packages/msgpack-c/package.py b/var/spack/repos/builtin/packages/msgpack-c/package.py
index d42ac255d0..9a726e2356 100644
--- a/var/spack/repos/builtin/packages/msgpack-c/package.py
+++ b/var/spack/repos/builtin/packages/msgpack-c/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class MsgpackC(Package):
     """A small, fast binary interchange format convertible to/from JSON"""
     homepage = "http://www.msgpack.org"
diff --git a/var/spack/repos/builtin/packages/mumps/package.py b/var/spack/repos/builtin/packages/mumps/package.py
index b85a6d2b94..32bc42a9c3 100644
--- a/var/spack/repos/builtin/packages/mumps/package.py
+++ b/var/spack/repos/builtin/packages/mumps/package.py
@@ -36,15 +36,24 @@ class Mumps(Package):
 
     version('5.0.1', 'b477573fdcc87babe861f62316833db0')
 
-    variant('mpi', default=True, description='Activate the compilation of MUMPS with the MPI support')
-    variant('scotch', default=False, description='Activate Scotch as a possible ordering library')
-    variant('ptscotch', default=False, description='Activate PT-Scotch as a possible ordering library')
-    variant('metis', default=False, description='Activate Metis as a possible ordering library')
-    variant('parmetis', default=False, description='Activate Parmetis as a possible ordering library')
-    variant('double', default=True, description='Activate the compilation of dmumps')
-    variant('float', default=True, description='Activate the compilation of smumps')
-    variant('complex', default=True, description='Activate the compilation of cmumps and/or zmumps')
-    variant('idx64', default=False, description='Use int64_t/integer*8 as default index type')
+    variant('mpi', default=True,
+            description='Compile MUMPS with MPI support')
+    variant('scotch', default=False,
+            description='Activate Scotch as a possible ordering library')
+    variant('ptscotch', default=False,
+            description='Activate PT-Scotch as a possible ordering library')
+    variant('metis', default=False,
+            description='Activate Metis as a possible ordering library')
+    variant('parmetis', default=False,
+            description='Activate Parmetis as a possible ordering library')
+    variant('double', default=True,
+            description='Activate the compilation of dmumps')
+    variant('float', default=True,
+            description='Activate the compilation of smumps')
+    variant('complex', default=True,
+            description='Activate the compilation of cmumps and/or zmumps')
+    variant('idx64', default=False,
+            description='Use int64_t/integer*8 as default index type')
     variant('shared', default=True, description='Build shared libraries')
 
     depends_on('scotch + esmumps', when='~ptscotch+scotch')
@@ -61,8 +70,10 @@ class Mumps(Package):
     # end before install
     # def patch(self):
     def write_makefile_inc(self):
-        if ('+parmetis' in self.spec or '+ptscotch' in self.spec) and '+mpi' not in self.spec:  # NOQA: ignore=E501
-            raise RuntimeError('You cannot use the variants parmetis or ptscotch without mpi')  # NOQA: ignore=E501
+        if ('+parmetis' in self.spec or '+ptscotch' in self.spec) and (
+                '+mpi' not in self.spec):
+            raise RuntimeError(
+                'You cannot use the variants parmetis or ptscotch without mpi')
 
         makefile_conf = ["LIBBLAS = %s" % to_link_flags(
             self.spec['blas'].blas_shared_lib)
@@ -115,7 +126,7 @@ class Mumps(Package):
                 # the fortran compilation flags most probably are
                 # working only for intel and gnu compilers this is
                 # perhaps something the compiler should provide
-                ['OPTF    = %s -O  -DALLOW_NON_INIT %s' % (fpic, '-fdefault-integer-8' if self.compiler.name == "gcc" else '-i8'),  # NOQA: ignore=E501
+                ['OPTF    = %s -O  -DALLOW_NON_INIT %s' % (fpic, '-fdefault-integer-8' if self.compiler.name == "gcc" else '-i8'),  # noqa
                  'OPTL    = %s -O ' % fpic,
                  'OPTC    = %s -O -DINTSIZE64' % fpic])
         else:
@@ -148,13 +159,13 @@ class Mumps(Package):
                 # 10.10. Use gfortran. (Homebrew)
                 makefile_conf.extend([
                     'LIBEXT=.dylib',
-                    'AR=%s -dynamiclib -Wl,-install_name -Wl,%s/$(notdir $@) -undefined dynamic_lookup -o ' % (os.environ['FC'], prefix.lib),  # NOQA: ignore=E501
+                    'AR=%s -dynamiclib -Wl,-install_name -Wl,%s/$(notdir $@) -undefined dynamic_lookup -o ' % (os.environ['FC'], prefix.lib),  # noqa
                     'RANLIB=echo'
                 ])
             else:
                 makefile_conf.extend([
                     'LIBEXT=.so',
-                    'AR=$(FL) -shared -Wl,-soname -Wl,%s/$(notdir $@) -o' % prefix.lib,  # NOQA: ignore=E501
+                    'AR=$(FL) -shared -Wl,-soname -Wl,%s/$(notdir $@) -o' % prefix.lib,  # noqa
                     'RANLIB=echo'
                 ])
         else:
diff --git a/var/spack/repos/builtin/packages/munge/package.py b/var/spack/repos/builtin/packages/munge/package.py
index ebe3e18882..51455006e9 100644
--- a/var/spack/repos/builtin/packages/munge/package.py
+++ b/var/spack/repos/builtin/packages/munge/package.py
@@ -25,12 +25,14 @@
 from spack import *
 import os
 
+
 class Munge(Package):
     """ MUNGE Uid 'N' Gid Emporium """
     homepage = "https://code.google.com/p/munge/"
     url      = "https://github.com/dun/munge/releases/download/munge-0.5.11/munge-0.5.11.tar.bz2"
 
-    version('0.5.11', 'bd8fca8d5f4c1fcbef1816482d49ee01', url='https://github.com/dun/munge/releases/download/munge-0.5.11/munge-0.5.11.tar.bz2')
+    version('0.5.11', 'bd8fca8d5f4c1fcbef1816482d49ee01',
+            url='https://github.com/dun/munge/releases/download/munge-0.5.11/munge-0.5.11.tar.bz2')
 
     depends_on('openssl')
     depends_on('libgcrypt')
@@ -41,4 +43,3 @@ class Munge(Package):
 
         make()
         make("install")
-
diff --git a/var/spack/repos/builtin/packages/muparser/package.py b/var/spack/repos/builtin/packages/muparser/package.py
index 47d1855329..1373c8cd7b 100644
--- a/var/spack/repos/builtin/packages/muparser/package.py
+++ b/var/spack/repos/builtin/packages/muparser/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Muparser(Package):
     """C++ math expression parser library."""
     homepage = "http://muparser.beltoforion.de/"
diff --git a/var/spack/repos/builtin/packages/muster/package.py b/var/spack/repos/builtin/packages/muster/package.py
index 64b7324415..81817e48dc 100644
--- a/var/spack/repos/builtin/packages/muster/package.py
+++ b/var/spack/repos/builtin/packages/muster/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Muster(Package):
     """The Muster library provides implementations of sequential and
        parallel K-Medoids clustering algorithms. It is intended as a
diff --git a/var/spack/repos/builtin/packages/mvapich2/package.py b/var/spack/repos/builtin/packages/mvapich2/package.py
index da386445bb..17124a0572 100644
--- a/var/spack/repos/builtin/packages/mvapich2/package.py
+++ b/var/spack/repos/builtin/packages/mvapich2/package.py
@@ -40,7 +40,8 @@ class Mvapich2(Package):
     provides('mpi@:2.2', when='@1.9')  # MVAPICH2-1.9 supports MPI 2.2
     provides('mpi@:3.0', when='@2.0:')  # MVAPICH2-2.0 supports MPI 3.0
 
-    variant('debug', default=False, description='Enables debug information and error messages at run-time')
+    variant('debug', default=False,
+            description='Enable debug info and error messages at run-time')
 
     ##########
     # TODO : Process managers should be grouped into the same variant,
@@ -51,10 +52,14 @@ class Mvapich2(Package):
     GFORKER = 'gforker'
     REMSHELL = 'remshell'
     SLURM_INCOMPATIBLE_PMS = (HYDRA, GFORKER, REMSHELL)
-    variant(SLURM, default=False, description='Sets slurm as the only process manager')
-    variant(HYDRA, default=False, description='Sets hydra as one of the process managers')
-    variant(GFORKER, default=False, description='Sets gforker as one of the process managers')
-    variant(REMSHELL, default=False, description='Sets remshell as one of the process managers')
+    variant(SLURM, default=False,
+            description='Set slurm as the only process manager')
+    variant(HYDRA, default=False,
+            description='Set hydra as one of the process managers')
+    variant(GFORKER, default=False,
+            description='Set gforker as one of the process managers')
+    variant(REMSHELL, default=False,
+            description='Set remshell as one of the process managers')
     ##########
 
     ##########
@@ -67,15 +72,28 @@ class Mvapich2(Package):
     NEMESIS = 'nemesis'
     MRAIL = 'mrail'
     SUPPORTED_NETWORKS = (PSM, SOCK, NEMESIS, NEMESISIB, NEMESISIBTCP)
-    variant(PSM, default=False, description='Configures a build for QLogic PSM-CH3')
-    variant(SOCK, default=False, description='Configures a build for TCP/IP-CH3')
-    variant(NEMESISIBTCP, default=False, description='Configures a build for both OFA-IB-Nemesis and TCP/IP-Nemesis')
-    variant(NEMESISIB, default=False, description='Configures a build for OFA-IB-Nemesis')
-    variant(NEMESIS, default=False, description='Configures a build for TCP/IP-Nemesis')
-    variant(MRAIL, default=False, description='Configures a build for OFA-IB-CH3')
+    variant(
+        PSM, default=False,
+        description='Configure for QLogic PSM-CH3')
+    variant(
+        SOCK, default=False,
+        description='Configure for TCP/IP-CH3')
+    variant(
+        NEMESISIBTCP, default=False,
+        description='Configure for both OFA-IB-Nemesis and TCP/IP-Nemesis')
+    variant(
+        NEMESISIB, default=False,
+        description='Configure for OFA-IB-Nemesis')
+    variant(
+        NEMESIS, default=False,
+        description='Configure for TCP/IP-Nemesis')
+    variant(
+        MRAIL, default=False,
+        description='Configure for OFA-IB-CH3')
     ##########
 
     # FIXME : CUDA support is missing
+    depends_on('libpciaccess')
 
     def url_for_version(self, version):
         base_url = "http://mvapich.cse.ohio-state.edu/download"
diff --git a/var/spack/repos/builtin/packages/mxml/package.py b/var/spack/repos/builtin/packages/mxml/package.py
index 254a5f1595..113c48c18f 100644
--- a/var/spack/repos/builtin/packages/mxml/package.py
+++ b/var/spack/repos/builtin/packages/mxml/package.py
@@ -1,3 +1,27 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/nag/package.py b/var/spack/repos/builtin/packages/nag/package.py
index 63269a50b1..792e3fe3c7 100644
--- a/var/spack/repos/builtin/packages/nag/package.py
+++ b/var/spack/repos/builtin/packages/nag/package.py
@@ -43,8 +43,8 @@ class Nag(Package):
     def url_for_version(self, version):
         # TODO: url and checksum are architecture dependent
         # TODO: We currently only support x86_64
-        return 'http://www.nag.com/downloads/impl/npl6a%sna_amd64.tgz' % \
-               str(version).replace('.', '')
+        return 'http://www.nag.com/downloads/impl/npl6a%sna_amd64.tgz' % str(
+            version).replace('.', '')
 
     def install(self, spec, prefix):
         # Set installation directories
diff --git a/var/spack/repos/builtin/packages/nasm/package.py b/var/spack/repos/builtin/packages/nasm/package.py
index c955e6d13e..9faccccaae 100644
--- a/var/spack/repos/builtin/packages/nasm/package.py
+++ b/var/spack/repos/builtin/packages/nasm/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Nasm(Package):
     """NASM (Netwide Assembler) is an 80x86 assembler designed for
        portability and modularity. It includes a disassembler as well."""
diff --git a/var/spack/repos/builtin/packages/nccmp/package.py b/var/spack/repos/builtin/packages/nccmp/package.py
index 68bddd6957..d59ca09381 100644
--- a/var/spack/repos/builtin/packages/nccmp/package.py
+++ b/var/spack/repos/builtin/packages/nccmp/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Nccmp(Package):
     """Compare NetCDF Files"""
     homepage = "http://nccmp.sourceforge.net/"
diff --git a/var/spack/repos/builtin/packages/ncdu/package.py b/var/spack/repos/builtin/packages/ncdu/package.py
index 0f2f9cda45..2147319d3f 100644
--- a/var/spack/repos/builtin/packages/ncdu/package.py
+++ b/var/spack/repos/builtin/packages/ncdu/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Ncdu(Package):
     """
     Ncdu is a disk usage analyzer with an ncurses interface. It is designed
@@ -38,15 +39,15 @@ class Ncdu(Package):
 
     version('1.11', '9e44240a5356b029f05f0e70a63c4d12')
     version('1.10', '7535decc8d54eca811493e82d4bfab2d')
-    version('1.9' , '93258079db897d28bb8890e2db89b1fb')
-    version('1.8' , '94d7a821f8a0d7ba8ef3dd926226f7d5')
-    version('1.7' , '172047c29d232724cc62e773e82e592a')
+    version('1.9', '93258079db897d28bb8890e2db89b1fb')
+    version('1.8', '94d7a821f8a0d7ba8ef3dd926226f7d5')
+    version('1.7', '172047c29d232724cc62e773e82e592a')
 
     depends_on("ncurses")
 
     def install(self, spec, prefix):
         configure('--prefix=%s' % prefix,
-            '--with-ncurses=%s' % spec['ncurses'])
+                  '--with-ncurses=%s' % spec['ncurses'])
 
         make()
         make("install")
diff --git a/var/spack/repos/builtin/packages/nco/package.py b/var/spack/repos/builtin/packages/nco/package.py
index 4bc4da68e3..16d72b4593 100644
--- a/var/spack/repos/builtin/packages/nco/package.py
+++ b/var/spack/repos/builtin/packages/nco/package.py
@@ -23,7 +23,7 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
-import os
+
 
 class Nco(Package):
     """The NCO toolkit manipulates and analyzes data stored in
@@ -39,9 +39,9 @@ class Nco(Package):
 
     depends_on('netcdf')
     depends_on('antlr@2.7.7+cxx')    # (required for ncap2)
-    depends_on('gsl')            #  (desirable for ncap2)
+    depends_on('gsl')  # (desirable for ncap2)
     depends_on('udunits2')       # (allows dimensional unit transformations)
-    # depends_on('opendap')      # (enables network transparency), 
+    # depends_on('opendap')      # (enables network transparency),
 
     def install(self, spec, prefix):
         opts = [
diff --git a/var/spack/repos/builtin/packages/ncurses/package.py b/var/spack/repos/builtin/packages/ncurses/package.py
index 3ab2b0477d..aaacbac7b1 100644
--- a/var/spack/repos/builtin/packages/ncurses/package.py
+++ b/var/spack/repos/builtin/packages/ncurses/package.py
@@ -24,11 +24,14 @@
 ##############################################################################
 from spack import *
 
+
 class Ncurses(Package):
-    """The ncurses (new curses) library is a free software emulation of curses
-       in System V Release 4.0, and more. It uses terminfo format, supports pads and
-       color and multiple highlights and forms characters and function-key mapping,
-       and has all the other SYSV-curses enhancements over BSD curses.
+    """The ncurses (new curses) library is a free software emulation of
+       curses in System V Release 4.0, and more. It uses terminfo format,
+       supports pads and color and multiple highlights and forms
+       characters and function-key mapping, and has all the other
+       SYSV-curses enhancements over BSD curses.
+
     """
 
     homepage = "http://invisible-island.net/ncurses/ncurses.html"
diff --git a/var/spack/repos/builtin/packages/ncview/package.py b/var/spack/repos/builtin/packages/ncview/package.py
index b39e17ca49..f61e6984b5 100644
--- a/var/spack/repos/builtin/packages/ncview/package.py
+++ b/var/spack/repos/builtin/packages/ncview/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Ncview(Package):
     """Simple viewer for NetCDF files."""
     homepage = "http://meteora.ucsd.edu/~pierce/ncview_home_page.html"
diff --git a/var/spack/repos/builtin/packages/ndiff/package.py b/var/spack/repos/builtin/packages/ndiff/package.py
index 3c9dd4054a..dc41add03f 100644
--- a/var/spack/repos/builtin/packages/ndiff/package.py
+++ b/var/spack/repos/builtin/packages/ndiff/package.py
@@ -24,11 +24,15 @@
 ##############################################################################
 from spack import *
 
+
 class Ndiff(Package):
-    """The ndiff tool is a binary utility that compares putatively similar files
-       while ignoring small numeric differernces. This utility is most often used
-       to compare files containing a lot of floating-point numeric data that
-       may be slightly different due to numeric error."""
+    """The ndiff tool is a binary utility that compares putatively similar
+       files while ignoring small numeric differernces. This utility is
+       most often used to compare files containing a lot of
+       floating-point numeric data that may be slightly different due to
+       numeric error.
+
+    """
 
     homepage = "http://ftp.math.utah.edu/pub/ndiff/"
     url      = "http://ftp.math.utah.edu/pub/ndiff/ndiff-2.00.tar.gz"
diff --git a/var/spack/repos/builtin/packages/netcdf-cxx/package.py b/var/spack/repos/builtin/packages/netcdf-cxx/package.py
index 994c51c0da..2c3ab73309 100644
--- a/var/spack/repos/builtin/packages/netcdf-cxx/package.py
+++ b/var/spack/repos/builtin/packages/netcdf-cxx/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class NetcdfCxx(Package):
     """Deprecated C++ compatibility bindings for NetCDF.
     These do NOT read or write NetCDF-4 files, and are no longer
diff --git a/var/spack/repos/builtin/packages/netcdf/package.py b/var/spack/repos/builtin/packages/netcdf/package.py
index ad4ee59640..ab40c14340 100644
--- a/var/spack/repos/builtin/packages/netcdf/package.py
+++ b/var/spack/repos/builtin/packages/netcdf/package.py
@@ -26,9 +26,11 @@ from spack import *
 
 
 class Netcdf(Package):
-    """NetCDF is a set of software libraries and self-describing, machine-independent
-    data formats that support the creation, access, and sharing of array-oriented
-    scientific data."""
+    """NetCDF is a set of software libraries and self-describing,
+    machine-independent data formats that support the creation, access,
+    and sharing of array-oriented scientific data.
+
+    """
 
     homepage = "http://www.unidata.ucar.edu/software/netcdf"
     url      = "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.3.3.tar.gz"
@@ -74,18 +76,19 @@ class Netcdf(Package):
             "--enable-dap"
         ]
 
-        # Make sure Netcdf links against Spack's curl
-        # Otherwise it may pick up system's curl, which could lead to link errors:
-        # /usr/lib/x86_64-linux-gnu/libcurl.so: undefined reference to `SSL_CTX_use_certificate_chain_file@OPENSSL_1.0.0'
+        # Make sure Netcdf links against Spack's curl, otherwise
+        # otherwise it may pick up system's curl, which can give link
+        # errors, e.g.:
+        # undefined reference to `SSL_CTX_use_certificate_chain_file`
         LIBS.append("-lcurl")
         CPPFLAGS.append("-I%s" % spec['curl'].prefix.include)
-        LDFLAGS.append( "-L%s" % spec['curl'].prefix.lib)
+        LDFLAGS.append("-L%s" % spec['curl'].prefix.lib)
 
         if '+mpi' in spec:
             config_args.append('--enable-parallel4')
 
         CPPFLAGS.append("-I%s/include" % spec['hdf5'].prefix)
-        LDFLAGS.append( "-L%s/lib"     % spec['hdf5'].prefix)
+        LDFLAGS.append("-L%s/lib"     % spec['hdf5'].prefix)
 
         # HDF4 support
         # As of NetCDF 4.1.3, "--with-hdf4=..." is no longer a valid option
@@ -93,13 +96,13 @@ class Netcdf(Package):
         if '+hdf4' in spec:
             config_args.append("--enable-hdf4")
             CPPFLAGS.append("-I%s/include" % spec['hdf'].prefix)
-            LDFLAGS.append( "-L%s/lib"     % spec['hdf'].prefix)
-            LIBS.append(    "-l%s"         % "jpeg")
+            LDFLAGS.append("-L%s/lib"     % spec['hdf'].prefix)
+            LIBS.append("-l%s"         % "jpeg")
 
         if 'szip' in spec:
             CPPFLAGS.append("-I%s/include" % spec['szip'].prefix)
-            LDFLAGS.append( "-L%s/lib"     % spec['szip'].prefix)
-            LIBS.append(    "-l%s"         % "sz")
+            LDFLAGS.append("-L%s/lib"     % spec['szip'].prefix)
+            LIBS.append("-l%s"         % "sz")
 
         # Fortran support
         # In version 4.2+, NetCDF-C and NetCDF-Fortran have split.
diff --git a/var/spack/repos/builtin/packages/netgauge/package.py b/var/spack/repos/builtin/packages/netgauge/package.py
index be9292fabb..b57cdbe5f3 100644
--- a/var/spack/repos/builtin/packages/netgauge/package.py
+++ b/var/spack/repos/builtin/packages/netgauge/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Netgauge(Package):
     """Netgauge is a high-precision network parameter measurement
     tool. It supports benchmarking of many different network protocols
diff --git a/var/spack/repos/builtin/packages/netlib-lapack/package.py b/var/spack/repos/builtin/packages/netlib-lapack/package.py
index 70015baf1c..08c94a5c9b 100644
--- a/var/spack/repos/builtin/packages/netlib-lapack/package.py
+++ b/var/spack/repos/builtin/packages/netlib-lapack/package.py
@@ -26,11 +26,12 @@ from spack import *
 
 
 class NetlibLapack(Package):
-    """
-    LAPACK version 3.X is a comprehensive FORTRAN library that does linear algebra operations including matrix
-    inversions, least squared solutions to linear sets of equations, eigenvector analysis, singular value
-    decomposition, etc. It is a very comprehensive and reputable package that has found extensive use in the
-    scientific community.
+    """LAPACK version 3.X is a comprehensive FORTRAN library that does
+    linear algebra operations including matrix inversions, least squared
+    solutions to linear sets of equations, eigenvector analysis, singular
+    value decomposition, etc. It is a very comprehensive and reputable
+    package that has found extensive use in the scientific community.
+
     """
     homepage = "http://www.netlib.org/lapack/"
     url = "http://www.netlib.org/lapack/lapack-3.5.0.tgz"
@@ -44,9 +45,11 @@ class NetlibLapack(Package):
 
     variant('debug', default=False, description='Activates the Debug build type')
     variant('shared', default=True, description="Build shared library version")
-    variant('external-blas', default=False, description='Build lapack with an external blas')
+    variant('external-blas', default=False,
+            description='Build lapack with an external blas')
 
-    variant('lapacke', default=True, description='Activates the build of the LAPACKE C interface')
+    variant('lapacke', default=True,
+            description='Activates the build of the LAPACKE C interface')
 
     # virtual dependency
     provides('blas', when='~external-blas')
@@ -55,26 +58,30 @@ class NetlibLapack(Package):
     depends_on('cmake', type='build')
     depends_on('blas', when='+external-blas')
 
-
     def patch(self):
         # Fix cblas CMakeLists.txt -- has wrong case for subdirectory name.
         if self.spec.satisfies('@3.6.0:'):
-            filter_file('${CMAKE_CURRENT_SOURCE_DIR}/CMAKE/',
-                        '${CMAKE_CURRENT_SOURCE_DIR}/cmake/', 'CBLAS/CMakeLists.txt', string=True)
+            filter_file(
+                '${CMAKE_CURRENT_SOURCE_DIR}/CMAKE/',
+                '${CMAKE_CURRENT_SOURCE_DIR}/cmake/',
+                'CBLAS/CMakeLists.txt', string=True)
 
     def install_one(self, spec, prefix, shared):
-        cmake_args = ['-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if shared else 'OFF'),
-                      '-DCMAKE_BUILD_TYPE:STRING=%s' % ('Debug' if '+debug' in spec else 'Release'),
-                      '-DLAPACKE:BOOL=%s' % ('ON' if '+lapacke' in spec else 'OFF')]
+        cmake_args = [
+            '-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if shared else 'OFF'),
+            '-DCMAKE_BUILD_TYPE:STRING=%s' % (
+                'Debug' if '+debug' in spec else 'Release'),
+            '-DLAPACKE:BOOL=%s' % ('ON' if '+lapacke' in spec else 'OFF')]
         if spec.satisfies('@3.6.0:'):
-            cmake_args.extend(['-DCBLAS=ON']) # always build CBLAS
+            cmake_args.extend(['-DCBLAS=ON'])  # always build CBLAS
 
         if '+external-blas' in spec:
-            # TODO : the mechanism to specify the library should be more general,
+            # TODO : mechanism to specify the library should be more general,
             # TODO : but this allows to have an hook to an external blas
             cmake_args.extend([
                 '-DUSE_OPTIMIZED_BLAS:BOOL=ON',
-                '-DBLAS_LIBRARIES:PATH=%s' % join_path(spec['blas'].prefix.lib, 'libblas.a')
+                '-DBLAS_LIBRARIES:PATH=%s' % join_path(
+                    spec['blas'].prefix.lib, 'libblas.a')
             ])
 
         cmake_args.extend(std_cmake_args)
@@ -85,7 +92,6 @@ class NetlibLapack(Package):
             make()
             make("install")
 
-
     def install(self, spec, prefix):
         # Always build static libraries.
         self.install_one(spec, prefix, False)
@@ -94,15 +100,17 @@ class NetlibLapack(Package):
         if '+shared' in spec:
             self.install_one(spec, prefix, True)
 
-
     def setup_dependent_package(self, module, dspec):
         # This is WIP for a prototype interface for virtual packages.
         # We can update this as more builds start depending on BLAS/LAPACK.
-        libdir = find_library_path('libblas.a', self.prefix.lib64, self.prefix.lib)
+        libdir = find_library_path(
+            'libblas.a', self.prefix.lib64, self.prefix.lib)
 
         self.spec.blas_static_lib   = join_path(libdir, 'libblas.a')
         self.spec.lapack_static_lib = join_path(libdir, 'liblapack.a')
 
         if '+shared' in self.spec:
-            self.spec.blas_shared_lib   = join_path(libdir, 'libblas.%s' % dso_suffix)
-            self.spec.lapack_shared_lib = join_path(libdir, 'liblapack.%s' % dso_suffix)
+            self.spec.blas_shared_lib   = join_path(
+                libdir, 'libblas.%s' % dso_suffix)
+            self.spec.lapack_shared_lib = join_path(
+                libdir, 'liblapack.%s' % dso_suffix)
diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py
index f7733249cf..49b8633209 100644
--- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py
+++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py
@@ -39,7 +39,8 @@ class NetlibScalapack(Package):
     # versions before 2.0.0 are not using cmake and requires blacs as
     # a separated package
 
-    variant('shared', default=True, description='Build the shared library version')
+    variant('shared', default=True,
+            description='Build the shared library version')
     variant('fpic', default=False, description="Build with -fpic compiler option")
 
     provides('scalapack')
diff --git a/var/spack/repos/builtin/packages/nettle/package.py b/var/spack/repos/builtin/packages/nettle/package.py
index 56e4836611..02e9ef5f1e 100644
--- a/var/spack/repos/builtin/packages/nettle/package.py
+++ b/var/spack/repos/builtin/packages/nettle/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Nettle(Package):
     """The Nettle package contains the low-level cryptographic library
     that is designed to fit easily in many contexts."""
diff --git a/var/spack/repos/builtin/packages/nextflow/package.py b/var/spack/repos/builtin/packages/nextflow/package.py
new file mode 100644
index 0000000000..54f3dbf915
--- /dev/null
+++ b/var/spack/repos/builtin/packages/nextflow/package.py
@@ -0,0 +1,42 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Nextflow(Package):
+    """Data-driven computational pipelines"""
+
+    homepage = "http://www.nextflow.io"
+
+    version('0.20.1', '0e4e0e3eca1c2c97f9b4bffd944b923a',
+            url='https://github.com/nextflow-io/nextflow/releases/download/v0.20.1/nextflow',
+            expand=False)
+
+    depends_on('jdk')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install("nextflow", join_path(prefix.bin, "nextflow"))
+        set_executable(join_path(prefix.bin, "nextflow"))
diff --git a/var/spack/repos/builtin/packages/ninja/package.py b/var/spack/repos/builtin/packages/ninja/package.py
index e3f3819289..dcd00576dd 100644
--- a/var/spack/repos/builtin/packages/ninja/package.py
+++ b/var/spack/repos/builtin/packages/ninja/package.py
@@ -25,6 +25,7 @@
 from spack import *
 import os
 
+
 class Ninja(Package):
     """ A small, fast Make alternative """
     homepage = "https://martine.github.io/ninja/"
@@ -35,7 +36,6 @@ class Ninja(Package):
     extends('python')
 
     def install(self, spec, prefix):
-        sh = which('sh')
         python('configure.py', '--bootstrap')
 
         cp = which('cp')
diff --git a/var/spack/repos/builtin/packages/numdiff/package.py b/var/spack/repos/builtin/packages/numdiff/package.py
index 97164165e0..fb897f560b 100644
--- a/var/spack/repos/builtin/packages/numdiff/package.py
+++ b/var/spack/repos/builtin/packages/numdiff/package.py
@@ -25,6 +25,7 @@
 from spack import *
 import sys
 
+
 class Numdiff(Package):
     """Numdiff is a little program that can be used to compare putatively
     similar files line by line and field by field, ignoring small numeric
@@ -35,7 +36,7 @@ class Numdiff(Package):
 
     version('5.8.1',    'a295eb391f6cb1578209fc6b4f9d994e')
 
-    depends_on('gettext', when=sys.platform=='darwin', type='build')
+    depends_on('gettext', when=sys.platform == 'darwin', type='build')
 
     def install(self, spec, prefix):
         options = ['--prefix=%s' % prefix]
diff --git a/var/spack/repos/builtin/packages/ocaml/package.py b/var/spack/repos/builtin/packages/ocaml/package.py
new file mode 100644
index 0000000000..9488d3b7a6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ocaml/package.py
@@ -0,0 +1,43 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Ocaml(Package):
+    """OCaml is an industrial strength programming language supporting
+       functional, imperative and object-oriented styles"""
+
+    homepage = "http://ocaml.org/"
+    url      = "http://caml.inria.fr/pub/distrib/ocaml-4.03/ocaml-4.03.0.tar.gz"
+
+    version('4.03.0', '43812739ea1b4641cf480f57f977c149')
+
+    depends_on('ncurses')
+
+    def install(self, spec, prefix):
+        configure('-prefix', '{0}'.format(prefix))
+
+        make('world.opt')
+        make('install')
diff --git a/var/spack/repos/builtin/packages/oce/package.py b/var/spack/repos/builtin/packages/oce/package.py
index 108c8f8a41..4f9f7b2e12 100644
--- a/var/spack/repos/builtin/packages/oce/package.py
+++ b/var/spack/repos/builtin/packages/oce/package.py
@@ -40,7 +40,8 @@ class Oce(Package):
     version('0.16.1', '4d591b240c9293e879f50d86a0cb2bb3')
     version('0.16',   '7a4b4df5a104d75a537e25e7dd387eca')
 
-    variant('tbb', default=True, description='Build with Intel Threading Building Blocks')
+    variant('tbb', default=True,
+            description='Build with Intel Threading Building Blocks')
 
     depends_on('cmake@2.8:', type='build')
     depends_on('tbb', when='+tbb')
diff --git a/var/spack/repos/builtin/packages/ompss/package.py b/var/spack/repos/builtin/packages/ompss/package.py
index c0848ffd70..02925974ea 100644
--- a/var/spack/repos/builtin/packages/ompss/package.py
+++ b/var/spack/repos/builtin/packages/ompss/package.py
@@ -26,19 +26,18 @@ from spack import *
 import os
 import glob
 
-# working config lines for ompss 14.06 :
-#./nanox-0.7/config.log:    $ ./configure --prefix=/usr/gapps/exmatex/ompss --with-mcc=/usr/gapps/exmatex/ompss/ --with-hwloc=/usr
-#./mcxx-1.99.2/config.log:    $ ./configure --prefix=/usr/gapps/exmatex/ompss --with-nanox=/usr/gapps/exmatex/ompss --enable-ompss --with-mpi=/opt/mvapich2-intel-shmem-1.7 --enable-tl-openmp-profile --enable-tl-openmp-intel
 
 class Ompss(Package):
-    """OmpSs is an effort to integrate features from the StarSs
-       programming model developed by BSC into a single programming
-       model. In particular, our objective is to extend OpenMP with
-       new directives to support asynchronous parallelism and
-       heterogeneity (devices like GPUs). However, it can also be
-       understood as new directives extending other accelerator based
-       APIs like CUDA or OpenCL. Our OmpSs environment is built on top
-       of our Mercurium compiler and Nanos++ runtime system."""
+    """OmpSs is an effort to integrate features from the StarSs programming
+       model developed by BSC into a single programming model. In
+       particular, our objective is to extend OpenMP with new directives
+       to support asynchronous parallelism and heterogeneity (devices
+       like GPUs). However, it can also be understood as new directives
+       extending other accelerator based APIs like CUDA or OpenCL. Our
+       OmpSs environment is built on top of our Mercurium compiler and
+       Nanos++ runtime system.
+
+    """
     homepage = "http://pm.bsc.es/"
     url      = "http://pm.bsc.es/sites/default/files/ftp/ompss/releases/ompss-14.10.tar.gz"
     list_url = 'http://pm.bsc.es/ompss-downloads'
@@ -47,7 +46,7 @@ class Ompss(Package):
 
     # all dependencies are optional, really
     depends_on("mpi")
-    #depends_on("openmp")
+    # depends_on("openmp")
     depends_on("hwloc")
     depends_on("extrae")
 
@@ -61,14 +60,22 @@ class Ompss(Package):
 
         openmp_options = ["--enable-tl-openmp-profile"]
         if spec.satisfies('%intel'):
-            openmp_options.append( "--enable-tl-openmp-intel" )
+            openmp_options.append("--enable-tl-openmp-intel")
 
         os.chdir(glob.glob('./nanox-*').pop())
-        configure("--prefix=%s" % prefix, "--with-mcc=%s" % prefix, "--with-extrae=%s" % spec['extrae'].prefix, "--with-hwloc=%s" % spec['hwloc'].prefix)
+        configure("--prefix=%s" % prefix,
+                  "--with-mcc=%s" % prefix,
+                  "--with-extrae=%s" %
+                  spec['extrae'].prefix,
+                  "--with-hwloc=%s" % spec['hwloc'].prefix)
         make()
         make("install")
 
         os.chdir(glob.glob('../mcxx-*').pop())
-        configure("--prefix=%s" % prefix, "--with-nanox=%s" % prefix, "--enable-ompss", "--with-mpi=%s" % mpi.prefix, *openmp_options)
+        configure("--prefix=%s" % prefix,
+                  "--with-nanox=%s" % prefix,
+                  "--enable-ompss",
+                  "--with-mpi=%s" % mpi.prefix,
+                  *openmp_options)
         make()
         make("install")
diff --git a/var/spack/repos/builtin/packages/ompt-openmp/package.py b/var/spack/repos/builtin/packages/ompt-openmp/package.py
index 800c04ae0e..40159e4c6c 100644
--- a/var/spack/repos/builtin/packages/ompt-openmp/package.py
+++ b/var/spack/repos/builtin/packages/ompt-openmp/package.py
@@ -24,8 +24,14 @@
 ##############################################################################
 from spack import *
 
+
 class OmptOpenmp(Package):
-    """LLVM/Clang OpenMP runtime with OMPT support. This is a fork of the OpenMPToolsInterface/LLVM-openmp fork of the official LLVM OpenMP mirror.  This library provides a drop-in replacement of the OpenMP runtimes for GCC, Intel and LLVM/Clang."""
+    """LLVM/Clang OpenMP runtime with OMPT support. This is a fork of the
+       OpenMPToolsInterface/LLVM-openmp fork of the official LLVM OpenMP
+       mirror.  This library provides a drop-in replacement of the OpenMP
+       runtimes for GCC, Intel and LLVM/Clang.
+
+    """
     homepage = "https://github.com/OpenMPToolsInterface/LLVM-openmp"
     url      = "http://github.com/khuck/LLVM-openmp/archive/v0.1.tar.gz"
 
@@ -35,13 +41,9 @@ class OmptOpenmp(Package):
 
     def install(self, spec, prefix):
         with working_dir("runtime/build", create=True):
-
-            # FIXME: Modify the configure line to suit your build system here.
-            cmake('-DCMAKE_C_COMPILER=%s' % self.compiler.cc, 
+            cmake('-DCMAKE_C_COMPILER=%s' % self.compiler.cc,
                   '-DCMAKE_CXX_COMPILER=%s' % self.compiler.cxx,
                   '-DCMAKE_INSTALL_PREFIX=%s' % prefix,
                   '..', *std_cmake_args)
-
-            # FIXME: Add logic to build and install here
             make()
             make("install")
diff --git a/var/spack/repos/builtin/packages/opari2/package.py b/var/spack/repos/builtin/packages/opari2/package.py
index 510fff9fc2..e901f8ed39 100644
--- a/var/spack/repos/builtin/packages/opari2/package.py
+++ b/var/spack/repos/builtin/packages/opari2/package.py
@@ -25,18 +25,24 @@
 
 from spack import *
 
+
 class Opari2(Package):
     """
-    OPARI2 is a source-to-source instrumentation tool for OpenMP and hybrid codes. It surrounds OpenMP directives and
-    runtime library calls with calls to the POMP2 measurement interface. OPARI2 will provide you with a new
-    initialization method that allows for multi-directory and parallel builds as well as the usage of pre-instrumented
-    libraries. Furthermore, an efficient way of tracking parent-child relationships was added. Additionally, we extended
-    OPARI2 to support instrumentation of OpenMP 3.0 tied tasks.
+    OPARI2 is a source-to-source instrumentation tool for OpenMP and hybrid
+    codes. It surrounds OpenMP directives and runtime library calls with calls
+    to the POMP2 measurement interface. OPARI2 will provide you with a new
+    initialization method that allows for multi-directory and parallel builds
+    as well as the usage of pre-instrumented libraries. Furthermore, an
+    efficient way of tracking parent-child relationships was added.
+    Additionally, we extended OPARI2 to support instrumentation of OpenMP 3.0
+    tied tasks.
     """
 
     homepage = "http://www.vi-hps.org/projects/score-p"
     url      = "http://www.vi-hps.org/upload/packages/opari2/opari2-1.1.2.tar.gz"
 
+    version('2.0', '72350dbdb6139f2e68a5055a4f0ba16c',
+            url='http://www.vi-hps.org/upload/packages/opari2/opari2-2.0.tar.gz')
     version('1.1.4', '245d3d11147a06de77909b0805f530c0',
             url='http://www.vi-hps.org/upload/packages/opari2/opari2-1.1.4.tar.gz')
     version('1.1.2', '9a262c7ca05ff0ab5f7775ae96f3539e')
diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py
index d09ebd6739..37f7a7005d 100644
--- a/var/spack/repos/builtin/packages/openblas/package.py
+++ b/var/spack/repos/builtin/packages/openblas/package.py
@@ -37,9 +37,12 @@ class Openblas(Package):
     version('0.2.16', 'fef46ab92463bdbb1479dcec594ef6dc')
     version('0.2.15', 'b1190f3d3471685f17cfd1ec1d252ac9')
 
-    variant('shared', default=True,  description="Build shared libraries as well as static libs.")  # NOQA: ignore=E501
-    variant('openmp', default=False, description="Enable OpenMP support.")
-    variant('fpic',   default=True,  description="Build position independent code")  # NOQA: ignore=E501
+    variant('shared', default=True,
+            description="Build shared libraries as well as static libs.")
+    variant('openmp', default=False,
+            description="Enable OpenMP support.")
+    variant('fpic',   default=True,
+            description="Build position independent code")
 
     # virtual dependency
     provides('blas')
diff --git a/var/spack/repos/builtin/packages/opencv/package.py b/var/spack/repos/builtin/packages/opencv/package.py
index ff551d0b92..8f592342b0 100644
--- a/var/spack/repos/builtin/packages/opencv/package.py
+++ b/var/spack/repos/builtin/packages/opencv/package.py
@@ -23,51 +23,186 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
+from glob import glob
 
 
 class Opencv(Package):
+    """OpenCV is released under a BSD license and hence it's free for both
+    academic and commercial use. It has C++, C, Python and Java interfaces and
+    supports Windows, Linux, Mac OS, iOS and Android. OpenCV was designed for
+    computational efficiency and with a strong focus on real-time applications.
+    Written in optimized C/C++, the library can take advantage of multi-core
+    processing. Enabled with OpenCL, it can take advantage of the hardware
+    acceleration of the underlying heterogeneous compute platform. Adopted all
+    around the world, OpenCV has more than 47 thousand people of user community
+    and estimated number of downloads exceeding 9 million. Usage ranges from
+    interactive art, to mines inspection, stitching maps on the web or through
+    advanced robotics.
     """
-    OpenCV is released under a BSD license and hence it's free for both academic and commercial use. It has C++, C,
-    Python and Java interfaces and supports Windows, Linux, Mac OS, iOS and Android. OpenCV was designed for
-    computational efficiency and with a strong focus on real-time applications. Written in optimized C/C++, the library
-    can take advantage of multi-core processing. Enabled with OpenCL, it can take advantage of the hardware
-    acceleration of the underlying heterogeneous compute platform. Adopted all around the world, OpenCV has more than
-    47 thousand people of user community and estimated number of downloads exceeding 9 million. Usage ranges from
-    interactive art, to mines inspection, stitching maps on the web or through advanced robotics.
-    """
+
     homepage = 'http://opencv.org/'
     url = 'https://github.com/Itseez/opencv/archive/3.1.0.tar.gz'
 
     version('3.1.0', '70e1dd07f0aa06606f1bc0e3fa15abd3')
 
-    variant('shared', default=True, description='Enables the build of shared libraries')
-    variant('debug', default=False, description='Builds a debug version of the libraries')
+    variant('shared', default=True,
+            description='Enables the build of shared libraries')
+    variant('debug', default=False,
+            description='Builds a debug version of the libraries')
 
     variant('eigen', default=True, description='Activates support for eigen')
     variant('ipp', default=True, description='Activates support for IPP')
+    variant('jasper', default=True, description='Activates support for JasPer')
+    variant('cuda', default=False, description='Activates support for CUDA')
+    variant('gtk', default=False, description='Activates support for GTK')
+    variant('vtk', default=False, description='Activates support for VTK')
+    variant('qt', default=False, description='Activates support for QT')
+    variant('python', default=False,
+            description='Enables the build of Python extensions')
+    variant('java', default=False,
+            description='Activates support for Java')
+
+    depends_on('cmake', type='build')
+    depends_on('eigen', when='+eigen', type='build')
 
     depends_on('zlib')
     depends_on('libpng')
     depends_on('libjpeg-turbo')
     depends_on('libtiff')
 
-    depends_on('python')
-    depends_on('py-numpy')
+    depends_on('jasper', when='+jasper')
+    depends_on('cuda', when='+cuda')
+    depends_on('gtkplus', when='+gtk')
+    depends_on('vtk', when='+vtk')
+    depends_on('qt', when='+qt')
+    depends_on('jdk', when='+java')
+    depends_on('py-numpy', when='+python')
 
-    depends_on('eigen', when='+eigen', type='build')
-    depends_on('cmake', type='build')
-
-    # FIXME : GUI extensions missing
-    # FIXME : CUDA extensions still missing
+    extends('python', when='+python')
 
     def install(self, spec, prefix):
         cmake_options = []
         cmake_options.extend(std_cmake_args)
 
-        cmake_options.extend(['-DCMAKE_BUILD_TYPE:STRING=%s' % ('Debug' if '+debug' in spec else 'Release'),
-                              '-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if '+shared' in spec else 'OFF'),
-                              '-DENABLE_PRECOMPILED_HEADERS:BOOL=OFF',
-                              '-DWITH_IPP:BOOL=%s' % ('ON' if '+ipp' in spec else 'OFF')])
+        cmake_options.extend([
+            '-DCMAKE_BUILD_TYPE:STRING={0}'.format((
+                'Debug' if '+debug' in spec else 'Release')),
+            '-DBUILD_SHARED_LIBS:BOOL={0}'.format((
+                'ON' if '+shared' in spec else 'OFF')),
+            '-DENABLE_PRECOMPILED_HEADERS:BOOL=OFF',
+            '-DWITH_IPP:BOOL={0}'.format((
+                'ON' if '+ipp' in spec else 'OFF')),
+            '-DWITH_CUDA:BOOL={0}'.format((
+                'ON' if '+cuda' in spec else 'OFF')),
+            '-DWITH_QT:BOOL={0}'.format((
+                'ON' if '+qt' in spec else 'OFF')),
+            '-DWITH_VTK:BOOL={0}'.format((
+                'ON' if '+vtk' in spec else 'OFF')),
+            '-DBUILD_opencv_java:BOOL={0}'.format((
+                'ON' if '+java' in spec else 'OFF')),
+        ])
+
+        # Media I/O
+        zlib = spec['zlib']
+        cmake_options.extend([
+            '-DZLIB_LIBRARY_{0}:FILEPATH={1}'.format((
+                'DEBUG' if '+debug' in spec else 'RELEASE'),
+                join_path(zlib.prefix.lib,
+                          'libz.{0}'.format(dso_suffix))),
+            '-DZLIB_INCLUDE_DIR:PATH={0}'.format(zlib.prefix.include)
+        ])
+
+        libpng = spec['libpng']
+        cmake_options.extend([
+            '-DPNG_LIBRARY_{0}:FILEPATH={1}'.format((
+                'DEBUG' if '+debug' in spec else 'RELEASE'),
+                join_path(libpng.prefix.lib,
+                          'libpng.{0}'.format(dso_suffix))),
+            '-DPNG_INCLUDE_DIR:PATH={0}'.format(libpng.prefix.include)
+        ])
+
+        libjpeg = spec['libjpeg-turbo']
+        cmake_options.extend([
+            '-DJPEG_LIBRARY:FILEPATH={0}'.format(
+                join_path(libjpeg.prefix.lib,
+                          'libjpeg.{0}'.format(dso_suffix))),
+            '-DJPEG_INCLUDE_DIR:PATH={0}'.format(libjpeg.prefix.include)
+        ])
+
+        libtiff = spec['libtiff']
+        cmake_options.extend([
+            '-DTIFF_LIBRARY_{0}:FILEPATH={1}'.format((
+                'DEBUG' if '+debug' in spec else 'RELEASE'),
+                join_path(libtiff.prefix.lib,
+                          'libtiff.{0}'.format(dso_suffix))),
+            '-DTIFF_INCLUDE_DIR:PATH={0}'.format(libtiff.prefix.include)
+        ])
+
+        jasper = spec['jasper']
+        cmake_options.extend([
+            '-DJASPER_LIBRARY_{0}:FILEPATH={1}'.format((
+                'DEBUG' if '+debug' in spec else 'RELEASE'),
+                join_path(jasper.prefix.lib,
+                          'libjasper.{0}'.format(dso_suffix))),
+            '-DJASPER_INCLUDE_DIR:PATH={0}'.format(jasper.prefix.include)
+        ])
+
+        # GUI
+        if '+gtk' not in spec:
+            cmake_options.extend([
+                '-DWITH_GTK:BOOL=OFF',
+                '-DWITH_GTK_2_X:BOOL=OFF'
+            ])
+        elif '^gtkplus@3:' in spec:
+            cmake_options.extend([
+                '-DWITH_GTK:BOOL=ON',
+                '-DWITH_GTK_2_X:BOOL=OFF'
+            ])
+        elif '^gtkplus@2:3' in spec:
+            cmake_options.extend([
+                '-DWITH_GTK:BOOL=OFF',
+                '-DWITH_GTK_2_X:BOOL=ON'
+            ])
+
+        # Python
+        if '+python' in spec:
+            python = spec['python']
+
+            try:
+                python_lib = glob(join_path(
+                    python.prefix.lib, 'libpython*.{0}'.format(dso_suffix)))[0]
+            except KeyError:
+                raise InstallError('Cannot find libpython')
+
+            try:
+                python_include_dir = glob(join_path(python.prefix.include,
+                                                    'python*'))[0]
+            except KeyError:
+                raise InstallError('Cannot find python include directory')
+
+            if '^python@3:' in spec:
+                python_exe = join_path(python.prefix.bin, 'python3')
+                cmake_options.extend([
+                    '-DBUILD_opencv_python3=ON',
+                    '-DPYTHON3_EXECUTABLE={0}'.format(python_exe),
+                    '-DPYTHON3_LIBRARY={0}'.format(python_lib),
+                    '-DPYTHON3_INCLUDE_DIR={0}'.format(python_include_dir),
+                    '-DBUILD_opencv_python2=OFF',
+                ])
+            elif '^python@2:3' in spec:
+                python_exe = join_path(python.prefix.bin, 'python2')
+                cmake_options.extend([
+                    '-DBUILD_opencv_python2=ON',
+                    '-DPYTHON2_EXECUTABLE={0}'.format(python_exe),
+                    '-DPYTHON2_LIBRARY={0}'.format(python_lib),
+                    '-DPYTHON2_INCLUDE_DIR={0}'.format(python_include_dir),
+                    '-DBUILD_opencv_python3=OFF',
+                ])
+        else:
+            cmake_options.extend([
+                '-DBUILD_opencv_python2=OFF',
+                '-DBUILD_opencv_python3=OFF'
+            ])
 
         with working_dir('spack_build', create=True):
             cmake('..', *cmake_options)
diff --git a/var/spack/repos/builtin/packages/openexr/package.py b/var/spack/repos/builtin/packages/openexr/package.py
new file mode 100644
index 0000000000..3619bd063c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/openexr/package.py
@@ -0,0 +1,54 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Openexr(Package):
+    """OpenEXR Graphics Tools (high dynamic-range image file format)"""
+
+    homepage = "http://www.openexr.com/"
+    url = "https://savannah.nongnu.org/download/openexr/openexr-2.2.0.tar.gz"
+
+    version('2.2.0', 'b64e931c82aa3790329c21418373db4e')
+    version('2.1.0', '33735d37d2ee01c6d8fbd0df94fb8b43')
+    version('2.0.1', '4387e6050d2faa65dd5215618ff2ddce')
+    version('1.7.0', '27113284f7d26a58f853c346e0851d7a')
+    version('1.6.1', '11951f164f9c872b183df75e66de145a')
+    version('1.5.0', '55342d2256ab3ae99da16f16b2e12ce9')
+    version('1.4.0a', 'd0a4b9a930c766fa51561b05fb204afe')
+    version('1.3.2', '1522fe69135016c52eb88fc7d8514409')
+
+    variant('debug', default=False,
+            description='Builds a debug version of the libraries')
+
+    depends_on('pkg-config', type='build')
+    depends_on('ilmbase')
+
+    def install(self, spec, prefix):
+        configure_options = ['--prefix={0}'.format(prefix)]
+        if '+debug' not in spec:
+            configure_options.append('--disable-debug')
+        configure(*configure_options)
+        make('install')
diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py
index 3fcf942f05..b0efe27def 100644
--- a/var/spack/repos/builtin/packages/openmpi/package.py
+++ b/var/spack/repos/builtin/packages/openmpi/package.py
@@ -108,7 +108,8 @@ class Openmpi(Package):
     depends_on('sqlite', when='+sqlite3')
 
     def url_for_version(self, version):
-        return "http://www.open-mpi.org/software/ompi/v%s/downloads/openmpi-%s.tar.bz2" % (version.up_to(2), version)  # NOQA: ignore=E501
+        return "http://www.open-mpi.org/software/ompi/v%s/downloads/openmpi-%s.tar.bz2" % (
+            version.up_to(2), version)
 
     def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
         spack_env.set('MPICC',  join_path(self.prefix.bin, 'mpicc'))
diff --git a/var/spack/repos/builtin/packages/openspeedshop/package.py b/var/spack/repos/builtin/packages/openspeedshop/package.py
index 4e2694a53c..5e141060b2 100644
--- a/var/spack/repos/builtin/packages/openspeedshop/package.py
+++ b/var/spack/repos/builtin/packages/openspeedshop/package.py
@@ -22,7 +22,7 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-################################################################################
+##########################################################################
 # Copyright (c) 2015-2016 Krell Institute. All Rights Reserved.
 #
 # This program is free software; you can redistribute it and/or modify it under
@@ -38,50 +38,72 @@
 # You should have received a copy of the GNU General Public License along with
 # this program; if not, write to the Free Software Foundation, Inc., 59 Temple
 # Place, Suite 330, Boston, MA  02111-1307  USA
-################################################################################
+##########################################################################
 
 from spack import *
 
+
 class Openspeedshop(Package):
-    """OpenSpeedShop is a community effort by The Krell Institute with current direct funding from DOEs NNSA.
-    It builds on top of a broad list of community infrastructures, most notably Dyninst and MRNet from UW,
-    libmonitor from Rice, and PAPI from UTK. OpenSpeedShop is an open source multi platform Linux performance
-    tool which is targeted to support performance analysis of applications running on both single node and
-    large scale IA64, IA32, EM64T, AMD64, PPC, ARM, Blue Gene and Cray platforms.  OpenSpeedShop development
-    is hosted by the Krell Institute. The infrastructure and base components of OpenSpeedShop are released
-    as open source code primarily under LGPL.
+    """OpenSpeedShop is a community effort by The Krell Institute with
+    current direct funding from DOEs NNSA.  It builds on top of a broad
+    list of community infrastructures, most notably Dyninst and MRNet
+    from UW, libmonitor from Rice, and PAPI from UTK. OpenSpeedShop is an
+    open source multi platform Linux performance tool which is targeted
+    to support performance analysis of applications running on both
+    single node and large scale IA64, IA32, EM64T, AMD64, PPC, ARM, Blue
+    Gene and Cray platforms.  OpenSpeedShop development is hosted by the
+    Krell Institute. The infrastructure and base components of
+    OpenSpeedShop are released as open source code primarily under LGPL.
+
     """
 
     homepage = "http://www.openspeedshop.org"
-    url		= "https://github.com/OpenSpeedShop"
+    url = "https://github.com/OpenSpeedShop"
     version('2.2', '16cb051179c2038de4e8a845edf1d573')
     # Use when the git repository is available
-    version('2.2', branch='master', git='https://github.com/OpenSpeedShop/openspeedshop.git')
+    version('2.2', branch='master',
+            git='https://github.com/OpenSpeedShop/openspeedshop.git')
 
     # Optional mirror template
-    #url = "file:/home/jeg/OpenSpeedShop_ROOT/SOURCES/openspeedshop-2.2.tar.gz"
-    #version('2.2', '643337740dc6c2faca60f42d3620b0e1')
+    # url="file:/home/jeg/OpenSpeedShop_ROOT/SOURCES/openspeedshop-2.2.tar.gz"
+    # version('2.2', '643337740dc6c2faca60f42d3620b0e1')
 
     parallel = False
 
-    variant('offline', default=True, description="build with offline instrumentor enabled.")
-    variant('cbtf', default=False, description="build with cbtf instrumentor enabled.")
-    variant('runtime', default=False, description="build only the runtime libraries and collectors.")
-    variant('frontend', default=False, description="build only the front-end tool using the runtime_dir to point to the target build.")
-    variant('cuda', default=False, description="build with cuda packages included.")
-    variant('ptgf', default=False, description="build with the PTGF based gui package enabled.")
-    variant('rtfe', default=False, description="build for generic cluster platforms that have different processors on the fe and be nodes.")
+    variant('offline', default=True,
+            description="build with offline instrumentor enabled.")
+    variant('cbtf', default=False,
+            description="build with cbtf instrumentor enabled.")
+    variant('runtime', default=False,
+            description="build only the runtime libraries and collectors.")
+    variant('frontend', default=False,
+            description="build only the front-end tool using the runtime_dir "
+                        "to point to the target build.")
+    variant('cuda', default=False,
+            description="build with cuda packages included.")
+    variant('ptgf', default=False,
+            description="build with the PTGF based gui package enabled.")
+    variant('rtfe', default=False,
+            description="build for generic cluster platforms that have "
+                        "different processors on the fe and be nodes.")
 
     # MPI variants
-    variant('openmpi', default=False, description="Build mpi experiment collector for openmpi MPI when this variant is enabled.")
-    variant('mpt', default=False, description="Build mpi experiment collector for SGI MPT MPI when this variant is enabled.")
-    variant('mvapich2', default=False, description="Build mpi experiment collector for mvapich2 MPI when this variant is enabled.")
-    variant('mvapich', default=False, description="Build mpi experiment collector for mvapich MPI when this variant is enabled.")
-    variant('mpich2', default=False, description="Build mpi experiment collector for mpich2 MPI when this variant is enabled.")
-    variant('mpich', default=False, description="Build mpi experiment collector for mpich MPI when this variant is enabled.")
+    variant('openmpi', default=False,
+            description="Build mpi experiment collector for openmpi MPI.")
+    variant('mpt', default=False,
+            description="Build mpi experiment collector for SGI MPT MPI.")
+    variant('mvapich2', default=False,
+            description="Build mpi experiment collector for mvapich2 MPI.")
+    variant('mvapich', default=False,
+            description="Build mpi experiment collector for mvapich MPI.")
+    variant('mpich2', default=False,
+            description="Build mpi experiment collector for mpich2 MPI.")
+    variant('mpich', default=False,
+            description="Build mpi experiment collector for mpich MPI.")
 
     depends_on("cmake@3.0.2", type='build')
-    # Dependencies for openspeedshop that are common to all the variants of the OpenSpeedShop build
+    # Dependencies for openspeedshop that are common to all the variants of
+    # the OpenSpeedShop build
     depends_on("bison")
     depends_on("flex")
     depends_on("binutils@2.24+krellpatch")
@@ -111,11 +133,13 @@ class Openspeedshop(Package):
     depends_on("mrnet@5.0.1:+lwthreads+krellpatch", when='+cbtf')
 
     def adjustBuildTypeParams_cmakeOptions(self, spec, cmakeOptions):
-        # Sets build type parameters into cmakeOptions the options that will enable the cbtf-krell built type settings
+        # Sets build type parameters into cmakeOptions the options that will
+        # enable the cbtf-krell built type settings
 
-        compile_flags="-O2 -g"
+        compile_flags = "-O2 -g"
         BuildTypeOptions = []
-        # Set CMAKE_BUILD_TYPE to what cbtf-krell wants it to be, not the stdcmakeargs
+        # Set CMAKE_BUILD_TYPE to what cbtf-krell wants it to be, not the
+        # stdcmakeargs
         for word in cmakeOptions[:]:
             if word.startswith('-DCMAKE_BUILD_TYPE'):
                 cmakeOptions.remove(word)
@@ -124,63 +148,64 @@ class Openspeedshop(Package):
             if word.startswith('-DCMAKE_C_FLAGS'):
                 cmakeOptions.remove(word)
         BuildTypeOptions.extend([
-                 '-DCMAKE_BUILD_TYPE=None',
-                 '-DCMAKE_CXX_FLAGS=%s'         % compile_flags,
-                 '-DCMAKE_C_FLAGS=%s'           % compile_flags
+            '-DCMAKE_BUILD_TYPE=None',
+            '-DCMAKE_CXX_FLAGS=%s'         % compile_flags,
+            '-DCMAKE_C_FLAGS=%s'           % compile_flags
         ])
 
         cmakeOptions.extend(BuildTypeOptions)
 
     def set_mpi_cmakeOptions(self, spec, cmakeOptions):
-        # Appends to cmakeOptions the options that will enable the appropriate MPI implementations
- 
+        # Appends to cmakeOptions the options that will enable the appropriate
+        # MPI implementations
+
         MPIOptions = []
 
         # openmpi
         if '+openmpi' in spec:
             MPIOptions.extend([
-                 '-DOPENMPI_DIR=%s' % spec['openmpi'].prefix
+                '-DOPENMPI_DIR=%s' % spec['openmpi'].prefix
             ])
         # mpich
         if '+mpich' in spec:
             MPIOptions.extend([
-                 '-DMPICH_DIR=%s' % spec['mpich'].prefix
+                '-DMPICH_DIR=%s' % spec['mpich'].prefix
             ])
         # mpich2
         if '+mpich2' in spec:
             MPIOptions.extend([
-                 '-DMPICH2_DIR=%s' % spec['mpich2'].prefix
+                '-DMPICH2_DIR=%s' % spec['mpich2'].prefix
             ])
         # mvapich
         if '+mvapich' in spec:
             MPIOptions.extend([
-                 '-DMVAPICH_DIR=%s' % spec['mvapich'].prefix
+                '-DMVAPICH_DIR=%s' % spec['mvapich'].prefix
             ])
         # mvapich2
         if '+mvapich2' in spec:
             MPIOptions.extend([
-                 '-DMVAPICH2_DIR=%s' % spec['mvapich2'].prefix
+                '-DMVAPICH2_DIR=%s' % spec['mvapich2'].prefix
             ])
         # mpt
         if '+mpt' in spec:
             MPIOptions.extend([
-                 '-DMPT_DIR=%s' % spec['mpt'].prefix
+                '-DMPT_DIR=%s' % spec['mpt'].prefix
             ])
 
         cmakeOptions.extend(MPIOptions)
 
-
     def install(self, spec, prefix):
 
-        #openmpi_prefix_path = "/opt/openmpi-1.8.2"
-        #mvapich_prefix_path = "/usr/local/tools/mvapich-gnu"
-                          #'-DOPENMPI_DIR=%s'            % spec['openmpi'].prefix,
-                          #'-DOPENMPI_DIR=%s'            % openmpi_prefix_path,
-                          #'-DMVAPICH_DIR=%s'            % mvapich_prefix_path,
+        # openmpi_prefix_path = "/opt/openmpi-1.8.2"
+        # mvapich_prefix_path = "/usr/local/tools/mvapich-gnu"
+        #    '-DOPENMPI_DIR=%s'            % spec['openmpi'].prefix,
+        #    '-DOPENMPI_DIR=%s'            % openmpi_prefix_path,
+        #    '-DMVAPICH_DIR=%s'            % mvapich_prefix_path,
 
-        # FIXME: How do we make this dynamic in spack?   That is, can we specify the paths to cuda dynamically?
-        # WAITING for external package support. 
-        #if '+cuda' in spec:
+        # FIXME: How do we make this dynamic in spack?
+        # FIXME: That is, can we specify the paths to cuda dynamically?
+        # WAITING for external package support.
+        # if '+cuda' in spec:
         #    cuda_prefix_path = "/usr/local/cuda-6.0"
         #    cupti_prefix_path = "/usr/local/cuda-6.0/extras/CUPTI"
 
@@ -190,19 +215,20 @@ class Openspeedshop(Package):
                 with working_dir('build_runtime', create=True):
 
                     cmakeOptions = []
-                    cmakeOptions.extend(['-DCMAKE_INSTALL_PREFIX=%s'   % prefix,
-                                         '-DCMAKE_LIBRARY_PATH=%s'     % prefix.lib64,
-                                         '-DINSTRUMENTOR=%s'           % instrumentor_setting,
-                                         '-DLIBMONITOR_DIR=%s'         % spec['libmonitor'].prefix,
-                                         '-DLIBUNWIND_DIR=%s'          % spec['libunwind'].prefix,
-                                         '-DPAPI_DIR=%s'               % spec['papi'].prefix 
-                                        ])
- 
+                    cmakeOptions.extend([
+                        '-DCMAKE_INSTALL_PREFIX=%s' % prefix,
+                        '-DCMAKE_LIBRARY_PATH=%s' % prefix.lib64,
+                        '-DINSTRUMENTOR=%s' % instrumentor_setting,
+                        '-DLIBMONITOR_DIR=%s' % spec['libmonitor'].prefix,
+                        '-DLIBUNWIND_DIR=%s' % spec['libunwind'].prefix,
+                        '-DPAPI_DIR=%s' % spec['papi'].prefix])
+
                     # Add any MPI implementations coming from variant settings
                     self.set_mpi_cmakeOptions(spec, cmakeOptions)
                     cmakeOptions.extend(std_cmake_args)
 
-                    # Adjust the build options to the favored ones for this build
+                    # Adjust the build options to the favored ones for this
+                    # build
                     self.adjustBuildTypeParams_cmakeOptions(spec, cmakeOptions)
 
                     cmake('..', *cmakeOptions)
@@ -214,43 +240,49 @@ class Openspeedshop(Package):
                 cmake_prefix_path = join_path(spec['dyninst'].prefix)
                 with working_dir('build', create=True):
 
-                    #python_vers=join_path(spec['python'].version[:2])
-                    #'-DOPENMPI_DIR=%s'            % openmpi_prefix_path,
-                    #'-DMVAPICH_DIR=%s'            % mvapich_prefix_path,
-                    #'-DMPICH_DIR=%s'              % spec['mpich'].prefix,
-                    #'-DMPICH2_DIR=%s'             % spec['mpich2'].prefix,
-                    #'-DBoost_NO_SYSTEM_PATHS=TRUE',
-                    #'-DBOOST_ROOT=%s'             % spec['boost'].prefix,
-                    #'-DOPENMPI_DIR=%s'            % spec['openmpi'].prefix,
+                    # python_vers=join_path(spec['python'].version[:2])
+                    # '-DOPENMPI_DIR=%s'            % openmpi_prefix_path,
+                    # '-DMVAPICH_DIR=%s'            % mvapich_prefix_path,
+                    # '-DMPICH_DIR=%s'              % spec['mpich'].prefix,
+                    # '-DMPICH2_DIR=%s'             % spec['mpich2'].prefix,
+                    # '-DBoost_NO_SYSTEM_PATHS=TRUE',
+                    # '-DBOOST_ROOT=%s'             % spec['boost'].prefix,
+                    # '-DOPENMPI_DIR=%s'            % spec['openmpi'].prefix,
 
-                    python_vers='%d.%d' % spec['python'].version[:2]
+                    python_vers = '%d.%d' % spec['python'].version[:2]
 
                     cmakeOptions = []
-                    cmakeOptions.extend(['-DCMAKE_INSTALL_PREFIX=%s'   % prefix,
-                                         '-DCMAKE_LIBRARY_PATH=%s'     % prefix.lib64,
-                                         '-DCMAKE_PREFIX_PATH=%s'      % cmake_prefix_path,
-                                         '-DINSTRUMENTOR=%s'           % instrumentor_setting,
-                                         '-DBINUTILS_DIR=%s'           % spec['binutils'].prefix,
-                                         '-DLIBELF_DIR=%s'             % spec['libelf'].prefix,
-                                         '-DLIBDWARF_DIR=%s'           % spec['libdwarf'].prefix,
-                                         '-DLIBMONITOR_DIR=%s'         % spec['libmonitor'].prefix,
-                                         '-DLIBUNWIND_DIR=%s'          % spec['libunwind'].prefix,
-                                         '-DPAPI_DIR=%s'               % spec['papi'].prefix,
-                                         '-DSQLITE3_DIR=%s'            % spec['sqlite'].prefix,
-                                         '-DQTLIB_DIR=%s'              % spec['qt'].prefix,
-                                         '-DPYTHON_EXECUTABLE=%s'      % join_path(spec['python'].prefix + '/bin/python'),
-                                         '-DPYTHON_INCLUDE_DIR=%s'     % join_path(spec['python'].prefix.include) + '/python' + python_vers,
-                                         '-DPYTHON_LIBRARY=%s'         % join_path(spec['python'].prefix.lib) + '/libpython' + python_vers + '.so',
-                                         '-DBoost_NO_SYSTEM_PATHS=TRUE',
-                                         '-DBOOST_ROOT=%s'             % spec['boost'].prefix,
-                                         '-DDYNINST_DIR=%s'            % spec['dyninst'].prefix
-                                        ])
+                    cmakeOptions.extend([
+                        '-DCMAKE_INSTALL_PREFIX=%s' % prefix,
+                        '-DCMAKE_LIBRARY_PATH=%s' % prefix.lib64,
+                        '-DCMAKE_PREFIX_PATH=%s' % cmake_prefix_path,
+                        '-DINSTRUMENTOR=%s'   % instrumentor_setting,
+                        '-DBINUTILS_DIR=%s'   % spec['binutils'].prefix,
+                        '-DLIBELF_DIR=%s'     % spec['libelf'].prefix,
+                        '-DLIBDWARF_DIR=%s'   % spec['libdwarf'].prefix,
+                        '-DLIBMONITOR_DIR=%s' % spec['libmonitor'].prefix,
+                        '-DLIBUNWIND_DIR=%s'  % spec['libunwind'].prefix,
+                        '-DPAPI_DIR=%s'       % spec['papi'].prefix,
+                        '-DSQLITE3_DIR=%s'    % spec['sqlite'].prefix,
+                        '-DQTLIB_DIR=%s'      % spec['qt'].prefix,
+                        '-DPYTHON_EXECUTABLE=%s' % join_path(
+                            spec['python'].prefix, '/bin/python'),
+                        '-DPYTHON_INCLUDE_DIR=%s' % join_path(
+                            spec['python'].prefix.include,
+                            'python' + python_vers),
+                        '-DPYTHON_LIBRARY=%s' % join_path(
+                            spec['python'].prefix.lib,
+                            'libpython' + python_vers + '.so'),
+                        '-DBoost_NO_SYSTEM_PATHS=TRUE',
+                        '-DBOOST_ROOT=%s'          % spec['boost'].prefix,
+                        '-DDYNINST_DIR=%s'         % spec['dyninst'].prefix])
 
                     # Add any MPI implementations coming from variant settings
                     self.set_mpi_cmakeOptions(spec, cmakeOptions)
                     cmakeOptions.extend(std_cmake_args)
 
-                    # Adjust the build options to the favored ones for this build
+                    # Adjust the build options to the favored ones for this
+                    # build
                     self.adjustBuildTypeParams_cmakeOptions(spec, cmakeOptions)
 
                     cmake('..', *cmakeOptions)
@@ -261,160 +293,171 @@ class Openspeedshop(Package):
 
         elif '+cbtf' in spec:
             instrumentor_setting = "cbtf"
-            resolve_symbols = "symtabapi"
-            cmake_prefix_path = join_path(spec['cbtf'].prefix) + ':' + join_path(spec['cbtf-krell'].prefix) + ':' + join_path(spec['dyninst'].prefix)
-            #runtime_platform_cray = "cray"
-            #if '+cray' in spec:
+            cmake_prefix_path = ':'.join(spec['cbtf'].prefix,
+                                         spec['cbtf-krell'].prefix,
+                                         spec['dyninst'].prefix)
+
+            # resolve_symbols = "symtabapi"
+            # runtime_platform_cray = "cray"
+            # if '+cray' in spec:
             #    if '+runtime' in spec:
-            #                   #-DCBTF_KRELL_CN_RUNTIME_DIR=${CBTF_KRELL_CN_INSTALL_DIR} \
-            #        with working_dir('build_cbtf_cray_runtime', create=True):
-            #            python_vers='%d.%d' % spec['python'].version[:2]
-            #            cmake('..',
-            #                  '-DCMAKE_INSTALL_PREFIX=%s'   % prefix,
-            #                  '-DCMAKE_LIBRARY_PATH=%s'     % prefix.lib64,
-            #                  '-DRUNTIME_PLATFORM=%s'		% runtime_platform_cray,
-            #                  '-DCMAKE_PREFIX_PATH=%s'      % cmake_prefix_path,
-            #                  '-DRESOLVE_SYMBOLS=%s'		% resolve_symbols,
-            #                  '-DINSTRUMENTOR=%s'           % instrumentor_setting,
-            #                  '-DCBTF_DIR=%s'			% spec['cbtf'].prefix,
-            #                  '-DCBTF_KRELL_DIR=%s'		% spec['cbtf-krell'].prefix,
-            #                  '-DCBTF_KRELL_CN_RUNTIME_DIR=%s'	% spec['cbtf-krell'].prefix,
-            #                  '-DBINUTILS_DIR=%s'           % spec['binutils'].prefix,
-            #                  '-DLIBELF_DIR=%s'             % spec['libelf'].prefix,
-            #                  '-DLIBDWARF_DIR=%s'           % spec['libdwarf'].prefix,
-            #                  '-DLIBUNWIND_DIR=%s'          % spec['libunwind'].prefix,
-            #                  '-DPAPI_DIR=%s'               % spec['papi'].prefix,
-            #                  '-DDYNINST_DIR=%s'            % spec['dyninst'].prefix,
-            #                  '-DXERCESC_DIR=%s'            % spec['xerces-c'].prefix,
-            #                  '-DMRNET_DIR=%s'              % spec['mrnet'].prefix,
-            #                  '-DBoost_NO_SYSTEM_PATHS=TRUE',
-            #                  '-DBOOST_ROOT=%s'             % spec['boost'].prefix,
-            #                  *std_cmake_args)
+            #      #-DCBTF_KRELL_CN_RUNTIME_DIR=${CBTF_KRELL_CN_INSTALL_DIR} \
+            #      with working_dir('build_cbtf_cray_runtime', create=True):
+            #        python_vers='%d.%d' % spec['python'].version[:2]
+            #        cmake('..',
+            #   '-DCMAKE_INSTALL_PREFIX=%s'   % prefix,
+            #   '-DCMAKE_LIBRARY_PATH=%s'     % prefix.lib64,
+            #   '-DRUNTIME_PLATFORM=%s' % runtime_platform_cray,
+            #   '-DCMAKE_PREFIX_PATH=%s'      % cmake_prefix_path,
+            #   '-DRESOLVE_SYMBOLS=%s' % resolve_symbols,
+            #   '-DINSTRUMENTOR=%s'           % instrumentor_setting,
+            #   '-DCBTF_DIR=%s' % spec['cbtf'].prefix,
+            #   '-DCBTF_KRELL_DIR=%s' % spec['cbtf-krell'].prefix,
+            #   '-DCBTF_KRELL_CN_RUNTIME_DIR=%s' % spec['cbtf-krell'].prefix,
+            #   '-DBINUTILS_DIR=%s'           % spec['binutils'].prefix,
+            #   '-DLIBELF_DIR=%s'             % spec['libelf'].prefix,
+            #   '-DLIBDWARF_DIR=%s'           % spec['libdwarf'].prefix,
+            #   '-DLIBUNWIND_DIR=%s'          % spec['libunwind'].prefix,
+            #   '-DPAPI_DIR=%s'               % spec['papi'].prefix,
+            #   '-DDYNINST_DIR=%s'            % spec['dyninst'].prefix,
+            #   '-DXERCESC_DIR=%s'            % spec['xerces-c'].prefix,
+            #   '-DMRNET_DIR=%s'              % spec['mrnet'].prefix,
+            #   '-DBoost_NO_SYSTEM_PATHS=TRUE',
+            #   '-DBOOST_ROOT=%s'             % spec['boost'].prefix,
+            #   *std_cmake_args)
 
             #           make("clean")
             #           make()
             #           make("install")
 
-
-            #elif '+mic' in spec:
-            # comment out else and shift over the default case below until arch detection is in
-            #else:
+            # elif '+mic' in spec:
+            # comment out else and shift over the default case below
+            # until arch detection is in else:
 
             if '+runtime' in spec:
                 with working_dir('build_cbtf_runtime', create=True):
-                    python_vers='%d.%d' % spec['python'].version[:2]
-                    cmake('..',
-                          '-DCMAKE_INSTALL_PREFIX=%s'   % prefix,
-                          '-DCMAKE_LIBRARY_PATH=%s'     % prefix.lib64,
-                          '-DCMAKE_PREFIX_PATH=%s'      % cmake_prefix_path,
-                          '-DINSTRUMENTOR=%s'           % instrumentor_setting,
-                          '-DBINUTILS_DIR=%s'           % spec['binutils'].prefix,
-                          '-DLIBELF_DIR=%s'             % spec['libelf'].prefix,
-                          '-DLIBDWARF_DIR=%s'           % spec['libdwarf'].prefix,
-                          '-DCBTF_DIR=%s'               % spec['cbtf'].prefix,
-                          '-DCBTF_KRELL_DIR=%s'         % spec['cbtf-krell'].prefix,
-                          '-DPYTHON_EXECUTABLE=%s'      % join_path(spec['python'].prefix + '/bin/python'),
-                          '-DPYTHON_INCLUDE_DIR=%s'     % join_path(spec['python'].prefix.include) + '/python' + python_vers,
-                          '-DPYTHON_LIBRARY=%s'         % join_path(spec['python'].prefix.lib) + '/libpython' + python_vers + '.so',
-                          '-DBoost_NO_SYSTEM_PATHS=TRUE',
-                          '-DBOOST_ROOT=%s'             % spec['boost'].prefix,
-                          '-DDYNINST_DIR=%s'            % spec['dyninst'].prefix,
-                          '-DMRNET_DIR=%s'              % spec['mrnet'].prefix,
-                          *std_cmake_args)
+                    python_vers = '%d.%d' % spec['python'].version[:2]
+                    cmake(
+                        '..',
+                        '-DCMAKE_INSTALL_PREFIX=%s' % prefix,
+                        '-DCMAKE_LIBRARY_PATH=%s' % prefix.lib64,
+                        '-DCMAKE_PREFIX_PATH=%s' % cmake_prefix_path,
+                        '-DINSTRUMENTOR=%s' % instrumentor_setting,
+                        '-DBINUTILS_DIR=%s' % spec['binutils'].prefix,
+                        '-DLIBELF_DIR=%s' % spec['libelf'].prefix,
+                        '-DLIBDWARF_DIR=%s' % spec['libdwarf'].prefix,
+                        '-DCBTF_DIR=%s' % spec['cbtf'].prefix,
+                        '-DCBTF_KRELL_DIR=%s' % spec['cbtf-krell'].prefix,
+                        '-DPYTHON_EXECUTABLE=%s' % join_path(
+                            spec['python'].prefix, 'bin', 'python'),
+                        '-DPYTHON_INCLUDE_DIR=%s' % join_path(
+                            spec['python'].prefix.include,
+                            'python' + python_vers),
+                        '-DPYTHON_LIBRARY=%s' % join_path(
+                            spec['python'].prefix.lib,
+                            'libpython' + python_vers + '.so'),
+                        '-DBoost_NO_SYSTEM_PATHS=TRUE',
+                        '-DBOOST_ROOT=%s' % spec['boost'].prefix,
+                        '-DDYNINST_DIR=%s' % spec['dyninst'].prefix,
+                        '-DMRNET_DIR=%s' % spec['mrnet'].prefix,
+                        *std_cmake_args)
+
                     make("clean")
                     make()
                     make("install")
 
             else:
                 with working_dir('build_cbtf', create=True):
-                    python_vers='%d.%d' % spec['python'].version[:2]
-                    #python_vers=join_path(spec['python'].version[:2])
-                    cmake('..',
-                          '-DCMAKE_INSTALL_PREFIX=%s'   % prefix,
-                          '-DCMAKE_LIBRARY_PATH=%s'     % prefix.lib64,
-                          '-DCMAKE_PREFIX_PATH=%s'      % cmake_prefix_path,
-                          '-DINSTRUMENTOR=%s'           % instrumentor_setting,
-                          '-DBINUTILS_DIR=%s'           % spec['binutils'].prefix,
-                          '-DLIBELF_DIR=%s'             % spec['libelf'].prefix,
-                          '-DLIBDWARF_DIR=%s'           % spec['libdwarf'].prefix,
-                          '-DSQLITE3_DIR=%s'            % spec['sqlite'].prefix,
-                          '-DCBTF_DIR=%s'               % spec['cbtf'].prefix,
-                          '-DCBTF_KRELL_DIR=%s'         % spec['cbtf-krell'].prefix,
-                          '-DQTLIB_DIR=%s'              % spec['qt'].prefix,
-                          '-DPYTHON_EXECUTABLE=%s'      % join_path(spec['python'].prefix + '/bin/python'),
-                          '-DPYTHON_INCLUDE_DIR=%s'     % join_path(spec['python'].prefix.include) + '/python' + python_vers,
-                          '-DPYTHON_LIBRARY=%s'         % join_path(spec['python'].prefix.lib) + '/libpython' + python_vers + '.so',
-                          '-DBoost_NO_SYSTEM_PATHS=TRUE',
-                          '-DBOOST_ROOT=%s'             % spec['boost'].prefix,
-                          '-DDYNINST_DIR=%s'            % spec['dyninst'].prefix,
-                          '-DMRNET_DIR=%s'              % spec['mrnet'].prefix,
-                          *std_cmake_args)
+                    python_vers = '%d.%d' % spec['python'].version[:2]
+                    # python_vers=join_path(spec['python'].version[:2])
+                    cmake(
+                        '..',
+                        '-DCMAKE_INSTALL_PREFIX=%s' % prefix,
+                        '-DCMAKE_LIBRARY_PATH=%s'   % prefix.lib64,
+                        '-DCMAKE_PREFIX_PATH=%s'    % cmake_prefix_path,
+                        '-DINSTRUMENTOR=%s'         % instrumentor_setting,
+                        '-DBINUTILS_DIR=%s'         % spec['binutils'].prefix,
+                        '-DLIBELF_DIR=%s'         % spec['libelf'].prefix,
+                        '-DLIBDWARF_DIR=%s'       % spec['libdwarf'].prefix,
+                        '-DSQLITE3_DIR=%s'        % spec['sqlite'].prefix,
+                        '-DCBTF_DIR=%s'           % spec['cbtf'].prefix,
+                        '-DCBTF_KRELL_DIR=%s'     % spec['cbtf-krell'].prefix,
+                        '-DQTLIB_DIR=%s'          % spec['qt'].prefix,
+                        '-DPYTHON_EXECUTABLE=%s' % join_path(
+                            spec['python'].prefix, 'bin', 'python'),
+                        '-DPYTHON_INCLUDE_DIR=%s' % join_path(
+                            spec['python'].prefix.include,
+                            'python' + python_vers),
+                        '-DPYTHON_LIBRARY=%s' % join_path(
+                            spec['python'].prefix.lib,
+                            'libpython' + python_vers + '.so'),
+                        '-DBoost_NO_SYSTEM_PATHS=TRUE',
+                        '-DBOOST_ROOT=%s' % spec['boost'].prefix,
+                        '-DDYNINST_DIR=%s' % spec['dyninst'].prefix,
+                        '-DMRNET_DIR=%s' % spec['mrnet'].prefix,
+                        *std_cmake_args)
+
                     make("clean")
                     make()
                     make("install")
 
-        #if '+frontend' in spec:
-        #    with working_dir('build_frontend', create=True):
-        #         tbd
-
-
-
-        #if '+cbtf' in spec:
-        #   if cray build type detected:
-        #        if '+runtime' in spec:
-        #            with working_dir('build_cray_cbtf_compute', create=True):
-        #                tbd
-        #        else:
-        #            with working_dir('build_cray_cbtf_frontend', create=True):
-        #                tbd
-        #            with working_dir('build_cray_osscbtf_frontend', create=True):
-        #                tbd
-        #        fi
-        #    elif '+intelmic' in spec:
-        #        if '+runtime' in spec:
-        #            with working_dir('build_intelmic_cbtf_compute', create=True):
-        #                tbd
-        #        else:
-        #            with working_dir('build_intelmic_cbtf_frontend', create=True):
-        #                tbd
-        #            with working_dir('build_intelmic_osscbtf_frontend', create=True):
-        #        fi
-        #    else
-        #        with working_dir('build_cluster_cbtf', create=True):
-        #             tbd
-        #        with working_dir('build_cluster osscbtf', create=True):
-        #             tbd
-        #    fi
-        #elif '+offline' in spec:
-        #   if cray build type detected:
-        #        if '+runtime' in spec:
-        #            with working_dir('build_cray_ossoff_compute', create=True):
-        #                tbd
-        #        else:
-        #            with working_dir('build_cray_ossoff_frontend', create=True):
-        #                tbd
-        #        fi
-        #    elif '+intelmic' in spec:
-        #        if '+runtime' in spec:
-        #            with working_dir('build_intelmic_ossoff_compute', create=True):
-        #                tbd
-        #        else:
-        #            with working_dir('build_intelmic_ossoff_frontend', create=True):
-        #                tbd
-        #        fi
-        #    elif bgq build type detected:
-        #        if '+runtime' in spec:
-        #            with working_dir('build_bgq_ossoff_compute', create=True):
-        #                tbd
-        #        else:
-        #            with working_dir('build_bgq_ossoff_frontend', create=True):
-        #                tbd
-        #        fi
-        #    else
-        #        with working_dir('build_cluster ossoff', create=True):
-        #             tbd
-        #    fi
-        #fi
-
-
-
+# if '+frontend' in spec:
+#    with working_dir('build_frontend', create=True):
+#         tbd
+
+# if '+cbtf' in spec:
+#   if cray build type detected:
+#        if '+runtime' in spec:
+#            with working_dir('build_cray_cbtf_compute', create=True):
+#                tbd
+#        else:
+#            with working_dir('build_cray_cbtf_frontend', create=True):
+#                tbd
+#            with working_dir('build_cray_osscbtf_frontend', create=True):
+#                tbd
+#        fi
+#    elif '+intelmic' in spec:
+#        if '+runtime' in spec:
+#            with working_dir('build_intelmic_cbtf_compute', create=True):
+#                tbd
+#        else:
+#            with working_dir('build_intelmic_cbtf_frontend', create=True):
+#                tbd
+#            with working_dir('build_intelmic_osscbtf_frontend', create=True):
+#        fi
+#    else
+#        with working_dir('build_cluster_cbtf', create=True):
+#             tbd
+#        with working_dir('build_cluster osscbtf', create=True):
+#             tbd
+#    fi
+# elif '+offline' in spec:
+#   if cray build type detected:
+#        if '+runtime' in spec:
+#            with working_dir('build_cray_ossoff_compute', create=True):
+#                tbd
+#        else:
+#            with working_dir('build_cray_ossoff_frontend', create=True):
+#                tbd
+#        fi
+#    elif '+intelmic' in spec:
+#        if '+runtime' in spec:
+#            with working_dir('build_intelmic_ossoff_compute', create=True):
+#                tbd
+#        else:
+#            with working_dir('build_intelmic_ossoff_frontend', create=True):
+#                tbd
+#        fi
+#    elif bgq build type detected:
+#        if '+runtime' in spec:
+#            with working_dir('build_bgq_ossoff_compute', create=True):
+#                tbd
+#        else:
+#            with working_dir('build_bgq_ossoff_frontend', create=True):
+#                tbd
+#        fi
+#    else
+#        with working_dir('build_cluster ossoff', create=True):
+#             tbd
+#    fi
+# fi
diff --git a/var/spack/repos/builtin/packages/openssl/package.py b/var/spack/repos/builtin/packages/openssl/package.py
index e7c105d5f5..8d9049a8f7 100644
--- a/var/spack/repos/builtin/packages/openssl/package.py
+++ b/var/spack/repos/builtin/packages/openssl/package.py
@@ -22,7 +22,6 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import urllib
 import llnl.util.tty as tty
 
 from spack import *
@@ -35,7 +34,7 @@ class Openssl(Package):
        Transport Layer Security (TLS v1) protocols as well as a
        full-strength general purpose cryptography library."""
     homepage = "http://www.openssl.org"
-    url = "https://www.openssl.org/source/openssl-1.0.1h.tar.gz"
+    url = "ftp://openssl.org/source/openssl-1.0.1h.tar.gz"
 
     version('1.0.1h', '8d6d684a9430d5cc98a62a5d8fbda8cf')
     version('1.0.1r', '1abd905e079542ccae948af37e393d28')
@@ -50,61 +49,15 @@ class Openssl(Package):
     parallel = False
 
     def url_for_version(self, version):
-        # This URL is computed pinging the place where the latest version is
-        # stored. To avoid slowdown due to repeated pinging, we store the URL
-        # in a private class attribute to do the job only once per version
-        openssl_urls = getattr(Openssl, '_openssl_url', {})
-        openssl_url = openssl_urls.get(version, None)
-        # Same idea, but just to avoid issuing the same message multiple times
-        warnings_given_to_user = getattr(Openssl, '_warnings_given', {})
-        if openssl_url is None:
-            if self.spec.satisfies('@system'):
-                # The version @system is reserved to system openssl. In that
-                # case return a fake url and exit
-                openssl_url = '@system (reserved version for system openssl)'
-                if not warnings_given_to_user.get(version, False):
-                    tty.msg('Using openssl@system: '
-                            'the version @system is reserved for system openssl')
-                    warnings_given_to_user[version] = True
-            else:
-                openssl_url = self.check_for_outdated_release(
-                    version, warnings_given_to_user)  # Store the computed URL
-            openssl_urls[version] = openssl_url
-            # Store the updated dictionary of URLS
-            Openssl._openssl_url = openssl_urls
-            # Store the updated dictionary of warnings
-            Openssl._warnings_given = warnings_given_to_user
-
-        return openssl_url
-
-    def check_for_outdated_release(self, version, warnings_given_to_user):
-        latest = 'ftp://ftp.openssl.org/source/openssl-{version}.tar.gz'
-        older = 'http://www.openssl.org/source/old/{version_number}/openssl-{version_full}.tar.gz'  # NOQA: ignore=E501
-        # Try to use the url where the latest tarballs are stored.
-        # If the url does not exist (404), then return the url for
-        # older format
-        version_number = '.'.join([str(x) for x in version[:-1]])
-        try:
-            openssl_url = latest.format(version=version)
-            urllib.urlopen(openssl_url)
-        except IOError:
-            openssl_url = older.format(
-                version_number=version_number, version_full=version)
-            # Checks if we already warned the user for this particular
-            # version of OpenSSL. If not we display a warning message
-            # and mark this version
-            if not warnings_given_to_user.get(version, False):
-                tty.warn(
-                    'This installation depends on an old version of OpenSSL, '
-                    'which may have known security issues. ')
-                tty.warn(
-                    'Consider updating to the latest version of this package.')
-                tty.warn('More details at {homepage}'.format(
-                    homepage=Openssl.homepage))
-                warnings_given_to_user[version] = True
-
-        return openssl_url
-
+        if '@system' in self.spec:
+            return '@system (reserved version for system openssl)'
+        else:
+            return super(Openssl, self).url_for_version(self.version)
+
+    def handle_fetch_error(self, error):
+        tty.warn("Fetching OpenSSL failed. This may indicate that OpenSSL has "
+                 "been updated, and the version in your instance of Spack is "
+                 "insecure. Consider updating to the latest OpenSSL version.")
 
     def install(self, spec, prefix):
         # OpenSSL uses a variable APPS in its Makefile. If it happens to be set
diff --git a/var/spack/repos/builtin/packages/opium/package.py b/var/spack/repos/builtin/packages/opium/package.py
new file mode 100644
index 0000000000..2c81d92cc0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/opium/package.py
@@ -0,0 +1,55 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Opium(Package):
+    """DFT pseudopotential generation project"""
+
+    homepage = "https://opium.sourceforge.net/index.html"
+    url      = "https://downloads.sourceforge.net/project/opium/opium/opium-v3.8/opium-v3.8-src.tgz"
+
+    version('3.8', 'f710c0f869e70352b4a510c31e13bf9f')
+
+    depends_on('blas')
+    depends_on('lapack')
+
+    def install(self, spec, prefix):
+        options = [
+            'LDFLAGS=%s %s' % (
+                to_link_flags(spec['lapack'].lapack_shared_lib),
+                to_link_flags(spec['blas'].blas_shared_lib)
+            )
+        ]
+
+        configure(*options)
+        with working_dir("src", create=False):
+            make("all-subdirs")
+            make("opium")
+
+        # opium not have a make install :-((
+        mkdirp(self.prefix.bin)
+        install(join_path(self.stage.source_path, 'opium'),
+                self.prefix.bin)
diff --git a/var/spack/repos/builtin/packages/osu-micro-benchmarks/package.py b/var/spack/repos/builtin/packages/osu-micro-benchmarks/package.py
index 2104bf842b..161ba6254a 100644
--- a/var/spack/repos/builtin/packages/osu-micro-benchmarks/package.py
+++ b/var/spack/repos/builtin/packages/osu-micro-benchmarks/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class OsuMicroBenchmarks(Package):
     """The Ohio MicroBenchmark suite is a collection of independent MPI
     message passing performance microbenchmarks developed and written at
@@ -41,7 +42,6 @@ class OsuMicroBenchmarks(Package):
     depends_on('mpi')
     depends_on('cuda', when='+cuda')
 
-
     def install(self, spec, prefix):
         config_args = [
             'CC=%s'  % spec['mpi'].prefix.bin + '/mpicc',
diff --git a/var/spack/repos/builtin/packages/otf/package.py b/var/spack/repos/builtin/packages/otf/package.py
index 4a7a00b212..39eb5a85aa 100644
--- a/var/spack/repos/builtin/packages/otf/package.py
+++ b/var/spack/repos/builtin/packages/otf/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Otf(Package):
     """To improve scalability for very large and massively parallel
        traces the Open Trace Format (OTF) is developed at ZIH as a
diff --git a/var/spack/repos/builtin/packages/otf2/package.py b/var/spack/repos/builtin/packages/otf2/package.py
index 131836f8ac..ee39f448eb 100644
--- a/var/spack/repos/builtin/packages/otf2/package.py
+++ b/var/spack/repos/builtin/packages/otf2/package.py
@@ -27,8 +27,8 @@ from spack import *
 
 
 class Otf2(Package):
-    """
-    The Open Trace Format 2 is a highly scalable, memory efficient event trace data format plus support library.
+    """The Open Trace Format 2 is a highly scalable, memory efficient event
+       trace data format plus support library.
     """
 
     homepage = "http://www.vi-hps.org/score-p"
@@ -46,10 +46,10 @@ class Otf2(Package):
             url="http://www.vi-hps.org/upload/packages/otf2/otf2-1.2.1.tar.gz")
 
     def install(self, spec, prefix):
-        configure_args=["--prefix=%s" % prefix,
-                        "--enable-shared",
-                        "CFLAGS=-fPIC",
-                        "CXXFLAGS=-fPIC"]
+        configure_args = ["--prefix=%s" % prefix,
+                          "--enable-shared",
+                          "CFLAGS=-fPIC",
+                          "CXXFLAGS=-fPIC"]
         configure(*configure_args)
         make()
         make("install")
diff --git a/var/spack/repos/builtin/packages/p4est/package.py b/var/spack/repos/builtin/packages/p4est/package.py
index 4bbf0c1311..114fd00011 100644
--- a/var/spack/repos/builtin/packages/p4est/package.py
+++ b/var/spack/repos/builtin/packages/p4est/package.py
@@ -24,46 +24,42 @@
 ##############################################################################
 from spack import *
 
+
 class P4est(Package):
-    """Dynamic management of a collection (a forest) of adaptive octrees in parallel"""
+    """Dynamic management of a collection (a forest) of adaptive octrees in
+    parallel"""
     homepage = "http://www.p4est.org"
     url      = "http://p4est.github.io/release/p4est-1.1.tar.gz"
 
     version('1.1', '37ba7f4410958cfb38a2140339dbf64f')
 
-    variant('tests', default=True, description='Run small tests')
-
     # build dependencies
     depends_on('automake', type='build')
     depends_on('autoconf', type='build')
     depends_on('libtool@2.4.2:', type='build')
 
     # other dependencies
-    depends_on('lua') # Needed for the submodule sc
+    depends_on('lua')  # Needed for the submodule sc
     depends_on('mpi')
     depends_on('zlib')
 
     def install(self, spec, prefix):
-        options = ['--enable-mpi',
-                   '--enable-shared',
-                   '--disable-vtk-binary',
-                   '--without-blas',
-                   'CPPFLAGS=-DSC_LOG_PRIORITY=SC_LP_ESSENTIAL',
-                   'CFLAGS=-O2',
-                   'CC=%s'  % self.spec['mpi'].mpicc,
-                   'CXX=%s' % self.spec['mpi'].mpicxx,
-                   'FC=%s'  % self.spec['mpi'].mpifc,
-                   'F77=%s' % self.spec['mpi'].mpif77
-                  ]
+        options = [
+            '--enable-mpi',
+            '--enable-shared',
+            '--disable-vtk-binary',
+            '--without-blas',
+            'CPPFLAGS=-DSC_LOG_PRIORITY=SC_LP_ESSENTIAL',
+            'CFLAGS=-O2',
+            'CC=%s'  % self.spec['mpi'].mpicc,
+            'CXX=%s' % self.spec['mpi'].mpicxx,
+            'FC=%s'  % self.spec['mpi'].mpifc,
+            'F77=%s' % self.spec['mpi'].mpif77
+        ]
 
         configure('--prefix=%s' % prefix, *options)
 
         make()
-        # Make tests optional as sometimes mpiexec can't be run with an error:
-        # mpiexec has detected an attempt to run as root.
-        # Running at root is *strongly* discouraged as any mistake (e.g., in
-        # defining TMPDIR) or bug can result in catastrophic damage to the OS
-        # file system, leaving your system in an unusable state.
-        if '+tests' in self.spec:
-          make("check")
+        if self.run_tests:
+            make("check")
         make("install")
diff --git a/var/spack/repos/builtin/packages/pango/package.py b/var/spack/repos/builtin/packages/pango/package.py
index a04f6d64e0..2da20e9dc2 100644
--- a/var/spack/repos/builtin/packages/pango/package.py
+++ b/var/spack/repos/builtin/packages/pango/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Pango(Package):
     """Pango is a library for laying out and rendering of text, with
        an emphasis on internationalization. It can be used anywhere
@@ -31,8 +32,11 @@ class Pango(Package):
        far has been done in the context of the GTK+ widget toolkit."""
     homepage = "http://www.pango.org"
     url      = "http://ftp.gnome.org/pub/gnome/sources/pango/1.36/pango-1.36.8.tar.xz"
+    list_url = "http://ftp.gnome.org/pub/gnome/sources/pango/"
+    list_depth = 2
 
     version('1.36.8', '217a9a753006275215fa9fa127760ece')
+    version('1.40.1', '6fc88c6529890d6c8e03074d57a3eceb')
 
     depends_on("harfbuzz")
     depends_on("cairo")
diff --git a/var/spack/repos/builtin/packages/papi/package.py b/var/spack/repos/builtin/packages/papi/package.py
index ecd958407f..5c4abe1730 100644
--- a/var/spack/repos/builtin/packages/papi/package.py
+++ b/var/spack/repos/builtin/packages/papi/package.py
@@ -28,6 +28,7 @@ import os
 import sys
 from llnl.util.filesystem import fix_darwin_install_name
 
+
 class Papi(Package):
     """PAPI provides the tool designer and application engineer with a
        consistent interface and methodology for use of the performance
@@ -47,7 +48,7 @@ class Papi(Package):
     def install(self, spec, prefix):
         with working_dir("src"):
 
-            configure_args=["--prefix=%s" % prefix]
+            configure_args = ["--prefix=%s" % prefix]
 
             # PAPI uses MPI if MPI is present; since we don't require
             # an MPI package, we ensure that all attempts to use MPI
diff --git a/var/spack/repos/builtin/packages/paradiseo/package.py b/var/spack/repos/builtin/packages/paradiseo/package.py
index 97d36d94a4..c91b01c964 100644
--- a/var/spack/repos/builtin/packages/paradiseo/package.py
+++ b/var/spack/repos/builtin/packages/paradiseo/package.py
@@ -23,40 +23,50 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
-import sys
+
 
 class Paradiseo(Package):
-    """A C++ white-box object-oriented framework dedicated to the reusable design of metaheuristics."""
+    """A C++ white-box object-oriented framework dedicated to the reusable
+       design of metaheuristics."""
     homepage = "http://paradiseo.gforge.inria.fr/"
 
-    # Installing from the development version is a better option at this 
+    # Installing from the development version is a better option at this
     # point than using the very old supplied packages
     version('head', git='https://gforge.inria.fr/git/paradiseo/paradiseo.git')
-    # This is a version that the package formula author has tested successfully.
-    # However, the clone is very large (~1Gb git history). The history in the 
-    # head version has been trimmed significantly.
-    version('dev-safe', git='https://gforge.inria.fr/git/paradiseo/paradiseo.git',
-             commit='dbb8fbe9a786efd4d1c26408ac1883442e7643a6')
 
-    variant('mpi',      default=True,  description='Compile with parallel and distributed metaheuristics module')
-    variant('smp',      default=True,  description='Compile with symmetric multi-processing module ')
-    variant('edo',      default=True,  description='Compile with (Experimental) EDO module')
-    #variant('tests',    default=False, description='Compile with build tests')
-    #variant('doc',      default=False, description='Compile with documentation')
-    variant('debug',    default=False, description='Builds a debug version of the libraries')
+    # This is a version that the package formula author has tested
+    # successfully.  However, the clone is very large (~1Gb git
+    # history). The history in the head version has been trimmed
+    # significantly.
+    version(
+        'dev-safe', git='https://gforge.inria.fr/git/paradiseo/paradiseo.git',
+        commit='dbb8fbe9a786efd4d1c26408ac1883442e7643a6')
+
+    variant('mpi',      default=True,
+            description='Compile with parallel and distributed '
+                        'metaheuristics module')
+    variant('smp',      default=True,
+            description='Compile with symmetric multi-processing module ')
+    variant('edo',      default=True,
+            description='Compile with (Experimental) EDO module')
+
+    # variant('tests', default=False, description='Compile with build tests')
+    # variant('doc', default=False, description='Compile with documentation')
+    variant('debug',    default=False,
+            description='Builds a debug version of the libraries')
     variant('openmp',   default=False, description='Enable OpenMP support')
     variant('gnuplot',  default=False, description='Enable GnuPlot support')
-    
+
     # Required dependencies
-    depends_on ("cmake", type='build')
+    depends_on("cmake", type='build')
 
     # Optional dependencies
-    depends_on ("mpi", when="+mpi")
-    depends_on ("doxygen", when='+doc', type='build')
-    depends_on ("gnuplot", when='+gnuplot')
-    depends_on ("eigen", when='+edo', type='build')
-    depends_on ("boost~mpi", when='+edo~mpi')
-    depends_on ("boost+mpi", when='+edo+mpi')
+    depends_on("mpi", when="+mpi")
+    depends_on("doxygen", when='+doc', type='build')
+    depends_on("gnuplot", when='+gnuplot')
+    depends_on("eigen", when='+edo', type='build')
+    depends_on("boost~mpi", when='+edo~mpi')
+    depends_on("boost+mpi", when='+edo+mpi')
 
     # Patches
     patch('enable_eoserial.patch')
@@ -69,16 +79,21 @@ class Paradiseo(Package):
         options.extend(std_cmake_args)
 
         options.extend([
-            '-DCMAKE_BUILD_TYPE:STRING=%s' % ('Debug' if '+debug' in spec else 'Release'),
+            '-DCMAKE_BUILD_TYPE:STRING=%s' % (
+                'Debug' if '+debug' in spec else 'Release'),
             '-DINSTALL_TYPE:STRING=MIN',
             '-DMPI:BOOL=%s' % ('TRUE' if '+mpi' in spec else 'FALSE'),
-            '-DSMP:BOOL=%s' % ('TRUE' if '+smp' in spec else 'FALSE'), # Note: This requires a C++11 compatible compiler
+            # Note: This requires a C++11 compatible compiler
+            '-DSMP:BOOL=%s' % ('TRUE' if '+smp' in spec else 'FALSE'),
             '-DEDO:BOOL=%s' % ('TRUE' if '+edo' in spec else 'FALSE'),
-            '-DENABLE_CMAKE_TESTING:BOOL=%s' % ('TRUE' if '+tests' in spec else 'FALSE'),
-            '-DENABLE_OPENMP:BOOL=%s' % ('TRUE' if '+openmp' in spec else 'FALSE'),
-            '-DENABLE_GNUPLOT:BOOL=%s' % ('TRUE' if '+gnuplot' in spec else 'FALSE')
+            '-DENABLE_CMAKE_TESTING:BOOL=%s' % (
+                'TRUE' if '+tests' in spec else 'FALSE'),
+            '-DENABLE_OPENMP:BOOL=%s' % (
+                'TRUE' if '+openmp' in spec else 'FALSE'),
+            '-DENABLE_GNUPLOT:BOOL=%s' % (
+                'TRUE' if '+gnuplot' in spec else 'FALSE')
         ])
- 
+
         with working_dir('spack-build', create=True):
             # Configure
             cmake('..', *options)
diff --git a/var/spack/repos/builtin/packages/parallel-netcdf/package.py b/var/spack/repos/builtin/packages/parallel-netcdf/package.py
index deee46df8f..be4a8bc38b 100644
--- a/var/spack/repos/builtin/packages/parallel-netcdf/package.py
+++ b/var/spack/repos/builtin/packages/parallel-netcdf/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class ParallelNetcdf(Package):
     """Parallel netCDF (PnetCDF) is a library providing high-performance
     parallel I/O while still maintaining file-format compatibility with
@@ -37,12 +38,14 @@ class ParallelNetcdf(Package):
 
     variant('cxx', default=True, description='Build the C++ Interface')
     variant('fortran', default=True, description='Build the Fortran Interface')
-    variant('fpic', default=True, description='Produce position-independent code (for use with shared libraries)')
+    variant('fpic', default=True,
+            description='Produce position-independent code (for shared libs)')
 
     depends_on("m4", type='build')
     depends_on("mpi")
 
-    # See: https://trac.mcs.anl.gov/projects/parallel-netcdf/browser/trunk/INSTALL
+    # See:
+    # https://trac.mcs.anl.gov/projects/parallel-netcdf/browser/trunk/INSTALL
     def install(self, spec, prefix):
         args = list()
         if '+fpic' in spec:
@@ -53,7 +56,7 @@ class ParallelNetcdf(Package):
             args.append('--disable-fortran')
 
         args.extend(["--prefix=%s" % prefix,
-                  "--with-mpi=%s" % spec['mpi'].prefix])
+                     "--with-mpi=%s" % spec['mpi'].prefix])
         configure(*args)
         make()
         make("install")
diff --git a/var/spack/repos/builtin/packages/parallel/package.py b/var/spack/repos/builtin/packages/parallel/package.py
new file mode 100644
index 0000000000..2306dace55
--- /dev/null
+++ b/var/spack/repos/builtin/packages/parallel/package.py
@@ -0,0 +1,45 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Parallel(Package):
+    """
+    GNU parallel is a shell tool for executing jobs in parallel using
+    one or more computers. A job can be a single command or a small
+    script that has to be run for each of the lines in the input.
+    """
+
+    homepage = "http://www.gnu.org/software/parallel/"
+    url      = "http://ftp.gnu.org/gnu/parallel/parallel-20160422.tar.bz2"
+
+    version('20160422', '24621f684130472694333709bd4454cb')
+    version('20160322', '4e81e0d36902ab4c4e969ee6f35e6e57')
+
+    def install(self, spec, prefix):
+        configure('--prefix=%s' % prefix)
+
+        make()
+        make("install")
diff --git a/var/spack/repos/builtin/packages/paraver/package.py b/var/spack/repos/builtin/packages/paraver/package.py
index 50ce6b79fb..1b6e3ce8e6 100644
--- a/var/spack/repos/builtin/packages/paraver/package.py
+++ b/var/spack/repos/builtin/packages/paraver/package.py
@@ -25,6 +25,7 @@
 from spack import *
 import os
 
+
 class Paraver(Package):
     """"A very powerful performance visualization and analysis tool
         based on traces that can be used to analyse any information that
@@ -36,7 +37,7 @@ class Paraver(Package):
     version('4.5.3', '625de9ec0d639acd18d1aaa644b38f72')
 
     depends_on("boost")
-    #depends_on("extrae")
+    # depends_on("extrae")
     depends_on("wx")
     depends_on("wxpropgrid")
 
@@ -47,8 +48,11 @@ class Paraver(Package):
         make("install")
 
         os.chdir("../paraver-kernel")
-		#"--with-extrae=%s" % spec['extrae'].prefix,
-        configure("--prefix=%s" % prefix, "--with-ptools-common-files=%s" % prefix, "--with-boost=%s" % spec['boost'].prefix, "--with-boost-serialization=boost_serialization")
+        # "--with-extrae=%s" % spec['extrae'].prefix,
+        configure("--prefix=%s" % prefix,
+                  "--with-ptools-common-files=%s" % prefix,
+                  "--with-boost=%s" % spec['boost'].prefix,
+                  "--with-boost-serialization=boost_serialization")
         make()
         make("install")
 
@@ -58,8 +62,11 @@ class Paraver(Package):
         make("install")
 
         os.chdir("../wxparaver")
-		#"--with-extrae=%s" % spec['extrae'].prefix,
-        configure("--prefix=%s" % prefix, "--with-paraver=%s" % prefix, "--with-boost=%s" % spec['boost'].prefix, "--with-boost-serialization=boost_serialization", "--with-wxdir=%s" % spec['wx'].prefix.bin)
+        # "--with-extrae=%s" % spec['extrae'].prefix,
+        configure("--prefix=%s" % prefix,
+                  "--with-paraver=%s" % prefix,
+                  "--with-boost=%s" % spec['boost'].prefix,
+                  "--with-boost-serialization=boost_serialization",
+                  "--with-wxdir=%s" % spec['wx'].prefix.bin)
         make()
         make("install")
-
diff --git a/var/spack/repos/builtin/packages/paraview/package.py b/var/spack/repos/builtin/packages/paraview/package.py
index 75f5272006..68c781734e 100644
--- a/var/spack/repos/builtin/packages/paraview/package.py
+++ b/var/spack/repos/builtin/packages/paraview/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Paraview(Package):
     homepage = 'http://www.paraview.org'
     url      = 'http://www.paraview.org/files/v5.0/ParaView-v'
@@ -52,23 +53,22 @@ class Paraview(Package):
     depends_on('cmake', type='build')
     depends_on('bzip2')
     depends_on('freetype')
-    #depends_on('hdf5+mpi', when='+mpi')
-    #depends_on('hdf5~mpi', when='~mpi')
+    # depends_on('hdf5+mpi', when='+mpi')
+    # depends_on('hdf5~mpi', when='~mpi')
     depends_on('jpeg')
     depends_on('libpng')
     depends_on('libtiff')
     depends_on('libxml2')
-    #depends_on('netcdf')
-    #depends_on('netcdf-cxx')
-    #depends_on('protobuf') # version mismatches?
-    #depends_on('sqlite') # external version not supported
+    # depends_on('netcdf')
+    # depends_on('netcdf-cxx')
+    # depends_on('protobuf') # version mismatches?
+    # depends_on('sqlite') # external version not supported
     depends_on('zlib')
 
     def url_for_version(self, version):
         """Handle ParaView version-based custom URLs."""
         return self._url_str % (version.up_to(2), version)
 
-
     def install(self, spec, prefix):
         with working_dir('spack-build', create=True):
             def feature_to_bool(feature, on='ON', off='OFF'):
@@ -80,34 +80,46 @@ class Paraview(Package):
                 return feature_to_bool(feature, on='OFF', off='ON')
 
             feature_args = std_cmake_args[:]
-            feature_args.append('-DPARAVIEW_BUILD_QT_GUI:BOOL=%s' % feature_to_bool('+qt'))
-            feature_args.append('-DPARAVIEW_ENABLE_PYTHON:BOOL=%s' % feature_to_bool('+python'))
+            feature_args.append(
+                '-DPARAVIEW_BUILD_QT_GUI:BOOL=%s' % feature_to_bool('+qt'))
+            feature_args.append('-DPARAVIEW_ENABLE_PYTHON:BOOL=%s' %
+                                feature_to_bool('+python'))
             if '+python' in spec:
-                feature_args.append('-DPYTHON_EXECUTABLE:FILEPATH=%s/bin/python' % spec['python'].prefix)
-            feature_args.append('-DPARAVIEW_USE_MPI:BOOL=%s' % feature_to_bool('+mpi'))
+                feature_args.append(
+                    '-DPYTHON_EXECUTABLE:FILEPATH=%s/bin/python'
+                    % spec['python'].prefix)
+            feature_args.append('-DPARAVIEW_USE_MPI:BOOL=%s' %
+                                feature_to_bool('+mpi'))
             if '+mpi' in spec:
-                feature_args.append('-DMPIEXEC:FILEPATH=%s/bin/mpiexec' % spec['mpi'].prefix)
-            feature_args.append('-DVTK_ENABLE_TCL_WRAPPING:BOOL=%s' % feature_to_bool('+tcl'))
-            feature_args.append('-DVTK_OPENGL_HAS_OSMESA:BOOL=%s' % feature_to_bool('+osmesa'))
-            feature_args.append('-DVTK_USE_X:BOOL=%s' % nfeature_to_bool('+osmesa'))
-            feature_args.append('-DVTK_RENDERING_BACKEND:STRING=%s' % feature_to_bool('+opengl2', 'OpenGL2', 'OpenGL'))
+                feature_args.append(
+                    '-DMPIEXEC:FILEPATH=%s/bin/mpiexec' % spec['mpi'].prefix)
+            feature_args.append(
+                '-DVTK_ENABLE_TCL_WRAPPING:BOOL=%s' % feature_to_bool('+tcl'))
+            feature_args.append('-DVTK_OPENGL_HAS_OSMESA:BOOL=%s' %
+                                feature_to_bool('+osmesa'))
+            feature_args.append('-DVTK_USE_X:BOOL=%s' %
+                                nfeature_to_bool('+osmesa'))
+            feature_args.append(
+                '-DVTK_RENDERING_BACKEND:STRING=%s' %
+                feature_to_bool('+opengl2', 'OpenGL2', 'OpenGL'))
 
             feature_args.extend(std_cmake_args)
 
             if 'darwin' in self.spec.architecture:
                 feature_args.append('-DVTK_USE_X:BOOL=OFF')
-                feature_args.append('-DPARAVIEW_DO_UNIX_STYLE_INSTALLS:BOOL=ON')
+                feature_args.append(
+                    '-DPARAVIEW_DO_UNIX_STYLE_INSTALLS:BOOL=ON')
 
             cmake('..',
-                '-DCMAKE_INSTALL_PREFIX:PATH=%s' % prefix,
-                '-DBUILD_TESTING:BOOL=OFF',
-                '-DVTK_USE_SYSTEM_FREETYPE:BOOL=ON',
-                '-DVTK_USE_SYSTEM_HDF5:BOOL=OFF',
-                '-DVTK_USE_SYSTEM_JPEG:BOOL=ON',
-                '-DVTK_USE_SYSTEM_LIBXML2:BOOL=ON',
-                '-DVTK_USE_SYSTEM_NETCDF:BOOL=OFF',
-                '-DVTK_USE_SYSTEM_TIFF:BOOL=ON',
-                '-DVTK_USE_SYSTEM_ZLIB:BOOL=ON',
-                *feature_args)
+                  '-DCMAKE_INSTALL_PREFIX:PATH=%s' % prefix,
+                  '-DBUILD_TESTING:BOOL=OFF',
+                  '-DVTK_USE_SYSTEM_FREETYPE:BOOL=ON',
+                  '-DVTK_USE_SYSTEM_HDF5:BOOL=OFF',
+                  '-DVTK_USE_SYSTEM_JPEG:BOOL=ON',
+                  '-DVTK_USE_SYSTEM_LIBXML2:BOOL=ON',
+                  '-DVTK_USE_SYSTEM_NETCDF:BOOL=OFF',
+                  '-DVTK_USE_SYSTEM_TIFF:BOOL=ON',
+                  '-DVTK_USE_SYSTEM_ZLIB:BOOL=ON',
+                  *feature_args)
             make()
             make('install')
diff --git a/var/spack/repos/builtin/packages/parmetis/package.py b/var/spack/repos/builtin/packages/parmetis/package.py
index b2ceadc128..2750df2bdb 100644
--- a/var/spack/repos/builtin/packages/parmetis/package.py
+++ b/var/spack/repos/builtin/packages/parmetis/package.py
@@ -38,8 +38,10 @@ class Parmetis(Package):
     version('4.0.3', 'f69c479586bf6bb7aff6a9bc0c739628')
     version('4.0.2', '0912a953da5bb9b5e5e10542298ffdce')
 
-    variant('shared', default=True, description='Enables the build of shared libraries')
-    variant('debug', default=False, description='Builds the library in debug mode')
+    variant('shared', default=True,
+            description='Enables the build of shared libraries')
+    variant('debug', default=False,
+            description='Builds the library in debug mode')
     variant('gdb', default=False, description='Enables gdb support')
 
     depends_on('cmake@2.8:', type='build')  # build dependency
@@ -48,9 +50,9 @@ class Parmetis(Package):
 
     patch('enable_external_metis.patch')
     # bug fixes from PETSc developers
-    # https://bitbucket.org/petsc/pkg-parmetis/commits/1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b/raw/  # NOQA: ignore=E501
+    # https://bitbucket.org/petsc/pkg-parmetis/commits/1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b/raw/
     patch('pkg-parmetis-1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b.patch')
-    # https://bitbucket.org/petsc/pkg-parmetis/commits/82409d68aa1d6cbc70740d0f35024aae17f7d5cb/raw/  # NOQA: ignore=E501
+    # https://bitbucket.org/petsc/pkg-parmetis/commits/82409d68aa1d6cbc70740d0f35024aae17f7d5cb/raw/
     patch('pkg-parmetis-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch')
 
     def url_for_version(self, version):
diff --git a/var/spack/repos/builtin/packages/parpack/package.py b/var/spack/repos/builtin/packages/parpack/package.py
index 5930dada85..84bc88b3b0 100644
--- a/var/spack/repos/builtin/packages/parpack/package.py
+++ b/var/spack/repos/builtin/packages/parpack/package.py
@@ -26,6 +26,7 @@ from spack import *
 import os
 import shutil
 
+
 class Parpack(Package):
     """ARPACK is a collection of Fortran77 subroutines designed to solve large
        scale eigenvalue problems."""
@@ -52,13 +53,13 @@ class Parpack(Package):
         mf.filter('^PLAT.*',      'PLAT = ')
         mf.filter('^home.*',      'home = %s' % os.getcwd())
         mf.filter('^BLASdir.*',   'BLASdir = %s' % self.spec['blas'].prefix)
-        mf.filter('^LAPACKdir.*', 'LAPACKdir = %s' % self.spec['lapack'].prefix)
+        mf.filter('^LAPACKdir.*', 'LAPACKdir = %s' %
+                  self.spec['lapack'].prefix)
         mf.filter('^MAKE.*',      'MAKE = make')
 
         # build the library in our own prefix.
         mf.filter('^ARPACKLIB.*', 'PARPACKLIB = %s/libparpack.a' % os.getcwd())
 
-
     def install(self, spec, prefix):
         with working_dir('PARPACK/SRC/MPI'):
             make('all')
diff --git a/var/spack/repos/builtin/packages/patchelf/package.py b/var/spack/repos/builtin/packages/patchelf/package.py
index 3860875bcc..cd1f679062 100644
--- a/var/spack/repos/builtin/packages/patchelf/package.py
+++ b/var/spack/repos/builtin/packages/patchelf/package.py
@@ -24,8 +24,10 @@
 ##############################################################################
 from spack import *
 
+
 class Patchelf(Package):
-    """PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables."""
+    """PatchELF is a small utility to modify the dynamic linker and RPATH of
+       ELF executables."""
 
     homepage = "https://nixos.org/patchelf.html"
     url      = "http://nixos.org/releases/patchelf/patchelf-0.8/patchelf-0.8.tar.gz"
diff --git a/var/spack/repos/builtin/packages/pcre/package.py b/var/spack/repos/builtin/packages/pcre/package.py
index a43729a1ac..6f306ab0f9 100644
--- a/var/spack/repos/builtin/packages/pcre/package.py
+++ b/var/spack/repos/builtin/packages/pcre/package.py
@@ -29,7 +29,6 @@ class Pcre(Package):
     """The PCRE package contains Perl Compatible Regular Expression
        libraries. These are useful for implementing regular expression
        pattern matching using the same syntax and semantics as Perl 5."""
-
     homepage = "http://www.pcre.org"""
     url      = "ftp://ftp.csx.cam.ac.uk/pub/software/programming/pcre/pcre-8.36.tar.bz2"
 
@@ -46,6 +45,7 @@ class Pcre(Package):
         configure_args = ['--prefix=%s' % prefix]
         if '+utf' in spec:
             configure_args.append('--enable-utf')
+            configure_args.append('--enable-unicode-properties')
 
         configure(*configure_args)
         make()
diff --git a/var/spack/repos/builtin/packages/pcre2/package.py b/var/spack/repos/builtin/packages/pcre2/package.py
index b013685f05..a2739e0584 100644
--- a/var/spack/repos/builtin/packages/pcre2/package.py
+++ b/var/spack/repos/builtin/packages/pcre2/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Pcre2(Package):
     """The PCRE2 package contains Perl Compatible Regular Expression
        libraries. These are useful for implementing regular expression
diff --git a/var/spack/repos/builtin/packages/pdt/package.py b/var/spack/repos/builtin/packages/pdt/package.py
index 60136fc0cd..074d28540b 100644
--- a/var/spack/repos/builtin/packages/pdt/package.py
+++ b/var/spack/repos/builtin/packages/pdt/package.py
@@ -27,17 +27,21 @@ from spack import *
 
 
 class Pdt(Package):
-    """
-    Program Database Toolkit (PDT) is a framework for analyzing source code written in several programming languages
-    and for making rich program knowledge accessible to developers of static and dynamic analysis tools. PDT implements
-    a standard program representation, the program database (PDB), that can be accessed in a uniform way through a
-    class library supporting common PDB operations.
+    """Program Database Toolkit (PDT) is a framework for analyzing source
+       code written in several programming languages and for making rich
+       program knowledge accessible to developers of static and dynamic
+       analysis tools. PDT implements a standard program representation,
+       the program database (PDB), that can be accessed in a uniform way
+       through a class library supporting common PDB operations.
+
     """
     homepage = "https://www.cs.uoregon.edu/research/pdt/home.php"
-    url      = "https://www.cs.uoregon.edu/research/tau/pdt_releases/pdt-3.21.tar.gz"
 
-    version('3.21', '8df94298b71703decf680709a4ddf68f')
-    version('3.19', 'ba5591994998771fdab216699e362228')
+    version('3.21', '3092ca0d8833b69992c17e63ae66c263')
+    version('3.19', '5c5e1e6607086aa13bf4b1b9befc5864')
+
+    def url_for_version(self, version):
+        return 'https://www.cs.uoregon.edu/research/tau/pdt_releases/pdtoolkit-%s.tar.gz' % (version)
 
     def install(self, spec, prefix):
         configure('-prefix=%s' % prefix)
diff --git a/var/spack/repos/builtin/packages/perl/package.py b/var/spack/repos/builtin/packages/perl/package.py
new file mode 100644
index 0000000000..d71a7492ba
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl/package.py
@@ -0,0 +1,75 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+#
+# Author: George Hartzell <hartzell@alerce.com>
+# Date: July 21, 2016
+# Author: Justin Too <justin@doubleotoo.com>
+# Date: September 6, 2015
+#
+from spack import *
+
+
+class Perl(Package):
+    """Perl 5 is a highly capable, feature-rich programming language with over
+       27 years of development."""
+    homepage = "http://www.perl.org"
+    url      = "http://www.cpan.org/src/5.0/perl-5.22.2.tar.gz"
+
+    version('5.24.0', 'c5bf7f3285439a2d3b6a488e14503701')
+    version('5.22.2', '5767e2a10dd62a46d7b57f74a90d952b')
+    version('5.20.3', 'd647d0ea5a7a8194c34759ab9f2610cd')
+    # 5.18.4 fails with gcc-5
+    # https://rt.perl.org/Public/Bug/Display.html?id=123784
+    # version('5.18.4' , '1f9334ff730adc05acd3dd7130d295db')
+
+    # Installing cpanm alongside the core makes it safe and simple for
+    # people/projects to install their own sets of perl modules.  Not
+    # having it in core increases the "energy of activation" for doing
+    # things cleanly.
+    variant('cpanm', default=True,
+            description='Optionally install cpanm with the core packages.')
+
+    resource(
+        name="cpanm",
+        url="http://search.cpan.org/CPAN/authors/id/M/MI/MIYAGAWA/App-cpanminus-1.7042.tar.gz",
+        md5="e87f55fbcb3c13a4754500c18e89219f",
+        destination="cpanm",
+        placement="cpanm"
+    )
+
+    def install(self, spec, prefix):
+        configure = Executable('./Configure')
+        configure("-des", "-Dprefix=" + prefix)
+        make()
+        if self.run_tests:
+            make("test")
+        make("install")
+
+        if '+cpanm' in spec:
+            with working_dir(join_path('cpanm', 'cpanm')):
+                perl = Executable(join_path(prefix.bin, 'perl'))
+                perl('Makefile.PL')
+                make()
+                make('install')
diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py
index 11f5c36c22..66e1abdf1a 100644
--- a/var/spack/repos/builtin/packages/petsc/package.py
+++ b/var/spack/repos/builtin/packages/petsc/package.py
@@ -44,18 +44,25 @@ class Petsc(Package):
     version('3.5.1', 'a557e029711ebf425544e117ffa44d8f')
     version('3.4.4', '7edbc68aa6d8d6a3295dd5f6c2f6979d')
 
-    variant('shared',  default=True,  description='Enables the build of shared libraries')
+    variant('shared',  default=True,
+            description='Enables the build of shared libraries')
     variant('mpi',     default=True,  description='Activates MPI support')
-    variant('double',  default=True,  description='Switches between single and double precision')
+    variant('double',  default=True,
+            description='Switches between single and double precision')
     variant('complex', default=False, description='Build with complex numbers')
     variant('debug',   default=False, description='Compile in debug mode')
 
-    variant('metis',   default=True,  description='Activates support for metis and parmetis')
-    variant('hdf5',    default=True,  description='Activates support for HDF5 (only parallel)')
+    variant('metis',   default=True,
+            description='Activates support for metis and parmetis')
+    variant('hdf5',    default=True,
+            description='Activates support for HDF5 (only parallel)')
     variant('boost',   default=True,  description='Activates support for Boost')
-    variant('hypre',   default=True,  description='Activates support for Hypre (only parallel)')
-    variant('mumps',   default=True,  description='Activates support for MUMPS (only parallel)')
-    variant('superlu-dist', default=True, description='Activates support for SuperluDist (only parallel)')
+    variant('hypre',   default=True,
+            description='Activates support for Hypre (only parallel)')
+    variant('mumps',   default=True,
+            description='Activates support for MUMPS (only parallel)')
+    variant('superlu-dist', default=True,
+            description='Activates support for SuperluDist (only parallel)')
 
     # Virtual dependencies
     depends_on('blas')
@@ -74,7 +81,7 @@ class Petsc(Package):
     # Hypre does not support complex numbers.
     # Also PETSc prefer to build it without internal superlu, likely due to
     # conflict in headers see
-    # https://bitbucket.org/petsc/petsc/src/90564b43f6b05485163c147b464b5d6d28cde3ef/config/BuildSystem/config/packages/hypre.py  # NOQA: ignore=E501
+    # https://bitbucket.org/petsc/petsc/src/90564b43f6b05485163c147b464b5d6d28cde3ef/config/BuildSystem/config/packages/hypre.py
     depends_on('hypre~internal-superlu', when='+hypre+mpi~complex')
     depends_on('superlu-dist@:4.3', when='@:3.6.4+superlu-dist+mpi')
     depends_on('superlu-dist@5.0.0:', when='@3.7:+superlu-dist+mpi')
@@ -85,17 +92,21 @@ class Petsc(Package):
         if '~mpi' in self.spec:
             compiler_opts = [
                 '--with-cc=%s' % os.environ['CC'],
-                '--with-cxx=%s' % (os.environ['CXX'] if self.compiler.cxx is not None else '0'),  # NOQA: ignore=E501
-                '--with-fc=%s' % (os.environ['FC'] if self.compiler.fc is not None else '0'),  # NOQA: ignore=E501
+                '--with-cxx=%s' % (os.environ['CXX']
+                                   if self.compiler.cxx is not None else '0'),
+                '--with-fc=%s' % (os.environ['FC']
+                                  if self.compiler.fc is not None else '0'),
                 '--with-mpi=0'
             ]
-            error_message_fmt = '\t{library} support requires "+mpi" to be activated'  # NOQA: ignore=E501
+            error_message_fmt = \
+                '\t{library} support requires "+mpi" to be activated'
 
             # If mpi is disabled (~mpi), it's an error to have any of these
             # enabled. This generates a list of any such errors.
-            errors = [error_message_fmt.format(library=x)
-                      for x in ('hdf5', 'hypre', 'parmetis', 'mumps', 'superlu-dist')  # NOQA: ignore=E501
-                      if ('+' + x) in self.spec]
+            errors = [
+                error_message_fmt.format(library=x)
+                for x in ('hdf5', 'hypre', 'parmetis', 'mumps', 'superlu-dist')
+                if ('+' + x) in self.spec]
             if errors:
                 errors = ['incompatible variants given'] + errors
                 raise RuntimeError('\n'.join(errors))
@@ -110,8 +121,10 @@ class Petsc(Package):
         options = ['--with-ssl=0']
         options.extend(self.mpi_dependent_options())
         options.extend([
-            '--with-precision=%s' % ('double' if '+double' in spec else 'single'),  # NOQA: ignore=E501
-            '--with-scalar-type=%s' % ('complex' if '+complex' in spec else 'real'),  # NOQA: ignore=E501
+            '--with-precision=%s' % (
+                'double' if '+double' in spec else 'single'),
+            '--with-scalar-type=%s' % (
+                'complex' if '+complex' in spec else 'real'),
             '--with-shared-libraries=%s' % ('1' if '+shared' in spec else '0'),
             '--with-debugging=%s' % ('1' if '+debug' in spec else '0'),
             '--with-blas-lapack-dir=%s' % spec['lapack'].prefix
@@ -120,11 +133,13 @@ class Petsc(Package):
         for library in ('metis', 'boost', 'hdf5', 'hypre', 'parmetis',
                         'mumps', 'scalapack'):
             options.append(
-                '--with-{library}={value}'.format(library=library, value=('1' if library in spec else '0'))  # NOQA: ignore=E501
+                '--with-{library}={value}'.format(
+                    library=library, value=('1' if library in spec else '0'))
             )
             if library in spec:
                 options.append(
-                    '--with-{library}-dir={path}'.format(library=library, path=spec[library].prefix)  # NOQA: ignore=E501
+                    '--with-{library}-dir={path}'.format(
+                        library=library, path=spec[library].prefix)
                 )
         # PETSc does not pick up SuperluDist from the dir as they look for
         # superlu_dist_4.1.a
@@ -158,13 +173,25 @@ class Petsc(Package):
                 run = Executable(join_path(spec['mpi'].prefix.bin, 'mpirun'))
                 run('ex50', '-da_grid_x', '4', '-da_grid_y', '4')
                 if 'superlu-dist' in spec:
-                    run('ex50', '-da_grid_x', '4', '-da_grid_y', '4', '-pc_type', 'lu', '-pc_factor_mat_solver_package', 'superlu_dist')  # NOQA: ignore=E501
+                    run('ex50',
+                        '-da_grid_x', '4',
+                        '-da_grid_y', '4',
+                        '-pc_type', 'lu',
+                        '-pc_factor_mat_solver_package', 'superlu_dist')
 
                 if 'mumps' in spec:
-                    run('ex50', '-da_grid_x', '4', '-da_grid_y', '4', '-pc_type', 'lu', '-pc_factor_mat_solver_package', 'mumps')  # NOQA: ignore=E501
+                    run('ex50',
+                        '-da_grid_x', '4',
+                        '-da_grid_y', '4',
+                        '-pc_type', 'lu',
+                        '-pc_factor_mat_solver_package', 'mumps')
 
                 if 'hypre' in spec:
-                    run('ex50', '-da_grid_x', '4', '-da_grid_y', '4', '-pc_type', 'hypre', '-pc_hypre_type', 'boomeramg')  # NOQA: ignore=E501
+                    run('ex50',
+                        '-da_grid_x', '4',
+                        '-da_grid_y', '4',
+                        '-pc_type', 'hypre',
+                        '-pc_hypre_type', 'boomeramg')
 
     def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
         # set up PETSC_DIR for everyone using PETSc package
diff --git a/var/spack/repos/builtin/packages/pgi/package.py b/var/spack/repos/builtin/packages/pgi/package.py
index 7170c65303..c58d563682 100644
--- a/var/spack/repos/builtin/packages/pgi/package.py
+++ b/var/spack/repos/builtin/packages/pgi/package.py
@@ -41,6 +41,7 @@ class Pgi(Package):
     homepage = "http://www.pgroup.com/"
     url = "file://%s/pgi-16.3.tar.gz" % os.getcwd()
 
+    version('16.5', 'a40e8852071b5d600cb42f31631b3de1')
     version('16.3', '618cb7ddbc57d4e4ed1f21a0ab25f427')
 
     variant('network', default=True,
diff --git a/var/spack/repos/builtin/packages/pidx/package.py b/var/spack/repos/builtin/packages/pidx/package.py
index e7b18ce7a8..e19bb9e470 100644
--- a/var/spack/repos/builtin/packages/pidx/package.py
+++ b/var/spack/repos/builtin/packages/pidx/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Pidx(Package):
     """PIDX Parallel I/O Library.
 
diff --git a/var/spack/repos/builtin/packages/pixman/package.py b/var/spack/repos/builtin/packages/pixman/package.py
index 34d8dfea0d..3d7e332a3f 100644
--- a/var/spack/repos/builtin/packages/pixman/package.py
+++ b/var/spack/repos/builtin/packages/pixman/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Pixman(Package):
     """The Pixman package contains a library that provides low-level
        pixel manipulation features such as image compositing and
diff --git a/var/spack/repos/builtin/packages/pkg-config/g_date_strftime.patch b/var/spack/repos/builtin/packages/pkg-config/g_date_strftime.patch
new file mode 100644
index 0000000000..9538f23875
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pkg-config/g_date_strftime.patch
@@ -0,0 +1,34 @@
+From 00148329967adb196138372771052a3f606a6ea3 Mon Sep 17 00:00:00 2001
+From: coypu <coypu@sdf.org>
+Date: Wed, 2 Mar 2016 19:43:10 +0200
+Subject: [PATCH 2/2] gdate: Suppress string format literal warning
+
+Newer versions of GCC emit an error here, but we know it's safe.
+https://bugzilla.gnome.org/761550
+---
+ glib/glib/gdate.c | 5 +++++
+ 1 file changed, 5 insertions(+)
+
+diff --git a/glib/glib/gdate.c b/glib/glib/gdate.c
+index 4aece02..92c34d2 100644
+--- a/glib/glib/gdate.c
++++ b/glib/glib/gdate.c
+@@ -2439,6 +2439,9 @@ win32_strftime_helper (const GDate     *d,
+  *
+  * Returns: number of characters written to the buffer, or 0 the buffer was too small
+  */
++#pragma GCC diagnostic push
++#pragma GCC diagnostic ignored "-Wformat-nonliteral"
++
+ gsize     
+ g_date_strftime (gchar       *s, 
+                  gsize        slen, 
+@@ -2549,3 +2552,5 @@ g_date_strftime (gchar       *s,
+   return retval;
+ #endif
+ }
++
++#pragma GCC diagnostic pop
+-- 
+2.7.1
+
diff --git a/var/spack/repos/builtin/packages/pkg-config/package.py b/var/spack/repos/builtin/packages/pkg-config/package.py
index ddbc151767..45e8e8b74e 100644
--- a/var/spack/repos/builtin/packages/pkg-config/package.py
+++ b/var/spack/repos/builtin/packages/pkg-config/package.py
@@ -24,23 +24,29 @@
 ##############################################################################
 from spack import *
 
+
 class PkgConfig(Package):
-    """pkg-config is a helper tool used when compiling applications and libraries"""
+    """pkg-config is a helper tool used when compiling applications
+    and libraries"""
+
     homepage = "http://www.freedesktop.org/wiki/Software/pkg-config/"
     url      = "http://pkgconfig.freedesktop.org/releases/pkg-config-0.28.tar.gz"
 
-    version('0.28', 'aa3c86e67551adc3ac865160e34a2a0d')
+    version('0.29.1', 'f739a28cae4e0ca291f82d1d41ef107d')
+    version('0.28',   'aa3c86e67551adc3ac865160e34a2a0d')
 
     parallel = False
 
+    # The following patch is needed for gcc-6.1
+    patch('g_date_strftime.patch')
+
     def install(self, spec, prefix):
-        configure("--prefix=%s" %prefix,
-                "--enable-shared",
-                "--with-internal-glib") # There's a bootstrapping problem here;
-                                        # glib uses pkg-config as well, so
-                                        # break the cycle by using the internal
-                                        # glib.
+        configure("--prefix={0}".format(prefix),
+                  "--enable-shared",
+                  # There's a bootstrapping problem here;
+                  # glib uses pkg-config as well, so break
+                  # the cycle by using the internal glib.
+                  "--with-internal-glib")
 
         make()
         make("install")
-
diff --git a/var/spack/repos/builtin/packages/plumed/package.py b/var/spack/repos/builtin/packages/plumed/package.py
new file mode 100644
index 0000000000..b670b4c2b8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/plumed/package.py
@@ -0,0 +1,112 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+import subprocess
+
+from spack import *
+
+
+class Plumed(Package):
+    """PLUMED is an open source library for free energy calculations in
+    molecular systems which works together with some of the most popular
+    molecular dynamics engines.
+
+    Free energy calculations can be performed as a function of many order
+    parameters with a particular focus on biological problems, using state
+    of the art methods such as metadynamics, umbrella sampling and
+    Jarzynski-equation based steered MD.
+
+    The software, written in C++, can be easily interfaced with both fortran
+    and C/C++ codes.
+    """
+    homepage = 'http://www.plumed.org/'
+    url = 'https://github.com/plumed/plumed2/archive/v2.2.3.tar.gz'
+
+    version('2.2.3', 'a6e3863e40aac07eb8cf739cbd14ecf8')
+
+    variant('shared', default=True, description='Builds shared libraries')
+    variant('mpi', default=True, description='Activates MPI support')
+    variant('gsl', default=True, description='Activates GSL support')
+
+    depends_on('zlib')
+    depends_on('blas')
+    depends_on('lapack')
+
+    depends_on('mpi', when='+mpi')
+    depends_on('gsl', when='+gsl')
+
+    # Dictionary mapping PLUMED versions to the patches it provides
+    # interactively
+    plumed_patches = {
+        '2.2.3': {
+            'amber-14': '1',
+            'gromacs-4.5.7': '2',
+            'gromacs-4.6.7': '3',
+            'gromacs-5.0.7': '4',
+            'gromacs-5.1.2': '5',
+            'lammps-6Apr13': '6',
+            'namd-2.8': '7',
+            'namd-2.9': '8',
+            'espresso-5.0.2': '9'
+        }
+    }
+
+    def apply_patch(self, other):
+        plumed = subprocess.Popen(
+            [join_path(self.spec.prefix.bin, 'plumed'), 'patch', '-p'],
+            stdin=subprocess.PIPE
+        )
+        opts = Plumed.plumed_patches[str(self.version)]
+        search = '{0.name}-{0.version}'.format(other)
+        choice = opts[search] + '\n'
+        plumed.stdin.write(choice)
+        plumed.wait()
+
+    def setup_dependent_package(self, module, ext_spec):
+        # Make plumed visible from dependent packages
+        module.plumed = Executable(join_path(self.spec.prefix.bin, 'plumed'))
+
+    def install(self, spec, prefix):
+        # From plumed docs :
+        # Also consider that this is different with respect to what some other
+        # configure script does in that variables such as MPICXX are
+        # completely ignored here. In case you work on a machine where CXX is
+        # set to a serial compiler and MPICXX to a MPI compiler, to compile
+        # with MPI you should use:
+        #
+        # > ./configure CXX="$MPICXX"
+        configure_opts = [
+            'CXX={0}'.format(spec['mpi'].mpicxx)
+        ] if '+mpi' in self.spec else []
+
+        configure_opts.extend([
+            '--prefix={0}'.format(prefix),
+            '--enable-shared={0}'.format('yes' if '+shared' in spec else 'no'),
+            '--enable-mpi={0}'.format('yes' if '+mpi' in spec else 'no'),
+            '--enable-gsl={0}'.format('yes' if '+gsl' in spec else 'no')
+        ])
+
+        configure(*configure_opts)
+        make()
+        make('install')
diff --git a/var/spack/repos/builtin/packages/pmgr_collective/package.py b/var/spack/repos/builtin/packages/pmgr_collective/package.py
index a6e3b8e2a2..f6466a7954 100644
--- a/var/spack/repos/builtin/packages/pmgr_collective/package.py
+++ b/var/spack/repos/builtin/packages/pmgr_collective/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class PmgrCollective(Package):
     """PMGR_COLLECTIVE provides a scalable network for bootstrapping
        MPI jobs."""
diff --git a/var/spack/repos/builtin/packages/ppl/package.py b/var/spack/repos/builtin/packages/ppl/package.py
index a54c6ce221..73404103f0 100644
--- a/var/spack/repos/builtin/packages/ppl/package.py
+++ b/var/spack/repos/builtin/packages/ppl/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Ppl(Package):
     """The Parma Polyhedra Library (PPL) provides numerical
     abstractions especially targeted at applications in the field of
diff --git a/var/spack/repos/builtin/packages/prank/package.py b/var/spack/repos/builtin/packages/prank/package.py
new file mode 100644
index 0000000000..d627e8a0b6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/prank/package.py
@@ -0,0 +1,44 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Prank(Package):
+    """A powerful multiple sequence alignment browser."""
+
+    homepage = "http://wasabiapp.org/software/prank/"
+    url      = "http://wasabiapp.org/download/prank/prank.source.140603.tgz"
+
+    version('150803', '71ac2659e91c385c96473712c0a23e8a')
+
+    depends_on('mafft')
+    depends_on('exonerate')
+    depends_on('bpp-suite')      # for bppancestor
+
+    def install(self, spec, prefix):
+        with working_dir('src'):
+            make()
+            mkdirp(prefix.bin)
+            install('prank', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/proj/package.py b/var/spack/repos/builtin/packages/proj/package.py
index 20dd4f5f69..06ab6108b6 100644
--- a/var/spack/repos/builtin/packages/proj/package.py
+++ b/var/spack/repos/builtin/packages/proj/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Proj(Package):
     """Cartographic Projections"""
     homepage = "https://github.com/OSGeo/proj.4/wiki"
diff --git a/var/spack/repos/builtin/packages/protobuf/package.py b/var/spack/repos/builtin/packages/protobuf/package.py
index d4befc34ab..bf0073b16a 100644
--- a/var/spack/repos/builtin/packages/protobuf/package.py
+++ b/var/spack/repos/builtin/packages/protobuf/package.py
@@ -22,9 +22,9 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import os
 from spack import *
 
+
 class Protobuf(Package):
     """Google's data interchange format."""
 
diff --git a/var/spack/repos/builtin/packages/psi4/package.py b/var/spack/repos/builtin/packages/psi4/package.py
index 192dd86e0e..6296d0cee6 100644
--- a/var/spack/repos/builtin/packages/psi4/package.py
+++ b/var/spack/repos/builtin/packages/psi4/package.py
@@ -39,7 +39,15 @@ class Psi4(Package):
     # Required dependencies
     depends_on('blas')
     depends_on('lapack')
-    depends_on('boost+chrono+filesystem+python+regex+serialization+system+timer+thread')
+    depends_on('boost'
+               '+chrono'
+               '+filesystem'
+               '+python'
+               '+regex'
+               '+serialization'
+               '+system'
+               '+timer'
+               '+thread')
     depends_on('python')
     depends_on('cmake', type='build')
     depends_on('py-numpy', type=nolink)
diff --git a/var/spack/repos/builtin/packages/py-SQLAlchemy/package.py b/var/spack/repos/builtin/packages/py-SQLAlchemy/package.py
index 05f4616ff5..ca59105b4c 100644
--- a/var/spack/repos/builtin/packages/py-SQLAlchemy/package.py
+++ b/var/spack/repos/builtin/packages/py-SQLAlchemy/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class PySqlalchemy(Package):
     """The Python SQL Toolkit and Object Relational Mapper"""
 
diff --git a/var/spack/repos/builtin/packages/py-argcomplete/package.py b/var/spack/repos/builtin/packages/py-argcomplete/package.py
index ace9320424..2549972a6d 100644
--- a/var/spack/repos/builtin/packages/py-argcomplete/package.py
+++ b/var/spack/repos/builtin/packages/py-argcomplete/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class PyArgcomplete(Package):
     """Bash tab completion for argparse."""
 
diff --git a/var/spack/repos/builtin/packages/py-astroid/package.py b/var/spack/repos/builtin/packages/py-astroid/package.py
index e1ea71fb67..a47b7ffa33 100644
--- a/var/spack/repos/builtin/packages/py-astroid/package.py
+++ b/var/spack/repos/builtin/packages/py-astroid/package.py
@@ -43,4 +43,3 @@ class PyAstroid(Package):
 
     def install(self, spec, prefix):
         python('setup.py', 'install', '--prefix=%s' % prefix)
-
diff --git a/var/spack/repos/builtin/packages/py-autopep8/package.py b/var/spack/repos/builtin/packages/py-autopep8/package.py
index 507664949b..f6c08e2728 100644
--- a/var/spack/repos/builtin/packages/py-autopep8/package.py
+++ b/var/spack/repos/builtin/packages/py-autopep8/package.py
@@ -1,5 +1,6 @@
 from spack import *
 
+
 class PyAutopep8(Package):
     """Automatic pep8 formatter"""
     homepage = "https://github.com/hhatto/autopep8"
@@ -13,4 +14,3 @@ class PyAutopep8(Package):
 
     def install(self, spec, prefix):
         python('setup.py', 'install', '--prefix=%s' % prefix)
-
diff --git a/var/spack/repos/builtin/packages/py-biopython/package.py b/var/spack/repos/builtin/packages/py-biopython/package.py
index bcc889756e..c3edf9735b 100644
--- a/var/spack/repos/builtin/packages/py-biopython/package.py
+++ b/var/spack/repos/builtin/packages/py-biopython/package.py
@@ -24,8 +24,13 @@
 ##############################################################################
 from spack import *
 
+
 class PyBiopython(Package):
-    """It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics."""
+    """A distributed collaborative effort to develop Python libraries and
+       applications which address the needs of current and future work in
+       bioinformatics.
+
+    """
     homepage = "http://biopython.org/wiki/Main_Page"
     url      = "http://biopython.org/DIST/biopython-1.65.tar.gz"
 
diff --git a/var/spack/repos/builtin/packages/py-blessings/package.py b/var/spack/repos/builtin/packages/py-blessings/package.py
index 8d7a2343d1..e6fc6aa983 100644
--- a/var/spack/repos/builtin/packages/py-blessings/package.py
+++ b/var/spack/repos/builtin/packages/py-blessings/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class PyBlessings(Package):
     """A nicer, kinder way to write to the terminal """
     homepage = "https://github.com/erikrose/blessings"
diff --git a/var/spack/repos/builtin/packages/py-bottleneck/package.py b/var/spack/repos/builtin/packages/py-bottleneck/package.py
index 2483fab85f..ad2ee749d3 100644
--- a/var/spack/repos/builtin/packages/py-bottleneck/package.py
+++ b/var/spack/repos/builtin/packages/py-bottleneck/package.py
@@ -24,8 +24,9 @@
 ##############################################################################
 from spack import *
 
+
 class PyBottleneck(Package):
-    """Bottleneck is a collection of fast NumPy array functions written in Cython."""
+    """A collection of fast NumPy array functions written in Cython."""
     homepage = "https://pypi.python.org/pypi/Bottleneck/1.0.0"
     url      = "https://pypi.python.org/packages/source/B/Bottleneck/Bottleneck-1.0.0.tar.gz"
 
diff --git a/var/spack/repos/builtin/packages/py-cffi/package.py b/var/spack/repos/builtin/packages/py-cffi/package.py
index e54d50fa50..3c1044783f 100644
--- a/var/spack/repos/builtin/packages/py-cffi/package.py
+++ b/var/spack/repos/builtin/packages/py-cffi/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class PyCffi(Package):
     """Foreign Function Interface for Python calling C code"""
     homepage = "http://cffi.readthedocs.org/en/latest/"
diff --git a/var/spack/repos/builtin/packages/py-coverage/package.py b/var/spack/repos/builtin/packages/py-coverage/package.py
index b7eaf58cd6..c2a698b0bd 100644
--- a/var/spack/repos/builtin/packages/py-coverage/package.py
+++ b/var/spack/repos/builtin/packages/py-coverage/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class PyCoverage(Package):
     """ Testing coverage checker for python """
     # FIXME: add a proper url for your package's homepage here.
diff --git a/var/spack/repos/builtin/packages/py-csvkit/package.py b/var/spack/repos/builtin/packages/py-csvkit/package.py
index 2deaa2f74e..5f50e3b6c2 100644
--- a/var/spack/repos/builtin/packages/py-csvkit/package.py
+++ b/var/spack/repos/builtin/packages/py-csvkit/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class PyCsvkit(Package):
     """A library of utilities for working with CSV, the king of tabular file
     formats"""
diff --git a/var/spack/repos/builtin/packages/py-cython/package.py b/var/spack/repos/builtin/packages/py-cython/package.py
index 5ccc508697..4b3e1cabe1 100644
--- a/var/spack/repos/builtin/packages/py-cython/package.py
+++ b/var/spack/repos/builtin/packages/py-cython/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class PyCython(Package):
     """The Cython compiler for writing C extensions for the Python language."""
     homepage = "https://pypi.python.org/pypi/cython"
diff --git a/var/spack/repos/builtin/packages/py-dask/package.py b/var/spack/repos/builtin/packages/py-dask/package.py
index b7dbab3d97..4bc2c6fc99 100644
--- a/var/spack/repos/builtin/packages/py-dask/package.py
+++ b/var/spack/repos/builtin/packages/py-dask/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class PyDask(Package):
     """Minimal task scheduling abstraction"""
     homepage = "https://github.com/dask/dask/"
diff --git a/var/spack/repos/builtin/packages/py-dateutil/package.py b/var/spack/repos/builtin/packages/py-dateutil/package.py
index dfd1e143d9..40945232c1 100644
--- a/var/spack/repos/builtin/packages/py-dateutil/package.py
+++ b/var/spack/repos/builtin/packages/py-dateutil/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class PyDateutil(Package):
     """Extensions to the standard Python datetime module."""
     homepage = "https://pypi.python.org/pypi/dateutil"
diff --git a/var/spack/repos/builtin/packages/py-dbf/package.py b/var/spack/repos/builtin/packages/py-dbf/package.py
index 09c93de428..7f83bce75e 100644
--- a/var/spack/repos/builtin/packages/py-dbf/package.py
+++ b/var/spack/repos/builtin/packages/py-dbf/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class PyDbf(Package):
     """Pure python package for reading/writing dBase, FoxPro, and Visual FoxPro
     .dbf files (including memos)"""
diff --git a/var/spack/repos/builtin/packages/py-decorator/package.py b/var/spack/repos/builtin/packages/py-decorator/package.py
index bd78f262f4..9101b07a0d 100644
--- a/var/spack/repos/builtin/packages/py-decorator/package.py
+++ b/var/spack/repos/builtin/packages/py-decorator/package.py
@@ -24,8 +24,11 @@
 ##############################################################################
 from spack import *
 
+
 class PyDecorator(Package):
-    """The aim of the decorator module it to simplify the usage of decorators for the average programmer, and to popularize decorators by showing various non-trivial examples."""
+    """The aim of the decorator module it to simplify the usage of decorators
+       for the average programmer, and to popularize decorators by showing
+       various non-trivial examples."""
     homepage = "https://github.com/micheles/decorator"
     url      = "https://pypi.python.org/packages/source/d/decorator/decorator-4.0.9.tar.gz"
 
diff --git a/var/spack/repos/builtin/packages/py-epydoc/package.py b/var/spack/repos/builtin/packages/py-epydoc/package.py
index b370075e02..9d4b93dad4 100644
--- a/var/spack/repos/builtin/packages/py-epydoc/package.py
+++ b/var/spack/repos/builtin/packages/py-epydoc/package.py
@@ -24,8 +24,10 @@
 ##############################################################################
 from spack import *
 
+
 class PyEpydoc(Package):
-    """Epydoc is a tool for generating API documentation documentation for Python modules, based on their docstrings."""
+    """Epydoc is a tool for generating API documentation documentation for
+       Python modules, based on their docstrings."""
     homepage = "https://pypi.python.org/pypi/epydoc"
     url      = "https://pypi.python.org/packages/source/e/epydoc/epydoc-3.0.1.tar.gz"
 
diff --git a/var/spack/repos/builtin/packages/py-funcsigs/package.py b/var/spack/repos/builtin/packages/py-funcsigs/package.py
index 11ba639b85..c3d37f6b98 100644
--- a/var/spack/repos/builtin/packages/py-funcsigs/package.py
+++ b/var/spack/repos/builtin/packages/py-funcsigs/package.py
@@ -23,7 +23,7 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
-import os
+
 
 class PyFuncsigs(Package):
     """Python function signatures from PEP362 for Python 2.6, 2.7 and 3.2."""
@@ -38,6 +38,3 @@ class PyFuncsigs(Package):
 
     def install(self, spec, prefix):
         python('setup.py', 'install', '--prefix=%s' % prefix)
-
-
-
diff --git a/var/spack/repos/builtin/packages/py-genders/package.py b/var/spack/repos/builtin/packages/py-genders/package.py
index 44f6cb1ef4..f919a7e6c2 100644
--- a/var/spack/repos/builtin/packages/py-genders/package.py
+++ b/var/spack/repos/builtin/packages/py-genders/package.py
@@ -24,16 +24,19 @@
 ##############################################################################
 from spack import *
 
+
 class PyGenders(Package):
-    """Genders is a static cluster configuration database used for cluster configuration management. It is used by a variety of tools and scripts for management of large clusters."""
+    """Genders is a static cluster configuration database used for cluster
+       configuration management. It is used by a variety of tools and scripts
+       for management of large clusters."""
     homepage = "https://github.com/chaos/genders"
     url      = "https://github.com/chaos/genders/releases/download/genders-1-22-1/genders-1.22.tar.gz"
 
-    version('1.22', '9ea59a024dcbddb85b0ed25ddca9bc8e', url='https://github.com/chaos/genders/releases/download/genders-1-22-1/genders-1.22.tar.gz')
+    version('1.22', '9ea59a024dcbddb85b0ed25ddca9bc8e',
+            url='https://github.com/chaos/genders/releases/download/genders-1-22-1/genders-1.22.tar.gz')
     extends('python')
 
     def install(self, spec, prefix):
-        configure("--prefix=%s" %prefix)
+        configure("--prefix=%s" % prefix)
         make(parallel=False)
         make("install")
-
diff --git a/var/spack/repos/builtin/packages/py-gnuplot/package.py b/var/spack/repos/builtin/packages/py-gnuplot/package.py
index b08b03d1f1..a448a66e51 100644
--- a/var/spack/repos/builtin/packages/py-gnuplot/package.py
+++ b/var/spack/repos/builtin/packages/py-gnuplot/package.py
@@ -24,8 +24,10 @@
 ##############################################################################
 from spack import *
 
+
 class PyGnuplot(Package):
-    """Gnuplot.py is a Python package that allows you to create graphs from within Python using the gnuplot plotting program."""
+    """Gnuplot.py is a Python package that allows you to create graphs from
+       within Python using the gnuplot plotting program."""
     homepage = "http://gnuplot-py.sourceforge.net/"
     url      = "http://downloads.sourceforge.net/project/gnuplot-py/Gnuplot-py/1.8/gnuplot-py-1.8.tar.gz"
 
diff --git a/var/spack/repos/builtin/packages/py-h5py/package.py b/var/spack/repos/builtin/packages/py-h5py/package.py
index f96cb9b4cd..90a67c51bd 100644
--- a/var/spack/repos/builtin/packages/py-h5py/package.py
+++ b/var/spack/repos/builtin/packages/py-h5py/package.py
@@ -43,6 +43,7 @@ class PyH5py(Package):
     # Build dependencies
     depends_on('py-cython@0.19:', type='build')
     depends_on('pkg-config', type='build')
+    depends_on('py-setuptools', type='build')
     depends_on('hdf5@1.8.4:')
     depends_on('hdf5+mpi', when='+mpi')
     depends_on('mpi', when='+mpi')
diff --git a/var/spack/repos/builtin/packages/py-ipython/package.py b/var/spack/repos/builtin/packages/py-ipython/package.py
index b583609953..ac3291e21e 100644
--- a/var/spack/repos/builtin/packages/py-ipython/package.py
+++ b/var/spack/repos/builtin/packages/py-ipython/package.py
@@ -24,8 +24,10 @@
 ##############################################################################
 from spack import *
 
+
 class PyIpython(Package):
-    """IPython provides a rich toolkit to help you make the most out of using Python interactively."""
+    """IPython provides a rich toolkit to help you make the most out of using
+       Python interactively."""
     homepage = "https://pypi.python.org/pypi/ipython"
     url      = "https://pypi.python.org/packages/source/i/ipython/ipython-2.3.1.tar.gz"
 
diff --git a/var/spack/repos/builtin/packages/py-jdcal/package.py b/var/spack/repos/builtin/packages/py-jdcal/package.py
index fd1d6b4419..32acf75131 100644
--- a/var/spack/repos/builtin/packages/py-jdcal/package.py
+++ b/var/spack/repos/builtin/packages/py-jdcal/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class PyJdcal(Package):
     """Julian dates from proleptic Gregorian and Julian calendars"""
 
diff --git a/var/spack/repos/builtin/packages/py-jinja2/package.py b/var/spack/repos/builtin/packages/py-jinja2/package.py
index 57f26e3b90..943edf521a 100644
--- a/var/spack/repos/builtin/packages/py-jinja2/package.py
+++ b/var/spack/repos/builtin/packages/py-jinja2/package.py
@@ -48,4 +48,3 @@ class PyJinja2(Package):
 
     def install(self, spec, prefix):
         python('setup.py', 'install', '--prefix=%s' % prefix)
-
diff --git a/var/spack/repos/builtin/packages/py-lockfile/package.py b/var/spack/repos/builtin/packages/py-lockfile/package.py
index 38cc81b895..b873625bdb 100644
--- a/var/spack/repos/builtin/packages/py-lockfile/package.py
+++ b/var/spack/repos/builtin/packages/py-lockfile/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class PyLockfile(Package):
     """The lockfile package exports a LockFile class which provides a
        simple API for locking files. Unlike the Windows msvcrt.locking
diff --git a/var/spack/repos/builtin/packages/py-logilab-common/package.py b/var/spack/repos/builtin/packages/py-logilab-common/package.py
index 6dab4a40e4..ac1b933e43 100644
--- a/var/spack/repos/builtin/packages/py-logilab-common/package.py
+++ b/var/spack/repos/builtin/packages/py-logilab-common/package.py
@@ -39,4 +39,3 @@ class PyLogilabCommon(Package):
 
     def install(self, spec, prefix):
         python('setup.py', 'install', '--prefix=%s' % prefix)
-
diff --git a/var/spack/repos/builtin/packages/py-mako/package.py b/var/spack/repos/builtin/packages/py-mako/package.py
index 56741ec11f..18a8dc0e68 100644
--- a/var/spack/repos/builtin/packages/py-mako/package.py
+++ b/var/spack/repos/builtin/packages/py-mako/package.py
@@ -24,12 +24,13 @@
 ##############################################################################
 from spack import *
 
+
 class PyMako(Package):
-    """A super-fast templating language that borrows the best 
-    ideas from the existing templating languages."""
+    """A super-fast templating language that borrows the best
+       ideas from the existing templating languages."""
 
     homepage = "https://pypi.python.org/pypi/mako"
-    url      = "https://pypi.python.org/packages/source/M/Mako/Mako-1.0.1.tar.gz"
+    url = "https://pypi.python.org/packages/source/M/Mako/Mako-1.0.1.tar.gz"
 
     version('1.0.1', '9f0aafd177b039ef67b90ea350497a54')
 
diff --git a/var/spack/repos/builtin/packages/py-markupsafe/package.py b/var/spack/repos/builtin/packages/py-markupsafe/package.py
index ee396de7be..0a039d1d47 100644
--- a/var/spack/repos/builtin/packages/py-markupsafe/package.py
+++ b/var/spack/repos/builtin/packages/py-markupsafe/package.py
@@ -48,4 +48,3 @@ class PyMarkupsafe(Package):
 
     def install(self, spec, prefix):
         python('setup.py', 'install', '--prefix=%s' % prefix)
-
diff --git a/var/spack/repos/builtin/packages/py-matplotlib/package.py b/var/spack/repos/builtin/packages/py-matplotlib/package.py
index b5eb8a53c4..c454a47ec3 100644
--- a/var/spack/repos/builtin/packages/py-matplotlib/package.py
+++ b/var/spack/repos/builtin/packages/py-matplotlib/package.py
@@ -25,6 +25,7 @@
 from spack import *
 import os
 
+
 class PyMatplotlib(Package):
     """Python plotting package."""
     homepage = "https://pypi.python.org/pypi/matplotlib"
@@ -65,12 +66,12 @@ class PyMatplotlib(Package):
         if str(self.version) in ['1.4.2', '1.4.3']:
             # hack to fix configuration file
             config_file = None
-            for p,d,f in os.walk(prefix.lib):
+            for p, d, f in os.walk(prefix.lib):
                 for file in f:
                     if file.find('matplotlibrc') != -1:
                         config_file = join_path(p, 'matplotlibrc')
                         print config_file
-            if config_file == None:
+            if config_file is None:
                 raise InstallError('could not find config file')
             filter_file(r'backend      : pyside',
                         'backend      : Qt4Agg',
diff --git a/var/spack/repos/builtin/packages/py-meep/package.py b/var/spack/repos/builtin/packages/py-meep/package.py
new file mode 100644
index 0000000000..269ac55c67
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-meep/package.py
@@ -0,0 +1,75 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class PyMeep(Package):
+    """Python-meep is a wrapper around libmeep. It allows the scripting of
+    Meep-simulations with Python"""
+
+    homepage = "https://launchpad.net/python-meep"
+    url      = "https://launchpad.net/python-meep/1.4/1.4/+download/python-meep-1.4.2.tar"
+
+    version('1.4.2', 'f8913542d18b0dda92ebc64f0a10ce56')
+
+    variant('mpi', default=True, description='Enable MPI support')
+
+    extends('python')
+    depends_on('py-numpy', type=nolink)
+    depends_on('py-scipy', type=nolink)
+    depends_on('py-matplotlib', type=nolink)
+
+    depends_on('mpi', when='+mpi')
+    depends_on('meep~mpi', when='~mpi')
+    depends_on('meep+mpi', when='+mpi')
+
+    # As of SWIG 3.0.3, Python-style comments are now treated as
+    # pre-processor directives. Use older SWIG. But not too old,
+    # or else it can't handle newer C++ compilers and flags.
+    depends_on('swig@1.3.39:3.0.2')
+
+    def install(self, spec, prefix):
+        setup = 'setup-mpi.py' if '+mpi' in spec else 'setup.py'
+
+        include_dirs = [
+            spec['meep'].prefix.include,
+            spec['py-numpy'].include
+        ]
+
+        library_dirs = [
+            spec['meep'].prefix.lib
+        ]
+
+        if '+mpi' in spec:
+            include_dirs.append(spec['mpi'].prefix.include)
+            library_dirs.append(spec['mpi'].prefix.lib)
+
+        include_flags = '-I{0}'.format(','.join(include_dirs))
+        library_flags = '-L{0}'.format(','.join(library_dirs))
+
+        python(setup, 'clean', '--all')
+        python(setup, 'build_ext', include_flags, library_flags)
+        python(setup, 'install', '--prefix={0}'.format(prefix))
+        python(setup, 'bdist', include_flags, library_flags)
diff --git a/var/spack/repos/builtin/packages/py-mock/package.py b/var/spack/repos/builtin/packages/py-mock/package.py
index f4c178de67..2c70535f19 100644
--- a/var/spack/repos/builtin/packages/py-mock/package.py
+++ b/var/spack/repos/builtin/packages/py-mock/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class PyMock(Package):
     """mock is a library for testing in Python. It allows you to replace parts
     of your system under test with mock objects and make assertions about how
diff --git a/var/spack/repos/builtin/packages/py-mpi4py/package.py b/var/spack/repos/builtin/packages/py-mpi4py/package.py
index a749e16779..1f0e52804e 100644
--- a/var/spack/repos/builtin/packages/py-mpi4py/package.py
+++ b/var/spack/repos/builtin/packages/py-mpi4py/package.py
@@ -24,8 +24,14 @@
 ##############################################################################
 from spack import *
 
+
 class PyMpi4py(Package):
-    """This package provides Python bindings for the Message Passing Interface (MPI) standard. It is implemented on top of the MPI-1/MPI-2 specification and exposes an API which grounds on the standard MPI-2 C++ bindings."""
+    """This package provides Python bindings for the Message Passing
+       Interface (MPI) standard. It is implemented on top of the
+       MPI-1/MPI-2 specification and exposes an API which grounds on the
+       standard MPI-2 C++ bindings.
+
+    """
     homepage = "https://pypi.python.org/pypi/mpi4py"
     url      = "https://pypi.python.org/packages/source/m/mpi4py/mpi4py-1.3.1.tar.gz"
 
diff --git a/var/spack/repos/builtin/packages/py-mpmath/package.py b/var/spack/repos/builtin/packages/py-mpmath/package.py
index 899ff053a9..e5bae34694 100644
--- a/var/spack/repos/builtin/packages/py-mpmath/package.py
+++ b/var/spack/repos/builtin/packages/py-mpmath/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class PyMpmath(Package):
     """A Python library for arbitrary-precision floating-point arithmetic."""
     homepage = "http://mpmath.org"
diff --git a/var/spack/repos/builtin/packages/py-mx/package.py b/var/spack/repos/builtin/packages/py-mx/package.py
index d0f9f7cadf..f5631916f6 100644
--- a/var/spack/repos/builtin/packages/py-mx/package.py
+++ b/var/spack/repos/builtin/packages/py-mx/package.py
@@ -24,8 +24,14 @@
 ##############################################################################
 from spack import *
 
+
 class PyMx(Package):
-    """The eGenix.com mx Base Distribution for Python is a collection of professional quality software tools which enhance Python's usability in many important areas such as fast text searching, date/time processing and high speed data types."""
+    """The eGenix.com mx Base Distribution for Python is a collection of
+       professional quality software tools which enhance Python's
+       usability in many important areas such as fast text searching,
+       date/time processing and high speed data types.
+
+    """
     homepage = "http://www.egenix.com/products/python/mxBase/"
     url      = "https://downloads.egenix.com/python/egenix-mx-base-3.2.8.tar.gz"
 
diff --git a/var/spack/repos/builtin/packages/py-mysqldb1/package.py b/var/spack/repos/builtin/packages/py-mysqldb1/package.py
index 46b44f34dd..693fda6dbb 100644
--- a/var/spack/repos/builtin/packages/py-mysqldb1/package.py
+++ b/var/spack/repos/builtin/packages/py-mysqldb1/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class PyMysqldb1(Package):
     """Legacy mysql bindings for python"""
     homepage = "https://github.com/farcepest/MySQLdb1"
@@ -36,4 +37,3 @@ class PyMysqldb1(Package):
 
     def install(self, spec, prefix):
         python('setup.py', 'install', '--prefix=%s' % prefix)
-
diff --git a/var/spack/repos/builtin/packages/py-netcdf/package.py b/var/spack/repos/builtin/packages/py-netcdf/package.py
index 9a354cb1c1..e4f67d75a6 100644
--- a/var/spack/repos/builtin/packages/py-netcdf/package.py
+++ b/var/spack/repos/builtin/packages/py-netcdf/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class PyNetcdf(Package):
     """Python interface to the netCDF Library."""
     homepage = "http://unidata.github.io/netcdf4-python"
diff --git a/var/spack/repos/builtin/packages/py-networkx/package.py b/var/spack/repos/builtin/packages/py-networkx/package.py
index d545717628..79ad420f8f 100644
--- a/var/spack/repos/builtin/packages/py-networkx/package.py
+++ b/var/spack/repos/builtin/packages/py-networkx/package.py
@@ -24,8 +24,10 @@
 ##############################################################################
 from spack import *
 
+
 class PyNetworkx(Package):
-    """NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks."""
+    """NetworkX is a Python package for the creation, manipulation, and study
+    of the structure, dynamics, and functions of complex networks."""
     homepage = "http://networkx.github.io/"
     url      = "https://pypi.python.org/packages/source/n/networkx/networkx-1.11.tar.gz"
 
@@ -34,6 +36,7 @@ class PyNetworkx(Package):
     extends('python')
 
     depends_on('py-decorator', type=nolink)
+    depends_on('py-setuptools', type='build')
 
     def install(self, spec, prefix):
         python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/repos/builtin/packages/py-nose/package.py b/var/spack/repos/builtin/packages/py-nose/package.py
index d15a1784d1..eb3dd77219 100644
--- a/var/spack/repos/builtin/packages/py-nose/package.py
+++ b/var/spack/repos/builtin/packages/py-nose/package.py
@@ -36,7 +36,7 @@ class PyNose(Package):
     version('1.3.6', '0ca546d81ca8309080fc80cb389e7a16')
     version('1.3.7', '4d3ad0ff07b61373d2cefc89c5d0b20b')
 
-    extends('python', ignore=r'bin/nosetests.*$')
+    extends('python')
     depends_on('py-setuptools', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/py-numexpr/package.py b/var/spack/repos/builtin/packages/py-numexpr/package.py
index fd8d7dc0c6..b3b2e1d47d 100644
--- a/var/spack/repos/builtin/packages/py-numexpr/package.py
+++ b/var/spack/repos/builtin/packages/py-numexpr/package.py
@@ -23,7 +23,7 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
-import re
+
 
 class PyNumexpr(Package):
     """Fast numerical expression evaluator for NumPy"""
diff --git a/var/spack/repos/builtin/packages/py-numpy/package.py b/var/spack/repos/builtin/packages/py-numpy/package.py
index 2febdac658..f800b5e834 100644
--- a/var/spack/repos/builtin/packages/py-numpy/package.py
+++ b/var/spack/repos/builtin/packages/py-numpy/package.py
@@ -23,6 +23,7 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
+import platform
 
 
 class PyNumpy(Package):
@@ -48,6 +49,18 @@ class PyNumpy(Package):
     depends_on('blas',   when='+blas')
     depends_on('lapack', when='+lapack')
 
+    def setup_dependent_package(self, module, dep_spec):
+        python_version = self.spec['python'].version.up_to(2)
+        arch = '{0}-{1}'.format(platform.system().lower(), platform.machine())
+
+        self.spec.include = join_path(
+            self.prefix.lib,
+            'python{0}'.format(python_version),
+            'site-packages',
+            'numpy-{0}-py{1}-{2}.egg'.format(
+                self.spec.version, python_version, arch),
+            'numpy/core/include')
+
     def install(self, spec, prefix):
         libraries    = []
         library_dirs = []
diff --git a/var/spack/repos/builtin/packages/py-openpyxl/package.py b/var/spack/repos/builtin/packages/py-openpyxl/package.py
index 624da58ff3..fa32cb879f 100644
--- a/var/spack/repos/builtin/packages/py-openpyxl/package.py
+++ b/var/spack/repos/builtin/packages/py-openpyxl/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class PyOpenpyxl(Package):
     """A Python library to read/write Excel 2007 xlsx/xlsm files"""
 
diff --git a/var/spack/repos/builtin/packages/py-pandas/package.py b/var/spack/repos/builtin/packages/py-pandas/package.py
index 8bd4227faf..37234ae652 100644
--- a/var/spack/repos/builtin/packages/py-pandas/package.py
+++ b/var/spack/repos/builtin/packages/py-pandas/package.py
@@ -23,10 +23,18 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
-import os
+
 
 class PyPandas(Package):
-    """pandas is a Python package providing fast, flexible, and expressive data structures designed to make working with relational or labeled data both easy and intuitive. It aims to be the fundamental high-level building block for doing practical, real world data analysis in Python. Additionally, it has the broader goal of becoming the most powerful and flexible open source data analysis / manipulation tool available in any language."""
+    """pandas is a Python package providing fast, flexible, and expressive
+       data structures designed to make working with relational or
+       labeled data both easy and intuitive. It aims to be the
+       fundamental high-level building block for doing practical, real
+       world data analysis in Python. Additionally, it has the broader
+       goal of becoming the most powerful and flexible open source data
+       analysis / manipulation tool available in any language.
+
+    """
     homepage = "http://pandas.pydata.org/"
     url      = "https://pypi.python.org/packages/source/p/pandas/pandas-0.16.0.tar.gz#md5=bfe311f05dc0c351f8955fbd1e296e73"
 
diff --git a/var/spack/repos/builtin/packages/py-pbr/package.py b/var/spack/repos/builtin/packages/py-pbr/package.py
index 8502b0b364..a0cfe0e5a5 100644
--- a/var/spack/repos/builtin/packages/py-pbr/package.py
+++ b/var/spack/repos/builtin/packages/py-pbr/package.py
@@ -23,10 +23,11 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
-import os
+
 
 class PyPbr(Package):
-    """PBR is a library that injects some useful and sensible default behaviors into your setuptools run."""
+    """PBR is a library that injects some useful and sensible default
+       behaviors into your setuptools run."""
     homepage = "https://pypi.python.org/pypi/pbr"
     url      = "https://pypi.python.org/packages/source/p/pbr/pbr-1.8.1.tar.gz"
 
@@ -38,5 +39,3 @@ class PyPbr(Package):
 
     def install(self, spec, prefix):
         python('setup.py', 'install', '--prefix=%s' % prefix)
-
-
diff --git a/var/spack/repos/builtin/packages/py-pep8/package.py b/var/spack/repos/builtin/packages/py-pep8/package.py
index ffcc2b318c..87d1da9ab0 100644
--- a/var/spack/repos/builtin/packages/py-pep8/package.py
+++ b/var/spack/repos/builtin/packages/py-pep8/package.py
@@ -1,5 +1,6 @@
 from spack import *
 
+
 class PyPep8(Package):
     """python pep8 format checker"""
     homepage = "https://github.com/PyCQA/pycodestyle"
@@ -12,4 +13,3 @@ class PyPep8(Package):
 
     def install(self, spec, prefix):
         python('setup.py', 'install', '--prefix=%s' % prefix)
-
diff --git a/var/spack/repos/builtin/packages/py-periodictable/package.py b/var/spack/repos/builtin/packages/py-periodictable/package.py
index 608f4e16c1..51d9cc2046 100644
--- a/var/spack/repos/builtin/packages/py-periodictable/package.py
+++ b/var/spack/repos/builtin/packages/py-periodictable/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class PyPeriodictable(Package):
     """nose extends the test loading and running features of unittest,
     making it easier to write, find and run tests."""
diff --git a/var/spack/repos/builtin/packages/py-pexpect/package.py b/var/spack/repos/builtin/packages/py-pexpect/package.py
index dd95af9643..8a99c0473b 100644
--- a/var/spack/repos/builtin/packages/py-pexpect/package.py
+++ b/var/spack/repos/builtin/packages/py-pexpect/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class PyPexpect(Package):
     """Pexpect allows easy control of interactive console applications."""
     homepage = "https://pypi.python.org/pypi/pexpect"
diff --git a/var/spack/repos/builtin/packages/py-phonopy/package.py b/var/spack/repos/builtin/packages/py-phonopy/package.py
index a3a4b7a9f7..d5b3313a98 100644
--- a/var/spack/repos/builtin/packages/py-phonopy/package.py
+++ b/var/spack/repos/builtin/packages/py-phonopy/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class PyPhonopy(Package):
     """Phonopy is an open source package for phonon
     calculations at harmonic and quasi-harmonic levels."""
diff --git a/var/spack/repos/builtin/packages/py-pillow/package.py b/var/spack/repos/builtin/packages/py-pillow/package.py
index 13a09f63cf..1d8b3faa6f 100644
--- a/var/spack/repos/builtin/packages/py-pillow/package.py
+++ b/var/spack/repos/builtin/packages/py-pillow/package.py
@@ -53,12 +53,15 @@ class PyPillow(Package):
     variant('tiff', default=False, description='Access to TIFF files')
     variant('freetype', default=False, description='Font related services')
     variant('lcms', default=False, description='Color management')
-    variant('jpeg2000', default=False, description='Provide JPEG 2000 functionality')
+    variant('jpeg2000', default=False,
+            description='Provide JPEG 2000 functionality')
 
     # Spack does not (yet) support these modes of building
     # variant('webp', default=False, description='Provide the WebP format')
-    # variant('webpmux', default=False, description='WebP metadata, relies on WebP support')  # NOQA: ignore=E501
-    # variant('imagequant', default=False, description='Provide improved color quantization') # NOQA: ignore=E501
+    # variant('webpmux', default=False,
+    #         description='WebP metadata, relies on WebP support')
+    # variant('imagequant', default=False,
+    #         description='Provide improved color quantization')
 
     # Required dependencies
     extends('python')
diff --git a/var/spack/repos/builtin/packages/py-pmw/package.py b/var/spack/repos/builtin/packages/py-pmw/package.py
index 062bfe9c03..e0a332a6bf 100644
--- a/var/spack/repos/builtin/packages/py-pmw/package.py
+++ b/var/spack/repos/builtin/packages/py-pmw/package.py
@@ -24,8 +24,10 @@
 ##############################################################################
 from spack import *
 
+
 class PyPmw(Package):
-    """Pmw is a toolkit for building high-level compound widgets, or megawidgets, constructed using other widgets as component parts."""
+    """Pmw is a toolkit for building high-level compound widgets, or
+       megawidgets, constructed using other widgets as component parts."""
     homepage = "https://pypi.python.org/pypi/Pmw"
     url      = "https://pypi.python.org/packages/source/P/Pmw/Pmw-2.0.0.tar.gz"
 
diff --git a/var/spack/repos/builtin/packages/py-py2neo/package.py b/var/spack/repos/builtin/packages/py-py2neo/package.py
index 02f37d8b78..a79c2e477b 100644
--- a/var/spack/repos/builtin/packages/py-py2neo/package.py
+++ b/var/spack/repos/builtin/packages/py-py2neo/package.py
@@ -43,4 +43,3 @@ class PyPy2neo(Package):
 
     def install(self, spec, prefix):
         python('setup.py', 'install', '--prefix=%s' % prefix)
-
diff --git a/var/spack/repos/builtin/packages/py-pychecker/package.py b/var/spack/repos/builtin/packages/py-pychecker/package.py
index 137c5f491c..e81c3dbc9b 100644
--- a/var/spack/repos/builtin/packages/py-pychecker/package.py
+++ b/var/spack/repos/builtin/packages/py-pychecker/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class PyPychecker(Package):
     """"""
     homepage = "http://pychecker.sourceforge.net/"
diff --git a/var/spack/repos/builtin/packages/py-pycparser/package.py b/var/spack/repos/builtin/packages/py-pycparser/package.py
index 9afba50077..ef1b772ffc 100644
--- a/var/spack/repos/builtin/packages/py-pycparser/package.py
+++ b/var/spack/repos/builtin/packages/py-pycparser/package.py
@@ -24,14 +24,14 @@
 ##############################################################################
 from spack import *
 
+
 class PyPycparser(Package):
-    """pycparser is a complete parser of the C language, written in pure python"""
+    """A complete parser of the C language, written in pure python."""
     homepage = "https://github.com/eliben/pycparser"
     url      = "https://pypi.python.org/packages/source/p/pycparser/pycparser-2.13.tar.gz"
 
     version('2.13', 'e4fe1a2d341b22e25da0d22f034ef32f')
 
-    
     extends('python')
     depends_on('py-setuptools', type='build')
 
diff --git a/var/spack/repos/builtin/packages/py-pyelftools/package.py b/var/spack/repos/builtin/packages/py-pyelftools/package.py
index 0c4a7a36cc..bf781daf83 100644
--- a/var/spack/repos/builtin/packages/py-pyelftools/package.py
+++ b/var/spack/repos/builtin/packages/py-pyelftools/package.py
@@ -24,8 +24,10 @@
 ##############################################################################
 from spack import *
 
+
 class PyPyelftools(Package):
-    """A pure-Python library for parsing and analyzing ELF files and DWARF debugging information"""
+    """A pure-Python library for parsing and analyzing ELF files and DWARF
+       debugging information"""
     homepage = "https://pypi.python.org/pypi/pyelftools"
     url      = "https://pypi.python.org/packages/source/p/pyelftools/pyelftools-0.23.tar.gz"
 
diff --git a/var/spack/repos/builtin/packages/py-pygments/package.py b/var/spack/repos/builtin/packages/py-pygments/package.py
index 0ca15dd10d..2d22bd9f03 100644
--- a/var/spack/repos/builtin/packages/py-pygments/package.py
+++ b/var/spack/repos/builtin/packages/py-pygments/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class PyPygments(Package):
     """Pygments is a syntax highlighting package written in Python."""
     homepage = "https://pypi.python.org/pypi/pygments"
diff --git a/var/spack/repos/builtin/packages/py-pylint/package.py b/var/spack/repos/builtin/packages/py-pylint/package.py
index 7107b2987f..c505d44530 100644
--- a/var/spack/repos/builtin/packages/py-pylint/package.py
+++ b/var/spack/repos/builtin/packages/py-pylint/package.py
@@ -23,7 +23,7 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
-import re
+
 
 class PyPylint(Package):
     """array processing for numbers, strings, records, and objects."""
diff --git a/var/spack/repos/builtin/packages/py-pypar/package.py b/var/spack/repos/builtin/packages/py-pypar/package.py
index f762789dea..6fef71304c 100644
--- a/var/spack/repos/builtin/packages/py-pypar/package.py
+++ b/var/spack/repos/builtin/packages/py-pypar/package.py
@@ -24,12 +24,16 @@
 ##############################################################################
 from spack import *
 
+
 class PyPypar(Package):
-    """Pypar is an efficient but easy-to-use module that allows programs written in Python to run in parallel on multiple processors and communicate using MPI."""
+    """Pypar is an efficient but easy-to-use module that allows programs
+       written in Python to run in parallel on multiple processors and
+       communicate using MPI."""
     homepage = "http://code.google.com/p/pypar/"
     url      = "https://pypar.googlecode.com/files/pypar-2.1.5_108.tgz"
 
-    version('2.1.5_108', '7a1f28327d2a3b679f9455c843d850b8', url='https://pypar.googlecode.com/files/pypar-2.1.5_108.tgz')
+    version('2.1.5_108', '7a1f28327d2a3b679f9455c843d850b8',
+            url='https://pypar.googlecode.com/files/pypar-2.1.5_108.tgz')
     extends('python')
     depends_on('mpi')
 
diff --git a/var/spack/repos/builtin/packages/py-pyparsing/package.py b/var/spack/repos/builtin/packages/py-pyparsing/package.py
index 0423aa3bdb..67d255b02d 100644
--- a/var/spack/repos/builtin/packages/py-pyparsing/package.py
+++ b/var/spack/repos/builtin/packages/py-pyparsing/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class PyPyparsing(Package):
     """A Python Parsing Module."""
     homepage = "https://pypi.python.org/pypi/pyparsing"
diff --git a/var/spack/repos/builtin/packages/py-pyqt/package.py b/var/spack/repos/builtin/packages/py-pyqt/package.py
index 05fb7aa22c..de68bfaa90 100644
--- a/var/spack/repos/builtin/packages/py-pyqt/package.py
+++ b/var/spack/repos/builtin/packages/py-pyqt/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class PyPyqt(Package):
     """PyQt is a set of Python v2 and v3 bindings for Digia's Qt
        application framework and runs on all platforms supported by Qt
diff --git a/var/spack/repos/builtin/packages/py-pyside/package.py b/var/spack/repos/builtin/packages/py-pyside/package.py
index cd174ce658..1cb3e4745f 100644
--- a/var/spack/repos/builtin/packages/py-pyside/package.py
+++ b/var/spack/repos/builtin/packages/py-pyside/package.py
@@ -25,6 +25,7 @@
 from spack import *
 import os
 
+
 class PyPyside(Package):
     """Python bindings for Qt."""
     homepage = "https://pypi.python.org/pypi/pyside"
@@ -43,7 +44,8 @@ class PyPyside(Package):
         # Figure out the special RPATH
         pypkg = self.spec['python'].package
         rpath = self.rpath
-        rpath.append(os.path.join(self.prefix, pypkg.site_packages_dir, 'PySide'))
+        rpath.append(os.path.join(
+            self.prefix, pypkg.site_packages_dir, 'PySide'))
 
         # Add Spack's standard CMake args to the sub-builds.
         # They're called BY setup.py so we have to patch it.
@@ -61,7 +63,6 @@ class PyPyside(Package):
             r'#rpath_cmd(pyside_path, srcpath)',
             'pyside_postinstall.py')
 
-
     def install(self, spec, prefix):
         python('setup.py', 'install',
                '--prefix=%s' % prefix,
diff --git a/var/spack/repos/builtin/packages/py-pytables/package.py b/var/spack/repos/builtin/packages/py-pytables/package.py
index 58ed067b21..f87e74211f 100644
--- a/var/spack/repos/builtin/packages/py-pytables/package.py
+++ b/var/spack/repos/builtin/packages/py-pytables/package.py
@@ -23,10 +23,11 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
-import re
+
 
 class PyPytables(Package):
-    """PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope with extremely large amounts of data."""
+    """PyTables is a package for managing hierarchical datasets and designed to
+    efficiently and easily cope with extremely large amounts of data."""
     homepage = "http://www.pytables.org/"
     url      = "https://github.com/PyTables/PyTables/archive/v.3.2.2.tar.gz"
 
@@ -37,6 +38,7 @@ class PyPytables(Package):
     depends_on('py-numpy', type=nolink)
     depends_on('py-numexpr', type=nolink)
     depends_on('py-cython', type=nolink)
+    depends_on('py-setuptools', type='build')
 
     def install(self, spec, prefix):
         env["HDF5_DIR"] = spec['hdf5'].prefix
diff --git a/var/spack/repos/builtin/packages/py-python-daemon/package.py b/var/spack/repos/builtin/packages/py-python-daemon/package.py
index c2c7c4de4f..a30dc00ba4 100644
--- a/var/spack/repos/builtin/packages/py-python-daemon/package.py
+++ b/var/spack/repos/builtin/packages/py-python-daemon/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class PyPythonDaemon(Package):
     """Library to implement a well-behaved Unix daemon process.
 
@@ -47,4 +48,3 @@ class PyPythonDaemon(Package):
 
     def install(self, spec, prefix):
         python('setup.py', 'install', '--prefix=%s' % prefix)
-
diff --git a/var/spack/repos/builtin/packages/py-pytz/package.py b/var/spack/repos/builtin/packages/py-pytz/package.py
index caf2c90e73..96f686d591 100644
--- a/var/spack/repos/builtin/packages/py-pytz/package.py
+++ b/var/spack/repos/builtin/packages/py-pytz/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class PyPytz(Package):
     """World timezone definitions, modern and historical."""
     homepage = "https://pypi.python.org/pypi/pytz"
diff --git a/var/spack/repos/builtin/packages/py-pyyaml/package.py b/var/spack/repos/builtin/packages/py-pyyaml/package.py
index c0e22ba681..8da391fac1 100644
--- a/var/spack/repos/builtin/packages/py-pyyaml/package.py
+++ b/var/spack/repos/builtin/packages/py-pyyaml/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class PyPyyaml(Package):
     """PyYAML is a YAML parser and emitter for Python."""
     homepage = "http://pyyaml.org/wiki/PyYAML"
diff --git a/var/spack/repos/builtin/packages/py-rpy2/package.py b/var/spack/repos/builtin/packages/py-rpy2/package.py
index 8f4771f0eb..f86d813766 100644
--- a/var/spack/repos/builtin/packages/py-rpy2/package.py
+++ b/var/spack/repos/builtin/packages/py-rpy2/package.py
@@ -24,10 +24,16 @@
 ##############################################################################
 from spack import *
 
+
 class PyRpy2(Package):
-    """rpy2 is a redesign and rewrite of rpy. It is providing a low-level interface to R from Python, a proposed high-level interface, including wrappers to graphical libraries, as well as R-like structures and functions."""
+    """rpy2 is a redesign and rewrite of rpy. It is providing a low-level
+       interface to R from Python, a proposed high-level interface,
+       including wrappers to graphical libraries, as well as R-like
+       structures and functions.
+
+    """
     homepage = "https://pypi.python.org/pypi/rpy2"
-    url      = "https://pypi.python.org/packages/source/r/rpy2/rpy2-2.5.4.tar.gz"
+    url = "https://pypi.python.org/packages/source/r/rpy2/rpy2-2.5.4.tar.gz"
 
     version('2.5.4', '115a20ac30883f096da2bdfcab55196d')
     version('2.5.6', 'a36e758b633ce6aec6a5f450bfee980f')
diff --git a/var/spack/repos/builtin/packages/py-scientificpython/package.py b/var/spack/repos/builtin/packages/py-scientificpython/package.py
index 7f7eb76b73..e2273dc164 100644
--- a/var/spack/repos/builtin/packages/py-scientificpython/package.py
+++ b/var/spack/repos/builtin/packages/py-scientificpython/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class PyScientificpython(Package):
     """ScientificPython is a collection of Python modules for
        scientific computing. It contains support for geometry,
diff --git a/var/spack/repos/builtin/packages/py-scikit-image/package.py b/var/spack/repos/builtin/packages/py-scikit-image/package.py
index 26c286e4be..fbeb5c95ca 100644
--- a/var/spack/repos/builtin/packages/py-scikit-image/package.py
+++ b/var/spack/repos/builtin/packages/py-scikit-image/package.py
@@ -42,6 +42,7 @@ class PyScikitImage(Package):
     depends_on('py-six', type=nolink)
     depends_on('py-scipy', type=nolink)
     depends_on('py-matplotlib', type=nolink)
+    depends_on('py-setuptools', type='build')
 
     def install(self, spec, prefix):
         python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/repos/builtin/packages/py-scikit-learn/package.py b/var/spack/repos/builtin/packages/py-scikit-learn/package.py
index 1a6112bcf3..3cd7ea74f3 100644
--- a/var/spack/repos/builtin/packages/py-scikit-learn/package.py
+++ b/var/spack/repos/builtin/packages/py-scikit-learn/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class PyScikitLearn(Package):
     """"""
     homepage = "https://pypi.python.org/pypi/scikit-learn"
diff --git a/var/spack/repos/builtin/packages/py-scipy/package.py b/var/spack/repos/builtin/packages/py-scipy/package.py
index ea3731cf1b..cab516e1df 100644
--- a/var/spack/repos/builtin/packages/py-scipy/package.py
+++ b/var/spack/repos/builtin/packages/py-scipy/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class PyScipy(Package):
     """Scientific Library for Python."""
     homepage = "http://www.scipy.org/"
@@ -41,7 +42,8 @@ class PyScipy(Package):
         if 'atlas' in spec:
             # libatlas.so actually isn't always installed, but this
             # seems to make the build autodetect things correctly.
-            env['ATLAS'] = join_path(spec['atlas'].prefix.lib, 'libatlas.' + dso_suffix)
+            env['ATLAS'] = join_path(
+                spec['atlas'].prefix.lib, 'libatlas.' + dso_suffix)
         else:
             env['BLAS']   = spec['blas'].blas_shared_lib
             env['LAPACK'] = spec['lapack'].lapack_shared_lib
diff --git a/var/spack/repos/builtin/packages/py-setuptools/package.py b/var/spack/repos/builtin/packages/py-setuptools/package.py
index 68032cb68d..08d5e5d552 100644
--- a/var/spack/repos/builtin/packages/py-setuptools/package.py
+++ b/var/spack/repos/builtin/packages/py-setuptools/package.py
@@ -24,8 +24,11 @@
 ##############################################################################
 from spack import *
 
+
 class PySetuptools(Package):
-    """Easily download, build, install, upgrade, and uninstall Python packages."""
+    """A Python utility that aids in the process of downloading, building,
+       upgrading, installing, and uninstalling Python packages."""
+
     homepage = "https://pypi.python.org/pypi/setuptools"
     url      = "https://pypi.python.org/packages/source/s/setuptools/setuptools-11.3.tar.gz"
 
@@ -40,4 +43,4 @@ class PySetuptools(Package):
     extends('python')
 
     def install(self, spec, prefix):
-        python('setup.py', 'install', '--prefix=%s' % prefix)
+        setup_py('install', '--prefix=%s' % prefix)
diff --git a/var/spack/repos/builtin/packages/py-shiboken/package.py b/var/spack/repos/builtin/packages/py-shiboken/package.py
index 27188e1417..0713f26ebc 100644
--- a/var/spack/repos/builtin/packages/py-shiboken/package.py
+++ b/var/spack/repos/builtin/packages/py-shiboken/package.py
@@ -25,8 +25,9 @@
 from spack import *
 import os
 
+
 class PyShiboken(Package):
-    """Shiboken generates bindings for C++ libraries using CPython source code."""
+    """Shiboken generates bindings for C++ libraries using CPython."""
     homepage = "https://shiboken.readthedocs.org/"
     url      = "https://pypi.python.org/packages/source/S/Shiboken/Shiboken-1.2.2.tar.gz"
 
@@ -45,7 +46,8 @@ class PyShiboken(Package):
         # They're called BY setup.py so we have to patch it.
         pypkg = self.spec['python'].package
         rpath = self.rpath
-        rpath.append(os.path.join(self.prefix, pypkg.site_packages_dir, 'Shiboken'))
+        rpath.append(os.path.join(
+            self.prefix, pypkg.site_packages_dir, 'Shiboken'))
 
         filter_file(
             r'OPTION_CMAKE,',
@@ -61,7 +63,6 @@ class PyShiboken(Package):
             r'#rpath_cmd(shiboken_path, srcpath)',
             'shiboken_postinstall.py')
 
-
     def install(self, spec, prefix):
         python('setup.py', 'install',
                '--prefix=%s' % prefix,
diff --git a/var/spack/repos/builtin/packages/py-sip/package.py b/var/spack/repos/builtin/packages/py-sip/package.py
index fc8e7f5296..9d97f08433 100644
--- a/var/spack/repos/builtin/packages/py-sip/package.py
+++ b/var/spack/repos/builtin/packages/py-sip/package.py
@@ -25,8 +25,10 @@
 from spack import *
 import os
 
+
 class PySip(Package):
-    """SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries."""
+    """SIP is a tool that makes it very easy to create Python bindings for C
+       and C++ libraries."""
     homepage = "http://www.riverbankcomputing.com/software/sip/intro"
     url      = "http://sourceforge.net/projects/pyqt/files/sip/sip-4.16.5/sip-4.16.5.tar.gz"
 
diff --git a/var/spack/repos/builtin/packages/py-six/package.py b/var/spack/repos/builtin/packages/py-six/package.py
index eb4846d5af..da0c7aa003 100644
--- a/var/spack/repos/builtin/packages/py-six/package.py
+++ b/var/spack/repos/builtin/packages/py-six/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class PySix(Package):
     """Python 2 and 3 compatibility utilities."""
     homepage = "https://pypi.python.org/pypi/six"
diff --git a/var/spack/repos/builtin/packages/py-sphinx/package.py b/var/spack/repos/builtin/packages/py-sphinx/package.py
index d00f1d128b..2295a6a0c3 100644
--- a/var/spack/repos/builtin/packages/py-sphinx/package.py
+++ b/var/spack/repos/builtin/packages/py-sphinx/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class PySphinx(Package):
     """Sphinx Documentation Generator."""
     homepage = "http://sphinx-doc.org"
diff --git a/var/spack/repos/builtin/packages/py-sympy/package.py b/var/spack/repos/builtin/packages/py-sympy/package.py
index 5e38fc5be1..3d8b86ac4d 100644
--- a/var/spack/repos/builtin/packages/py-sympy/package.py
+++ b/var/spack/repos/builtin/packages/py-sympy/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class PySympy(Package):
     """SymPy is a Python library for symbolic mathematics."""
     homepage = "https://pypi.python.org/pypi/sympy"
diff --git a/var/spack/repos/builtin/packages/py-tappy/package.py b/var/spack/repos/builtin/packages/py-tappy/package.py
index b10244acdd..03e9528ad7 100644
--- a/var/spack/repos/builtin/packages/py-tappy/package.py
+++ b/var/spack/repos/builtin/packages/py-tappy/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class PyTappy(Package):
     """Python TAP interface module for unit tests"""
     homepage = "https://github.com/mblayman/tappy"
diff --git a/var/spack/repos/builtin/packages/py-tuiview/package.py b/var/spack/repos/builtin/packages/py-tuiview/package.py
index 56056ebad1..672a3ee587 100644
--- a/var/spack/repos/builtin/packages/py-tuiview/package.py
+++ b/var/spack/repos/builtin/packages/py-tuiview/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class PyTuiview(Package):
     """
        TuiView is a lightweight raster GIS with powerful raster attribute
diff --git a/var/spack/repos/builtin/packages/py-twisted/package.py b/var/spack/repos/builtin/packages/py-twisted/package.py
index 2ce83cd24c..edf1e7b0d7 100644
--- a/var/spack/repos/builtin/packages/py-twisted/package.py
+++ b/var/spack/repos/builtin/packages/py-twisted/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class PyTwisted(Package):
     """An asynchronous networking framework written in Python"""
     homepage = "https://twistedmatrix.com/"
diff --git a/var/spack/repos/builtin/packages/py-urwid/package.py b/var/spack/repos/builtin/packages/py-urwid/package.py
index 48ba84e7bc..943fb250f6 100644
--- a/var/spack/repos/builtin/packages/py-urwid/package.py
+++ b/var/spack/repos/builtin/packages/py-urwid/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class PyUrwid(Package):
     """A full-featured console UI library"""
     homepage = "http://urwid.org/"
@@ -37,4 +38,3 @@ class PyUrwid(Package):
 
     def install(self, spec, prefix):
         python('setup.py', 'install', '--prefix=%s' % prefix)
-
diff --git a/var/spack/repos/builtin/packages/py-virtualenv/package.py b/var/spack/repos/builtin/packages/py-virtualenv/package.py
index d6b33ae175..0ed567df95 100644
--- a/var/spack/repos/builtin/packages/py-virtualenv/package.py
+++ b/var/spack/repos/builtin/packages/py-virtualenv/package.py
@@ -23,7 +23,7 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
-import shutil
+
 
 class PyVirtualenv(Package):
     """virtualenv is a tool to create isolated Python environments."""
diff --git a/var/spack/repos/builtin/packages/py-wheel/package.py b/var/spack/repos/builtin/packages/py-wheel/package.py
index 9e383a9a19..f0ad340835 100644
--- a/var/spack/repos/builtin/packages/py-wheel/package.py
+++ b/var/spack/repos/builtin/packages/py-wheel/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class PyWheel(Package):
     """A built-package format for Python."""
 
diff --git a/var/spack/repos/builtin/packages/py-xlrd/package.py b/var/spack/repos/builtin/packages/py-xlrd/package.py
index 9220f90340..81c3c928c0 100644
--- a/var/spack/repos/builtin/packages/py-xlrd/package.py
+++ b/var/spack/repos/builtin/packages/py-xlrd/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class PyXlrd(Package):
     """Library for developers to extract data from Microsoft Excel (tm)
     spreadsheet files"""
diff --git a/var/spack/repos/builtin/packages/py-yapf/package.py b/var/spack/repos/builtin/packages/py-yapf/package.py
index f7fe4037a1..bc26b82b07 100644
--- a/var/spack/repos/builtin/packages/py-yapf/package.py
+++ b/var/spack/repos/builtin/packages/py-yapf/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class PyYapf(Package):
     """ Yet Another Python Formatter """
     homepage = "https://github.com/google/yapf"
diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py
index bbb1e9c13a..c4e6754969 100644
--- a/var/spack/repos/builtin/packages/python/package.py
+++ b/var/spack/repos/builtin/packages/python/package.py
@@ -27,6 +27,7 @@ import re
 from contextlib import closing
 
 import spack
+import llnl.util.tty as tty
 from llnl.util.lang import match_predicate
 from spack import *
 from spack.util.environment import *
@@ -54,7 +55,8 @@ class Python(Package):
     extendable = True
 
     variant('tk',   default=False, description='Provide support for Tkinter')
-    variant('ucs4', default=False, description='Enable UCS4 (wide) unicode strings')
+    variant('ucs4', default=False,
+            description='Enable UCS4 (wide) unicode strings')
     # From https://docs.python.org/2/c-api/unicode.html: Python's default
     # builds use a 16-bit type for Py_UNICODE and store Unicode values
     # internally as UCS2. It is also possible to build a UCS4 version of Python
@@ -72,40 +74,41 @@ class Python(Package):
     depends_on("tk",  when="+tk")
     depends_on("tcl", when="+tk")
 
+    @when('@2.7,3.4:')
+    def patch(self):
+        # NOTE: Python's default installation procedure makes it possible for a
+        # user's local configurations to change the Spack installation.  In
+        # order to prevent this behavior for a full installation, we must
+        # modify the installation script so that it ignores user files.
+        ff = FileFilter('Makefile.pre.in')
+        ff.filter(
+            r'^(.*)setup\.py(.*)((build)|(install))(.*)$',
+            r'\1setup.py\2 --no-user-cfg \3\6'
+        )
+
     def install(self, spec, prefix):
+        # TODO: The '--no-user-cfg' option for Python installation is only in
+        # Python v2.7 and v3.4+ (see https://bugs.python.org/issue1180) and
+        # adding support for ignoring user configuration will require
+        # significant changes to this package for other Python versions.
+        if not spec.satisfies('@2.7,3.4:'):
+            tty.warn(('Python v{0} may not install properly if Python '
+                      'user configurations are present.').format(self.version))
+
         # Need this to allow python build to find the Python installation.
-        env['PYTHONHOME'] = prefix
+        env['PYTHONHOME'], env['PYTHONPATH'] = prefix, prefix
         env['MACOSX_DEPLOYMENT_TARGET'] = '10.6'
 
         # Rest of install is pretty standard except setup.py needs to
         # be able to read the CPPFLAGS and LDFLAGS as it scans for the
         # library and headers to build
-        include_dirs = [
-            spec['openssl'].prefix.include,  spec['bzip2'].prefix.include,
-            spec['readline'].prefix.include, spec['ncurses'].prefix.include,
-            spec['sqlite'].prefix.include,   spec['zlib'].prefix.include
-        ]
-
-        library_dirs = [
-            spec['openssl'].prefix.lib,  spec['bzip2'].prefix.lib,
-            spec['readline'].prefix.lib, spec['ncurses'].prefix.lib,
-            spec['sqlite'].prefix.lib,   spec['zlib'].prefix.lib
-        ]
-
-        if '+tk' in spec:
-            include_dirs.extend([
-                spec['tk'].prefix.include, spec['tcl'].prefix.include
-            ])
-            library_dirs.extend([
-                spec['tk'].prefix.lib, spec['tcl'].prefix.lib
-            ])
-
+        dep_pfxs = [dspec.prefix for dspec in spec.dependencies('link')]
         config_args = [
-            "--prefix={0}".format(prefix),
-            "--with-threads",
-            "--enable-shared",
-            "CPPFLAGS=-I{0}".format(" -I".join(include_dirs)),
-            "LDFLAGS=-L{0}".format(" -L".join(library_dirs))
+            '--prefix={0}'.format(prefix),
+            '--with-threads',
+            '--enable-shared',
+            'CPPFLAGS=-I{0}'.format(' -I'.join(dp.include for dp in dep_pfxs)),
+            'LDFLAGS=-L{0}'.format(' -L'.join(dp.lib for dp in dep_pfxs)),
         ]
 
         if '+ucs4' in spec:
@@ -115,15 +118,15 @@ class Python(Package):
                 config_args.append('--with-wide-unicode')
             elif spec.satisfies('@3.3:'):
                 # https://docs.python.org/3.3/whatsnew/3.3.html
-                raise ValueError('+ucs4 variant not compatible with Python 3.3 and beyond')  # NOQA: ignore=E501
+                raise ValueError(
+                    '+ucs4 variant not compatible with Python 3.3 and beyond')
 
         if spec.satisfies('@3:'):
             config_args.append('--without-ensurepip')
 
         configure(*config_args)
-
         make()
-        make("install")
+        make('install')
 
         self.filter_compilers(spec, prefix)
 
@@ -193,6 +196,8 @@ class Python(Package):
     def setup_dependent_environment(self, spack_env, run_env, extension_spec):
         """Set PYTHONPATH to include site-packages dir for the
         extension and any other python extensions it depends on."""
+        pythonhome = self.prefix
+        spack_env.set('PYTHONHOME', pythonhome)
 
         python_paths = []
         for d in extension_spec.traverse(deptype=nolink, deptype_query='run'):
@@ -214,15 +219,14 @@ class Python(Package):
 
         In most cases, extensions will only need to have one line::
 
-        python('setup.py', 'install', '--prefix={0}'.format(prefix))"""
+        setup_py('install', '--prefix={0}'.format(prefix))"""
+        python_path = join_path(
+            self.spec.prefix.bin,
+            'python{0}'.format('3' if self.spec.satisfies('@3') else '')
+        )
 
-        # Python extension builds can have a global python executable function
-        if Version("3.0.0") <= self.version < Version("4.0.0"):
-            module.python = Executable(join_path(self.spec.prefix.bin,
-                                                 'python3'))
-        else:
-            module.python = Executable(join_path(self.spec.prefix.bin,
-                                                 'python'))
+        module.python = Executable(python_path)
+        module.setup_py = Executable(python_path + ' setup.py --no-user-cfg')
 
         # Add variables for lib/pythonX.Y and lib/pythonX.Y/site-packages dirs.
         module.python_lib_dir     = join_path(ext_spec.prefix,
diff --git a/var/spack/repos/builtin/packages/qhull/package.py b/var/spack/repos/builtin/packages/qhull/package.py
index 3b0b22ae1f..eec517cb75 100644
--- a/var/spack/repos/builtin/packages/qhull/package.py
+++ b/var/spack/repos/builtin/packages/qhull/package.py
@@ -45,7 +45,7 @@ class Qhull(CMakePackage):
 
     # https://github.com/qhull/qhull/pull/5
     patch('qhull-iterator.patch', when='@1.0')
-    
+
     depends_on('cmake', type='build')
 
     @CMakePackage.sanity_check('build')
diff --git a/var/spack/repos/builtin/packages/qrupdate/package.py b/var/spack/repos/builtin/packages/qrupdate/package.py
index 314950dc36..f6b4c80cf4 100644
--- a/var/spack/repos/builtin/packages/qrupdate/package.py
+++ b/var/spack/repos/builtin/packages/qrupdate/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Qrupdate(Package):
     """qrupdate is a Fortran library for fast updates of QR and
     Cholesky decompositions."""
diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py
index f33e5c2d0e..e496a3e4d5 100644
--- a/var/spack/repos/builtin/packages/qt/package.py
+++ b/var/spack/repos/builtin/packages/qt/package.py
@@ -25,6 +25,7 @@
 from spack import *
 import os
 
+
 class Qt(Package):
     """Qt is a comprehensive cross-platform C++ application framework."""
     homepage = 'http://qt.io'
@@ -37,15 +38,17 @@ class Qt(Package):
     version('4.8.6',  '2edbe4d6c2eff33ef91732602f3518eb')
     version('3.3.8b', '9f05b4125cfe477cc52c9742c3c09009')
 
-    # Add patch for compile issues with qt3 found with use in the OpenSpeedShop project
-    variant('krellpatch', default=False, description="Build with openspeedshop based patch.")
+    # Add patch for compile issues with qt3 found with use in the
+    # OpenSpeedShop project
+    variant('krellpatch', default=False,
+            description="Build with openspeedshop based patch.")
     variant('mesa',       default=False, description="Depend on mesa.")
     variant('gtk',        default=False, description="Build with gtkplus.")
 
     patch('qt3krell.patch', when='@3.3.8b+krellpatch')
 
     # Use system openssl for security.
-    #depends_on("openssl")
+    # depends_on("openssl")
 
     depends_on("glib")
     depends_on("gtkplus", when='+gtk')
@@ -69,43 +72,39 @@ class Qt(Package):
     depends_on("mesa", when='@4:+mesa')
     depends_on("libxcb")
 
-
     def url_for_version(self, version):
         url = "http://download.qt.io/archive/qt/"
 
         if version >= Version('5'):
             url += "%s/%s/single/qt-everywhere-opensource-src-%s.tar.gz" % \
-                    (version.up_to(2), version, version)
+                (version.up_to(2), version, version)
         elif version >= Version('4.8'):
             url += "%s/%s/qt-everywhere-opensource-src-%s.tar.gz" % \
-                    (version.up_to(2), version, version)
+                (version.up_to(2), version, version)
         elif version >= Version('4.6'):
             url += "%s/qt-everywhere-opensource-src-%s.tar.gz" % \
-                    (version.up_to(2), version)
+                (version.up_to(2), version)
         elif version >= Version('4.0'):
             url += "%s/qt-x11-opensource-src-%s.tar.gz" % \
-                    (version.up_to(2), version)
+                (version.up_to(2), version)
         elif version >= Version('3'):
             url += "%s/qt-x11-free-%s.tar.gz" % \
-                    (version.up_to(1), version)
+                (version.up_to(1), version)
         elif version >= Version('2.1'):
             url += "%s/qt-x11-%s.tar.gz" % \
-                    (version.up_to(1), version)
+                (version.up_to(1), version)
         else:
             url += "%s/qt-%s.tar.gz" % \
-                    (version.up_to(1), version)
+                (version.up_to(1), version)
 
         return url
 
-
     def setup_environment(self, spack_env, env):
         env.set('QTDIR', self.prefix)
 
-
     def setup_dependent_environment(self, spack_env, run_env, dspec):
         spack_env.set('QTDIR', self.prefix)
 
-
     def patch(self):
         if self.spec.satisfies('@4'):
             qmake_conf      = 'mkspecs/common/g++-base.conf'
@@ -117,11 +116,14 @@ class Qt(Package):
             return
 
         # Fix qmake compilers in the default mkspec
-        filter_file(r'^QMAKE_COMPILER *=.*$',  'QMAKE_COMPILER = cc', qmake_conf)
-        filter_file(r'^QMAKE_CC *=.*$',        'QMAKE_CC = cc',       qmake_conf)
-        filter_file(r'^QMAKE_CXX *=.*$',       'QMAKE_CXX = c++',     qmake_conf)
-        filter_file(r'^QMAKE_LFLAGS_NOUNDEF *\+?=.*$',  'QMAKE_LFLAGS_NOUNDEF =', qmake_unix_conf)
-
+        filter_file(r'^QMAKE_COMPILER *=.*$',
+                    'QMAKE_COMPILER = cc', qmake_conf)
+        filter_file(r'^QMAKE_CC *=.*$',
+                    'QMAKE_CC = cc',       qmake_conf)
+        filter_file(r'^QMAKE_CXX *=.*$',
+                    'QMAKE_CXX = c++',     qmake_conf)
+        filter_file(r'^QMAKE_LFLAGS_NOUNDEF *\+?=.*$',
+                    'QMAKE_LFLAGS_NOUNDEF =', qmake_unix_conf)
 
     @property
     def common_config_args(self):
@@ -155,7 +157,7 @@ class Qt(Package):
     @when('@3')
     def configure(self):
         # An user report that this was necessary to link Qt3 on ubuntu
-        os.environ['LD_LIBRARY_PATH'] = os.getcwd()+'/lib' 
+        os.environ['LD_LIBRARY_PATH'] = os.getcwd() + '/lib'
         configure('-prefix', self.prefix,
                   '-v',
                   '-thread',
@@ -169,17 +171,16 @@ class Qt(Package):
                   '-no-webkit',
                   *self.common_config_args)
 
-
     @when('@5')
     def configure(self):
         configure('-no-eglfs',
                   '-no-directfb',
                   '-qt-xcb',
-                  # If someone wants to get a webkit build working, be my guest!
+                  # If someone wants to get a webkit build working, be my
+                  # guest!
                   '-skip', 'qtwebkit',
                   *self.common_config_args)
 
-
     def install(self, spec, prefix):
         self.configure()
         make()
diff --git a/var/spack/repos/builtin/packages/qthreads/package.py b/var/spack/repos/builtin/packages/qthreads/package.py
index 47b5706063..2eaff0a240 100644
--- a/var/spack/repos/builtin/packages/qthreads/package.py
+++ b/var/spack/repos/builtin/packages/qthreads/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Qthreads(Package):
     """The qthreads API is designed to make using large numbers of
        threads convenient and easy, and to allow portable access to
diff --git a/var/spack/repos/builtin/packages/r-base64enc/package.py b/var/spack/repos/builtin/packages/r-base64enc/package.py
new file mode 100644
index 0000000000..4c5d14a90f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-base64enc/package.py
@@ -0,0 +1,42 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RBase64enc(Package):
+    """This package provides tools for handling base64 encoding. It is more
+    flexible than the orphaned base64 package."""
+
+    homepage = "http://www.rforge.net/base64enc"
+    url      = "https://cran.r-project.org/src/contrib/base64enc_0.1-3.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/base64enc"
+
+    version('0.1-3', '0f476dacdd11a3e0ad56d13f5bc2f190')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-boot/package.py b/var/spack/repos/builtin/packages/r-boot/package.py
new file mode 100644
index 0000000000..1f2f541fec
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-boot/package.py
@@ -0,0 +1,43 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RBoot(Package):
+    """Functions and datasets for bootstrapping from the book "Bootstrap
+    Methods and Their Application" by A. C. Davison and D. V. Hinkley (1997,
+    CUP), originally written by Angelo Canty for S."""
+
+    homepage = "https://cran.r-project.org/package=boot"
+    url      = "https://cran.r-project.org/src/contrib/boot_1.3-18.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/boot"
+
+    version('1.3-18', '711dd58af14e1027eb8377d9202e9b6f')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-brew/package.py b/var/spack/repos/builtin/packages/r-brew/package.py
new file mode 100644
index 0000000000..111606d576
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-brew/package.py
@@ -0,0 +1,43 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RBrew(Package):
+    """brew implements a templating framework for mixing text and R code for
+    report generation. brew template syntax is similar to PHP, Ruby's erb
+    module, Java Server Pages, and Python's psp module."""
+
+    homepage = "https://cran.r-project.org/package=brew"
+    url      = "https://cran.r-project.org/src/contrib/brew_1.0-6.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/brew"
+
+    version('1.0-6', '4aaca5e6ec145e0fc0fe6375ce1f3806')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-car/package.py b/var/spack/repos/builtin/packages/r-car/package.py
new file mode 100644
index 0000000000..f4a3824983
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-car/package.py
@@ -0,0 +1,48 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RCar(Package):
+    """Functions and Datasets to Accompany J. Fox and S. Weisberg, An R
+    Companion to Applied Regression, Second Edition, Sage, 2011."""
+
+    homepage = "https://r-forge.r-project.org/projects/car/"
+    url      = "https://cran.r-project.org/src/contrib/car_2.1-2.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/car"
+
+    version('2.1-2', '0f78ad74ef7130126d319acec23951a0')
+
+    extends('R')
+
+    depends_on('r-mass', type=nolink)
+    depends_on('r-mgcv', type=nolink)
+    depends_on('r-nnet', type=nolink)
+    depends_on('r-pbkrtest', type=nolink)
+    depends_on('r-quantreg', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-caret/package.py b/var/spack/repos/builtin/packages/r-caret/package.py
new file mode 100644
index 0000000000..460526c7d3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-caret/package.py
@@ -0,0 +1,50 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RCaret(Package):
+    """Misc functions for training and plotting classification and regression
+    models."""
+
+    homepage = "https://github.com/topepo/caret/"
+    url      = "https://cran.r-project.org/src/contrib/caret_6.0-70.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/caret"
+
+    version('6.0-70', '202d7abb6a679af716ea69fb2573f108')
+
+    extends('R')
+
+    depends_on('r-lattice', type=nolink)
+    depends_on('r-ggplot2', type=nolink)
+    depends_on('r-car', type=nolink)
+    depends_on('r-foreach', type=nolink)
+    depends_on('r-plyr', type=nolink)
+    depends_on('r-nlme', type=nolink)
+    depends_on('r-reshape2', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-chron/package.py b/var/spack/repos/builtin/packages/r-chron/package.py
new file mode 100644
index 0000000000..9cd9d76e9e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-chron/package.py
@@ -0,0 +1,41 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RChron(Package):
+    """Chronological objects which can handle dates and times."""
+
+    homepage = "https://cran.r-project.org/package=chron"
+    url      = "https://cran.r-project.org/src/contrib/chron_2.3-47.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/chron"
+
+    version('2.3-47', 'b8890cdc5f2337f8fd775b0becdcdd1f')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-class/package.py b/var/spack/repos/builtin/packages/r-class/package.py
new file mode 100644
index 0000000000..f541ea3611
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-class/package.py
@@ -0,0 +1,44 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RClass(Package):
+    """Various functions for classification, including k-nearest neighbour,
+    Learning Vector Quantization and Self-Organizing Maps."""
+
+    homepage = "http://www.stats.ox.ac.uk/pub/MASS4/"
+    url      = "https://cran.r-project.org/src/contrib/class_7.3-14.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/class"
+
+    version('7.3-14', '6a21dd206fe4ea29c55faeb65fb2b71e')
+
+    extends('R')
+
+    depends_on('r-mass', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-cluster/package.py b/var/spack/repos/builtin/packages/r-cluster/package.py
new file mode 100644
index 0000000000..0fdf2ce5de
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-cluster/package.py
@@ -0,0 +1,43 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RCluster(Package):
+    """Methods for Cluster analysis. Much extended the original from Peter
+    Rousseeuw, Anja Struyf and Mia Hubert, based on Kaufman and Rousseeuw
+    (1990) "Finding Groups in Data"."""
+
+    homepage = "https://cran.r-project.org/web/packages/cluster/index.html"
+    url      = "https://cran.r-project.org/src/contrib/cluster_2.0.4.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/cluster"
+
+    version('2.0.4', 'bb4deceaafb1c42bb1278d5d0dc11e59')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-codetools/package.py b/var/spack/repos/builtin/packages/r-codetools/package.py
new file mode 100644
index 0000000000..bea2f78c82
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-codetools/package.py
@@ -0,0 +1,41 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RCodetools(Package):
+    """Code analysis tools for R."""
+
+    homepage = "https://cran.r-project.org/web/packages/codetools/index.html"
+    url      = "https://cran.r-project.org/src/contrib/codetools_0.2-14.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/codetools"
+
+    version('0.2-14', '7ec41d4f8bd6ba85facc8c5e6adc1f4d')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-crayon/package.py b/var/spack/repos/builtin/packages/r-crayon/package.py
new file mode 100644
index 0000000000..1e0befbca9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-crayon/package.py
@@ -0,0 +1,45 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RCrayon(Package):
+    """Colored terminal output on terminals that support 'ANSI' color and
+    highlight codes. It also works in 'Emacs' 'ESS'. 'ANSI' color support is
+    automatically detected. Colors and highlighting can be combined and nested.
+    New styles can also be created easily. This package was inspired by the
+    'chalk' 'JavaScript' project."""
+
+    homepage = "https://github.com/gaborcsardi/crayon"
+    url      = "https://cran.r-project.org/src/contrib/crayon_1.3.2.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/crayon"
+
+    version('1.3.2', 'fe29c6204d2d6ff4c2f9d107a03d0cb9')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-cubature/package.py b/var/spack/repos/builtin/packages/r-cubature/package.py
new file mode 100644
index 0000000000..1d8f837922
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-cubature/package.py
@@ -0,0 +1,41 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RCubature(Package):
+    """Adaptive multivariate integration over hypercubes"""
+
+    homepage = "https://cran.r-project.org/package=cubature"
+    url      = "https://cran.r-project.org/src/contrib/cubature_1.1-2.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/cubature"
+
+    version('1.1-2', '5617e1d82baa803a3814d92461da45c9')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-curl/package.py b/var/spack/repos/builtin/packages/r-curl/package.py
index c6e8f22a94..24c0eadb2d 100644
--- a/var/spack/repos/builtin/packages/r-curl/package.py
+++ b/var/spack/repos/builtin/packages/r-curl/package.py
@@ -38,8 +38,9 @@ class RCurl(Package):
 
     homepage = "https://github.com/jeroenooms/curl"
     url      = "https://cran.r-project.org/src/contrib/curl_0.9.7.tar.gz"
-    list_url = "https://cran.r-project.org/src/contrib/Archive/RCurl"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/curl"
 
+    version('1.0', '93d34926d6071e1fba7e728b482f0dd9')
     version('0.9.7', 'a101f7de948cb828fef571c730f39217')
 
     extends('R')
diff --git a/var/spack/repos/builtin/packages/r-datatable/package.py b/var/spack/repos/builtin/packages/r-datatable/package.py
new file mode 100644
index 0000000000..8b50643341
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-datatable/package.py
@@ -0,0 +1,46 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RDatatable(Package):
+    """Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins,
+    fast add/modify/delete of columns by group using no copies at all, list
+    columns and a fast file reader (fread). Offers a natural and flexible
+    syntax, for faster development."""
+
+    homepage = "https://github.com/Rdatatable/data.table/wiki"
+    url      = "https://cran.r-project.org/src/contrib/data.table_1.9.6.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/data.table"
+
+    version('1.9.6', 'b1c0c7cce490bdf42ab288541cc55372')
+
+    extends('R')
+
+    depends_on('r-chron')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-devtools/package.py b/var/spack/repos/builtin/packages/r-devtools/package.py
index 5f0b7b8779..75506dd257 100644
--- a/var/spack/repos/builtin/packages/r-devtools/package.py
+++ b/var/spack/repos/builtin/packages/r-devtools/package.py
@@ -36,14 +36,14 @@ class RDevtools(Package):
 
     extends('R')
 
-    depends_on('r-httr')
-    depends_on('r-memoise')
-    depends_on('r-whisker')
-    depends_on('r-digest')
-    depends_on('r-rstudioapi')
-    depends_on('r-jsonlite')
-    depends_on('r-git2r')
-    depends_on('r-withr')
+    depends_on('r-httr', type=nolink)
+    depends_on('r-memoise', type=nolink)
+    depends_on('r-whisker', type=nolink)
+    depends_on('r-digest', type=nolink)
+    depends_on('r-rstudioapi', type=nolink)
+    depends_on('r-jsonlite', type=nolink)
+    depends_on('r-git2r', type=nolink)
+    depends_on('r-withr', type=nolink)
 
     def install(self, spec, prefix):
         R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
diff --git a/var/spack/repos/builtin/packages/r-diagrammer/package.py b/var/spack/repos/builtin/packages/r-diagrammer/package.py
new file mode 100644
index 0000000000..7ff3b8548b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-diagrammer/package.py
@@ -0,0 +1,49 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RDiagrammer(Package):
+    """Create graph diagrams and flowcharts using R."""
+
+    homepage = "https://github.com/rich-iannone/DiagrammeR"
+    url      = "https://cran.r-project.org/src/contrib/DiagrammeR_0.8.4.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/DiagrammeR"
+
+    version('0.8.4', '9ee295c744f5d4ba9a84289ca7bdaf1a')
+
+    extends('R')
+
+    depends_on('r-htmlwidgets', type=nolink)
+    depends_on('r-igraph', type=nolink)
+    depends_on('r-influencer', type=nolink)
+    depends_on('r-rstudioapi@0.6:', type=nolink)
+    depends_on('r-stringr', type=nolink)
+    depends_on('r-visnetwork', type=nolink)
+    depends_on('r-scales', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-doparallel/package.py b/var/spack/repos/builtin/packages/r-doparallel/package.py
new file mode 100644
index 0000000000..7cebfd9e58
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-doparallel/package.py
@@ -0,0 +1,45 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RDoparallel(Package):
+    """Provides a parallel backend for the %dopar% function using the parallel
+    package."""
+
+    homepage = "https://cran.r-project.org/web/packages/doParallel/index.html"
+    url      = "https://cran.r-project.org/src/contrib/doParallel_1.0.10.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/doParallel"
+
+    version('1.0.10', 'd9fbde8f315d98d055483ee3493c9b43')
+
+    extends('R')
+
+    depends_on('r-foreach', type=nolink)
+    depends_on('r-iterators', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-dplyr/package.py b/var/spack/repos/builtin/packages/r-dplyr/package.py
index b065e0b817..ded7651278 100644
--- a/var/spack/repos/builtin/packages/r-dplyr/package.py
+++ b/var/spack/repos/builtin/packages/r-dplyr/package.py
@@ -36,14 +36,15 @@ class RDplyr(Package):
     version('0.5.0', '1fcafcacca70806eea2e6d465cdb94ef')
 
     extends('R')
-    depends_on('r-assertthat')
-    depends_on('r-R6')
-    depends_on('r-rcpp')
-    depends_on('r-tibble')
-    depends_on('r-magrittr')
-    depends_on('r-lazyeval')
-    depends_on('r-dbi')
-    depends_on('r-bh')
+
+    depends_on('r-assertthat', type=nolink)
+    depends_on('r-R6', type=nolink)
+    depends_on('r-rcpp', type=nolink)
+    depends_on('r-tibble', type=nolink)
+    depends_on('r-magrittr', type=nolink)
+    depends_on('r-lazyeval', type=nolink)
+    depends_on('r-dbi', type=nolink)
+    depends_on('r-bh', type=nolink)
 
     def install(self, spec, prefix):
         R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
diff --git a/var/spack/repos/builtin/packages/r-dt/package.py b/var/spack/repos/builtin/packages/r-dt/package.py
new file mode 100644
index 0000000000..f134ee8913
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-dt/package.py
@@ -0,0 +1,47 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RDt(Package):
+    """Data objects in R can be rendered as HTML tables using the JavaScript
+    library 'DataTables' (typically via R Markdown or Shiny). The 'DataTables'
+    library has been included in this R package. The package name 'DT' is an
+    abbreviation of 'DataTables'."""
+
+    homepage = "http://rstudio.github.io/DT"
+    url      = "https://cran.r-project.org/src/contrib/DT_0.1.tar.gz"
+
+    version('0.1', '5c8df984921fa484784ec4b8a4fb6f3c')
+
+    extends('R')
+
+    depends_on('r-htmltools', type=nolink)
+    depends_on('r-htmlwidgets', type=nolink)
+    depends_on('r-magrittr', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-dygraphs/package.py b/var/spack/repos/builtin/packages/r-dygraphs/package.py
new file mode 100644
index 0000000000..9b01d7aa18
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-dygraphs/package.py
@@ -0,0 +1,50 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RDygraphs(Package):
+    """An R interface to the 'dygraphs' JavaScript charting library (a copy of
+    which is included in the package). Provides rich facilities for charting
+    time-series data in R, including highly configurable series- and
+    axis-display and interactive features like zoom/pan and series/point
+    highlighting."""
+
+    homepage = "https://cran.r-project.org/web/packages/dygraphs/index.html"
+    url      = "https://cran.r-project.org/src/contrib/dygraphs_0.9.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/dygraphs"
+
+    version('0.9', '7f0ce4312bcd3f0a58b8c03b2772f833')
+
+    extends('R')
+
+    depends_on('r-magrittr', type=nolink)
+    depends_on('r-htmlwidgets', type=nolink)
+    depends_on('r-zoo', type=nolink)
+    depends_on('r-xts', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-e1071/package.py b/var/spack/repos/builtin/packages/r-e1071/package.py
new file mode 100644
index 0000000000..c2e7166403
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-e1071/package.py
@@ -0,0 +1,45 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RE1071(Package):
+    """Functions for latent class analysis, short time Fourier transform, fuzzy
+    clustering, support vector machines, shortest path computation, bagged
+    clustering, naive Bayes classifier, ..."""
+
+    homepage = "https://cran.r-project.org/package=e1071"
+    url      = "https://cran.r-project.org/src/contrib/e1071_1.6-7.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/e1071"
+
+    version('1.6-7', 'd109a7e3dd0c905d420e327a9a921f5a')
+
+    extends('R')
+
+    depends_on('r-class', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-foreach/package.py b/var/spack/repos/builtin/packages/r-foreach/package.py
new file mode 100644
index 0000000000..2a7324ae99
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-foreach/package.py
@@ -0,0 +1,50 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RForeach(Package):
+    """Support for the foreach looping construct. Foreach is an idiom that
+    allows for iterating over elements in a collection, without the use of an
+    explicit loop counter. This package in particular is intended to be used
+    for its return value, rather than for its side effects. In that sense, it
+    is similar to the standard lapply function, but doesn't require the
+    evaluation of a function. Using foreach without side effects also
+    facilitates executing the loop in parallel."""
+
+    homepage = "https://cran.r-project.org/web/packages/foreach/index.html"
+    url      = "https://cran.r-project.org/src/contrib/foreach_1.4.3.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/foreach"
+
+    version('1.4.3', 'ef45768126661b259f9b8994462c49a0')
+
+    extends('R')
+
+    depends_on('r-codetools', type=nolink)
+    depends_on('r-iterators', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-gdata/package.py b/var/spack/repos/builtin/packages/r-gdata/package.py
new file mode 100644
index 0000000000..0a09a1145b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-gdata/package.py
@@ -0,0 +1,59 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RGdata(Package):
+    """Various R programming tools for data manipulation, including: - medical
+    unit conversions ('ConvertMedUnits', 'MedUnits'), - combining objects
+    ('bindData', 'cbindX', 'combine', 'interleave'), - character vector
+    operations ('centerText', 'startsWith', 'trim'), - factor manipulation
+    ('levels', 'reorder.factor', 'mapLevels'), - obtaining information about R
+    objects ('object.size', 'elem', 'env', 'humanReadable', 'is.what', 'll',
+    'keep', 'ls.funs', 'Args','nPairs', 'nobs'), - manipulating MS-Excel
+    formatted files ('read.xls', 'installXLSXsupport', 'sheetCount',
+    'xlsFormats'), - generating fixed-width format files ('write.fwf'), -
+    extricating components of date & time objects ('getYear', 'getMonth',
+    'getDay', 'getHour', 'getMin', 'getSec'), - operations on columns of data
+    frames ('matchcols', 'rename.vars'), - matrix operations ('unmatrix',
+    'upperTriangle', 'lowerTriangle'), - operations on vectors ('case',
+    'unknownToNA', 'duplicated2', 'trimSum'), - operations on data frames
+    ('frameApply', 'wideByFactor'), - value of last evaluated expression
+    ('ans'), and - wrapper for 'sample' that ensures consistent behavior for
+    both scalar and vector arguments ('resample')."""
+
+    homepage = "https://cran.r-project.org/package=gdata"
+    url      = "https://cran.r-project.org/src/contrib/gdata_2.17.0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/gdata"
+
+    version('2.17.0', 'c716b663b9dc16ad8cafe6acc781a75f')
+
+    extends('R')
+
+    depends_on('r-gtools', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-geosphere/package.py b/var/spack/repos/builtin/packages/r-geosphere/package.py
new file mode 100644
index 0000000000..21ae07fd41
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-geosphere/package.py
@@ -0,0 +1,45 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RGeosphere(Package):
+    """Spherical trigonometry for geographic applications. That is, compute
+    distances and related measures for angular (longitude/latitude)
+    locations."""
+
+    homepage = "https://cran.r-project.org/package=geosphere"
+    url      = "https://cran.r-project.org/src/contrib/geosphere_1.5-5.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/geosphere"
+
+    version('1.5-5', '28efb7a8e266c7f076cdbcf642455f3e')
+
+    extends('R')
+
+    depends_on('r-sp', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-ggmap/package.py b/var/spack/repos/builtin/packages/r-ggmap/package.py
new file mode 100644
index 0000000000..2dfca19b51
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-ggmap/package.py
@@ -0,0 +1,57 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RGgmap(Package):
+    """A collection of functions to visualize spatial data and models on top of
+    static maps from various online sources (e.g Google Maps and Stamen Maps).
+    It includes tools common to those tasks, including functions for
+    geolocation and routing."""
+
+    homepage = "https://github.com/dkahle/ggmap"
+    url      = "https://cran.r-project.org/src/contrib/ggmap_2.6.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/ggmap"
+
+    version('2.6.1', '25ad414a3a1c6d59a227a9f22601211a')
+
+    extends('R')
+
+    depends_on('r-ggplot2', type=nolink)
+    depends_on('r-proto', type=nolink)
+    depends_on('r-rgooglemaps', type=nolink)
+    depends_on('r-png', type=nolink)
+    depends_on('r-plyr', type=nolink)
+    depends_on('r-reshape2', type=nolink)
+    depends_on('r-rjson', type=nolink)
+    depends_on('r-mapproj', type=nolink)
+    depends_on('r-jpeg', type=nolink)
+    depends_on('r-geosphere', type=nolink)
+    depends_on('r-digest', type=nolink)
+    depends_on('r-scales', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-ggplot2/package.py b/var/spack/repos/builtin/packages/r-ggplot2/package.py
index 2d1f53af26..a8cf21930f 100644
--- a/var/spack/repos/builtin/packages/r-ggplot2/package.py
+++ b/var/spack/repos/builtin/packages/r-ggplot2/package.py
@@ -42,12 +42,12 @@ class RGgplot2(Package):
 
     extends('R')
 
-    depends_on('r-digest')
-    depends_on('r-gtable')
-    depends_on('r-mass')
-    depends_on('r-plyr')
-    depends_on('r-reshape2')
-    depends_on('r-scales')
+    depends_on('r-digest', type=nolink)
+    depends_on('r-gtable', type=nolink)
+    depends_on('r-mass', type=nolink)
+    depends_on('r-plyr', type=nolink)
+    depends_on('r-reshape2', type=nolink)
+    depends_on('r-scales', type=nolink)
 
     def install(self, spec, prefix):
         R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
diff --git a/var/spack/repos/builtin/packages/r-ggvis/package.py b/var/spack/repos/builtin/packages/r-ggvis/package.py
index 8fc1f397c8..29b2069ae9 100644
--- a/var/spack/repos/builtin/packages/r-ggvis/package.py
+++ b/var/spack/repos/builtin/packages/r-ggvis/package.py
@@ -38,13 +38,13 @@ class RGgvis(Package):
 
     extends('R')
 
-    depends_on('r-assertthat')
-    depends_on('r-jsonlite')
-    depends_on('r-shiny')
-    depends_on('r-magrittr')
-    depends_on('r-dplyr')
-    depends_on('r-lazyeval')
-    depends_on('r-htmltools')
+    depends_on('r-assertthat', type=nolink)
+    depends_on('r-jsonlite', type=nolink)
+    depends_on('r-shiny', type=nolink)
+    depends_on('r-magrittr', type=nolink)
+    depends_on('r-dplyr', type=nolink)
+    depends_on('r-lazyeval', type=nolink)
+    depends_on('r-htmltools', type=nolink)
 
     def install(self, spec, prefix):
         R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
diff --git a/var/spack/repos/builtin/packages/r-glmnet/package.py b/var/spack/repos/builtin/packages/r-glmnet/package.py
new file mode 100644
index 0000000000..af6e1d1b63
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-glmnet/package.py
@@ -0,0 +1,49 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RGlmnet(Package):
+    """Extremely efficient procedures for fitting the entire lasso or
+    elastic-net regularization path for linear regression, logistic and
+    multinomial regression models, Poisson regression and the Cox model. Two
+    recent additions are the multiple-response Gaussian, and the grouped
+    multinomial. The algorithm uses cyclical coordinate descent in a path-wise
+    fashion, as described in the paper linked to via the URL below."""
+
+    homepage = "http://www.jstatsoft.org/v33/i01/"
+    url      = "https://cran.r-project.org/src/contrib/glmnet_2.0-5.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/glmnet"
+
+    version('2.0-5', '049b18caa29529614cd684db3beaec2a')
+
+    extends('R')
+
+    depends_on('r-matrix', type=nolink)
+    depends_on('r-foreach', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-googlevis/package.py b/var/spack/repos/builtin/packages/r-googlevis/package.py
new file mode 100644
index 0000000000..bcb7caa0fb
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-googlevis/package.py
@@ -0,0 +1,47 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RGooglevis(Package):
+    """R interface to Google Charts API, allowing users to create interactive
+    charts based on data frames. Charts are displayed locally via the R HTTP
+    help server. A modern browser with an Internet connection is required and
+    for some charts a Flash player. The data remains local and is not uploaded
+    to Google."""
+
+    homepage = "https://github.com/mages/googleVis#googlevis"
+    url      = "https://cran.r-project.org/src/contrib/googleVis_0.6.0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/googleVis"
+
+    version('0.6.0', 'ec36fd2a6884ddc7baa894007d0d0468')
+
+    extends('R')
+
+    depends_on('r-jsonlite', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-gridbase/package.py b/var/spack/repos/builtin/packages/r-gridbase/package.py
new file mode 100644
index 0000000000..a2f55b4470
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-gridbase/package.py
@@ -0,0 +1,41 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RGridbase(Package):
+    """Integration of base and grid graphics."""
+
+    homepage = "https://cran.r-project.org/web/packages/gridBase/index.html"
+    url      = "https://cran.r-project.org/src/contrib/gridBase_0.4-7.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/gridBase"
+
+    version('0.4-7', '6d5064a85f5c966a92ee468ae44c5f1f')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-gridextra/package.py b/var/spack/repos/builtin/packages/r-gridextra/package.py
index d215d10678..537426d42f 100644
--- a/var/spack/repos/builtin/packages/r-gridextra/package.py
+++ b/var/spack/repos/builtin/packages/r-gridextra/package.py
@@ -37,7 +37,7 @@ class RGridextra(Package):
 
     extends('R')
 
-    depends_on('r-gtable')
+    depends_on('r-gtable', type=nolink)
 
     def install(self, spec, prefix):
         R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
diff --git a/var/spack/repos/builtin/packages/r-gtools/package.py b/var/spack/repos/builtin/packages/r-gtools/package.py
new file mode 100644
index 0000000000..367bb30f87
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-gtools/package.py
@@ -0,0 +1,60 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RGtools(Package):
+    """Functions to assist in R programming, including: - assist in developing,
+    updating, and maintaining R and R packages ('ask', 'checkRVersion',
+    'getDependencies', 'keywords', 'scat'), - calculate the logit and inverse
+    logit transformations ('logit', 'inv.logit'), - test if a value is missing,
+    empty or contains only NA and NULL values ('invalid'), - manipulate R's
+    .Last function ('addLast'), - define macros ('defmacro'), - detect odd and
+    even integers ('odd', 'even'), - convert strings containing non-ASCII
+    characters (like single quotes) to plain ASCII ('ASCIIfy'), - perform a
+    binary search ('binsearch'), - sort strings containing both numeric and
+    character components ('mixedsort'), - create a factor variable from the
+    quantiles of a continuous variable ('quantcut'), - enumerate permutations
+    and combinations ('combinations', 'permutation'), - calculate and convert
+    between fold-change and log-ratio ('foldchange', 'logratio2foldchange',
+    'foldchange2logratio'), - calculate probabilities and generate random
+    numbers from Dirichlet distributions ('rdirichlet', 'ddirichlet'), - apply
+    a function over adjacent subsets of a vector ('running'), - modify the
+    TCP\_NODELAY ('de-Nagle') flag for socket objects, - efficient 'rbind' of
+    data frames, even if the column names don't match ('smartbind'), - generate
+    significance stars from p-values ('stars.pval'), - convert characters
+    to/from ASCII codes."""
+
+    homepage = "https://cran.r-project.org/package=gtools"
+    url      = "https://cran.r-project.org/src/contrib/gtools_3.5.0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/gtools"
+
+    version('3.5.0', '45f8800c0336d35046641fbacc56bdbb')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-htmltools/package.py b/var/spack/repos/builtin/packages/r-htmltools/package.py
index 0aea564372..21cdbe9184 100644
--- a/var/spack/repos/builtin/packages/r-htmltools/package.py
+++ b/var/spack/repos/builtin/packages/r-htmltools/package.py
@@ -36,8 +36,8 @@ class RHtmltools(Package):
 
     extends('R')
 
-    depends_on('r-digest')
-    depends_on('r-rcpp')
+    depends_on('r-digest', type=nolink)
+    depends_on('r-rcpp', type=nolink)
 
     def install(self, spec, prefix):
         R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
diff --git a/var/spack/repos/builtin/packages/r-htmlwidgets/package.py b/var/spack/repos/builtin/packages/r-htmlwidgets/package.py
new file mode 100644
index 0000000000..8090776f06
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-htmlwidgets/package.py
@@ -0,0 +1,47 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RHtmlwidgets(Package):
+    """A framework for creating HTML widgets that render in various contexts
+    including the R console, 'R Markdown' documents, and 'Shiny' web
+    applications."""
+
+    homepage = "https://github.com/ramnathv/htmlwidgets"
+    url      = "https://cran.r-project.org/src/contrib/htmlwidgets_0.6.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/htmlwidgets"
+
+    version('0.6', '7fa522d2eda97593978021bda9670c0e')
+
+    extends('R')
+
+    depends_on('r-htmltools', type=nolink)
+    depends_on('r-jsonlite', type=nolink)
+    depends_on('r-yaml', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-httpuv/package.py b/var/spack/repos/builtin/packages/r-httpuv/package.py
index 6ab12bcf9d..57025d3a3c 100644
--- a/var/spack/repos/builtin/packages/r-httpuv/package.py
+++ b/var/spack/repos/builtin/packages/r-httpuv/package.py
@@ -42,7 +42,7 @@ class RHttpuv(Package):
 
     extends('R')
 
-    depends_on('r-rcpp')
+    depends_on('r-rcpp', type=nolink)
 
     def install(self, spec, prefix):
         R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
diff --git a/var/spack/repos/builtin/packages/r-httr/package.py b/var/spack/repos/builtin/packages/r-httr/package.py
index 77ec34ab03..227594fc0d 100644
--- a/var/spack/repos/builtin/packages/r-httr/package.py
+++ b/var/spack/repos/builtin/packages/r-httr/package.py
@@ -38,11 +38,11 @@ class RHttr(Package):
 
     extends('R')
 
-    depends_on('r-jsonlite')
-    depends_on('r-mime')
-    depends_on('r-curl')
-    depends_on('r-openssl')
-    depends_on('r-R6')
+    depends_on('r-jsonlite', type=nolink)
+    depends_on('r-mime', type=nolink)
+    depends_on('r-curl', type=nolink)
+    depends_on('r-openssl', type=nolink)
+    depends_on('r-R6', type=nolink)
 
     def install(self, spec, prefix):
         R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
diff --git a/var/spack/repos/builtin/packages/r-igraph/package.py b/var/spack/repos/builtin/packages/r-igraph/package.py
new file mode 100644
index 0000000000..37925d4e02
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-igraph/package.py
@@ -0,0 +1,50 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RIgraph(Package):
+    """Routines for simple graphs and network analysis. It can handle large
+    graphs very well and provides functions for generating random and regular
+    graphs, graph visualization, centrality methods and much more."""
+
+    homepage = "http://igraph.org/"
+    url      = "https://cran.r-project.org/src/contrib/igraph_1.0.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/igraph"
+
+    version('1.0.1', 'ea33495e49adf4a331e4ba60ba559065')
+
+    extends('R')
+
+    depends_on('r-matrix', type=nolink)
+    depends_on('r-magrittr', type=nolink)
+    depends_on('r-nmf', type=nolink)
+    depends_on('r-irlba', type=nolink)
+    depends_on('gmp')
+    depends_on('libxml2')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-influencer/package.py b/var/spack/repos/builtin/packages/r-influencer/package.py
new file mode 100644
index 0000000000..dd525daf2b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-influencer/package.py
@@ -0,0 +1,50 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RInfluencer(Package):
+    """Provides functionality to compute various node centrality measures on
+    networks. Included are functions to compute betweenness centrality (by
+    utilizing Madduri and Bader's SNAP library), implementations of Burt's
+    constraint and effective network size (ENS) metrics, Borgatti's algorithm
+    to identify key players, and Valente's bridging metric. On Unix systems,
+    the betweenness, Key Players, and bridging implementations are parallelized
+    with OpenMP, which may run faster on systems which have OpenMP
+    configured."""
+
+    homepage = "https://github.com/rcc-uchicago/influenceR"
+    url      = "https://cran.r-project.org/src/contrib/influenceR_0.1.0.tar.gz"
+
+    version('0.1.0', '6c8b6decd78c341364b5811fb3050ba5')
+
+    extends('R')
+
+    depends_on('r-igraph', type=nolink)
+    depends_on('r-matrix', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-irlba/package.py b/var/spack/repos/builtin/packages/r-irlba/package.py
new file mode 100644
index 0000000000..42cc142e8a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-irlba/package.py
@@ -0,0 +1,45 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RIrlba(Package):
+    """Fast and memory efficient methods for truncated singular and eigenvalue
+    decompositions and principal component analysis of large sparse or dense
+    matrices."""
+
+    homepage = "https://cran.r-project.org/web/packages/irlba/index.html"
+    url      = "https://cran.r-project.org/src/contrib/irlba_2.0.0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/irlba"
+
+    version('2.0.0', '557674cf8b68fea5b9f231058c324d26')
+
+    extends('R')
+
+    depends_on('r-matrix', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-iterators/package.py b/var/spack/repos/builtin/packages/r-iterators/package.py
new file mode 100644
index 0000000000..f5a3489e7d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-iterators/package.py
@@ -0,0 +1,42 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RIterators(Package):
+    """Support for iterators, which allow a programmer to traverse through all
+    the elements of a vector, list, or other collection of data."""
+
+    homepage = "https://cran.r-project.org/web/packages/iterators/index.html"
+    url      = "https://cran.r-project.org/src/contrib/iterators_1.0.8.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/iterators"
+
+    version('1.0.8', '2ded7f82cddd8174f1ec98607946c6ee')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-jpeg/package.py b/var/spack/repos/builtin/packages/r-jpeg/package.py
new file mode 100644
index 0000000000..ef940720f8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-jpeg/package.py
@@ -0,0 +1,45 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RJpeg(Package):
+    """This package provides an easy and simple way to read, write and display
+    bitmap images stored in the JPEG format. It can read and write both files
+    and in-memory raw vectors."""
+
+    homepage = "http://www.rforge.net/jpeg/"
+    url      = "https://cran.r-project.org/src/contrib/jpeg_0.1-8.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/jpeg"
+
+    version('0.1-8', '696007451d14395b1ed1d0e9af667a57')
+
+    extends('R')
+
+    depends_on('jpeg')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-jsonlite/package.py b/var/spack/repos/builtin/packages/r-jsonlite/package.py
index 6e231ed345..d1cb4b52c1 100644
--- a/var/spack/repos/builtin/packages/r-jsonlite/package.py
+++ b/var/spack/repos/builtin/packages/r-jsonlite/package.py
@@ -38,9 +38,10 @@ class RJsonlite(Package):
     use with dynamic data in systems and applications."""
 
     homepage = "https://github.com/jeroenooms/jsonlite"
-    url      = "https://cran.r-project.org/src/contrib/jsonlite_0.9.21.tar.gz"
+    url      = "https://cran.r-project.org/src/contrib/jsonlite_1.0.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/jsonlite"
 
+    version('1.0', 'c8524e086de22ab39b8ac8000220cc87')
     version('0.9.21', '4fc382747f88a79ff0718a0d06bed45d')
 
     extends('R')
diff --git a/var/spack/repos/builtin/packages/r-leaflet/package.py b/var/spack/repos/builtin/packages/r-leaflet/package.py
new file mode 100644
index 0000000000..2a91100c34
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-leaflet/package.py
@@ -0,0 +1,54 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RLeaflet(Package):
+    """Create and customize interactive maps using the 'Leaflet' JavaScript
+    library and the 'htmlwidgets' package. These maps can be used directly from
+    the R console, from 'RStudio', in Shiny apps and R Markdown documents."""
+
+    homepage = "http://rstudio.github.io/leaflet/"
+    url      = "https://cran.r-project.org/src/contrib/leaflet_1.0.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/leaflet"
+
+    version('1.0.1', '7f3d8b17092604d87d4eeb579f73d5df')
+
+    extends('R')
+
+    depends_on('r-base64enc', type=nolink)
+    depends_on('r-htmlwidgets', type=nolink)
+    depends_on('r-htmltools', type=nolink)
+    depends_on('r-magrittr', type=nolink)
+    depends_on('r-markdown', type=nolink)
+    depends_on('r-png', type=nolink)
+    depends_on('r-rcolorbrewer', type=nolink)
+    depends_on('r-raster', type=nolink)
+    depends_on('r-scales', type=nolink)
+    depends_on('r-sp', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-lme4/package.py b/var/spack/repos/builtin/packages/r-lme4/package.py
new file mode 100644
index 0000000000..c52d9d0e27
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-lme4/package.py
@@ -0,0 +1,53 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RLme4(Package):
+    """Fit linear and generalized linear mixed-effects models. The models and
+    their components are represented using S4 classes and methods. The core
+    computational algorithms are implemented using the 'Eigen' C++ library for
+    numerical linear algebra and 'RcppEigen' "glue"."""
+
+    homepage = "https://github.com/lme4/lme4/"
+    url      = "https://cran.r-project.org/src/contrib/lme4_1.1-12.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/lme4"
+
+    version('1.1-12', 'da8aaebb67477ecb5631851c46207804')
+
+    extends('R')
+
+    depends_on('r-matrix', type=nolink)
+    depends_on('r-mass', type=nolink)
+    depends_on('r-lattice', type=nolink)
+    depends_on('r-nlme', type=nolink)
+    depends_on('r-minqa', type=nolink)
+    depends_on('r-nloptr', type=nolink)
+    depends_on('r-rcpp', type=nolink)
+    depends_on('r-rcppeigen', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-lmtest/package.py b/var/spack/repos/builtin/packages/r-lmtest/package.py
new file mode 100644
index 0000000000..31a36f1f7e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-lmtest/package.py
@@ -0,0 +1,45 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RLmtest(Package):
+    """A collection of tests, data sets, and examples for diagnostic checking
+    in linear regression models. Furthermore, some generic tools for inference
+    in parametric models are provided."""
+
+    homepage = "https://cran.r-project.org/package=lmtest"
+    url      = "https://cran.r-project.org/src/contrib/lmtest_0.9-34.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/lmtest"
+
+    version('0.9-34', 'fcdf7286bb5ccc2ca46be00bf25ac2fe')
+
+    extends('R')
+
+    depends_on('r-zoo', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-lubridate/package.py b/var/spack/repos/builtin/packages/r-lubridate/package.py
index 88576911f0..2e5661fa4d 100644
--- a/var/spack/repos/builtin/packages/r-lubridate/package.py
+++ b/var/spack/repos/builtin/packages/r-lubridate/package.py
@@ -40,7 +40,8 @@ class RLubridate(Package):
     version('1.5.6', 'a5dc44817548ee219d26a10bae92e611')
 
     extends('R')
-    depends_on('r-stringr')
+
+    depends_on('r-stringr', type=nolink)
 
     def install(self, spec, prefix):
         R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
diff --git a/var/spack/repos/builtin/packages/r-magic/package.py b/var/spack/repos/builtin/packages/r-magic/package.py
index f6ba97740b..2b8f95351a 100644
--- a/var/spack/repos/builtin/packages/r-magic/package.py
+++ b/var/spack/repos/builtin/packages/r-magic/package.py
@@ -39,7 +39,7 @@ class RMagic(Package):
 
     extends('R')
 
-    depends_on('r-abind')
+    depends_on('r-abind', type=nolink)
 
     def install(self, spec, prefix):
         R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
diff --git a/var/spack/repos/builtin/packages/r-mapproj/package.py b/var/spack/repos/builtin/packages/r-mapproj/package.py
new file mode 100644
index 0000000000..0f8bbe199b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-mapproj/package.py
@@ -0,0 +1,43 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RMapproj(Package):
+    """Converts latitude/longitude into projected coordinates."""
+
+    homepage = "https://cran.r-project.org/package=mapproj"
+    url      = "https://cran.r-project.org/src/contrib/mapproj_1.2-4.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/mapproj"
+
+    version('1.2-4', '10e22bde1c790e1540672f15ddcaee71')
+
+    extends('R')
+
+    depends_on('r-maps', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-maps/package.py b/var/spack/repos/builtin/packages/r-maps/package.py
new file mode 100644
index 0000000000..1e0bfd2d43
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-maps/package.py
@@ -0,0 +1,42 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RMaps(Package):
+    """Display of maps. Projection code and larger maps are in separate
+    packages ('mapproj' and 'mapdata')."""
+
+    homepage = "https://cran.r-project.org/"
+    url      = "https://cran.r-project.org/src/contrib/maps_3.1.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/maps"
+
+    version('3.1.1', 'ff045eccb6d5a658db5a539116ddf764')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-maptools/package.py b/var/spack/repos/builtin/packages/r-maptools/package.py
new file mode 100644
index 0000000000..8d045a4ed4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-maptools/package.py
@@ -0,0 +1,49 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RMaptools(Package):
+    """Set of tools for manipulating and reading geographic data, in particular
+    ESRI shapefiles; C code used from shapelib. It includes binary access to
+    GSHHG shoreline files. The package also provides interface wrappers for
+    exchanging spatial objects with packages such as PBSmapping, spatstat,
+    maps, RArcInfo, Stata tmap, WinBUGS, Mondrian, and others."""
+
+    homepage = "http://r-forge.r-project.org/projects/maptools/"
+    url      = "https://cran.r-project.org/src/contrib/maptools_0.8-39.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/maptools"
+
+    version('0.8-39', '3690d96afba8ef22c8e27ae540ffb836')
+
+    extends('R')
+
+    depends_on('r-sp', type=nolink)
+    depends_on('r-foreign', type=nolink)
+    depends_on('r-lattice', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-markdown/package.py b/var/spack/repos/builtin/packages/r-markdown/package.py
new file mode 100644
index 0000000000..c34727d2b0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-markdown/package.py
@@ -0,0 +1,47 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RMarkdown(Package):
+    """Provides R bindings to the 'Sundown' 'Markdown' rendering library
+    (https://github.com/vmg/sundown). 'Markdown' is a plain-text formatting
+    syntax that can be converted to 'XHTML' or other formats. See
+    http://en.wikipedia.org/wiki/Markdown for more information about
+    'Markdown'."""
+
+    homepage = "https://github.com/rstudio/markdown"
+    url      = "https://cran.r-project.org/src/contrib/markdown_0.7.7.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/markdown"
+
+    version('0.7.7', '72deca9c675c7cc9343048edbc29f7ff')
+
+    extends('R')
+
+    depends_on('r-mime', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-matrix/package.py b/var/spack/repos/builtin/packages/r-matrix/package.py
index fbd8a7b4df..1b45dc55ca 100644
--- a/var/spack/repos/builtin/packages/r-matrix/package.py
+++ b/var/spack/repos/builtin/packages/r-matrix/package.py
@@ -37,7 +37,7 @@ class RMatrix(Package):
 
     extends('R')
 
-    depends_on('r-lattice')
+    depends_on('r-lattice', type=nolink)
 
     def install(self, spec, prefix):
         R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
diff --git a/var/spack/repos/builtin/packages/r-matrixmodels/package.py b/var/spack/repos/builtin/packages/r-matrixmodels/package.py
new file mode 100644
index 0000000000..3cdce6fea6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-matrixmodels/package.py
@@ -0,0 +1,44 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RMatrixmodels(Package):
+    """Modelling with sparse and dense 'Matrix' matrices, using modular
+    prediction and response module classes."""
+
+    homepage = "http://matrix.r-forge.r-project.org/"
+    url      = "https://cran.r-project.org/src/contrib/MatrixModels_0.4-1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/MatrixModels"
+
+    version('0.4-1', '65b3ab56650c62bf1046a3eb1f1e19a0')
+
+    extends('R')
+
+    depends_on('r-matrix', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-memoise/package.py b/var/spack/repos/builtin/packages/r-memoise/package.py
index 6a0fb78650..81f3ff1dab 100644
--- a/var/spack/repos/builtin/packages/r-memoise/package.py
+++ b/var/spack/repos/builtin/packages/r-memoise/package.py
@@ -37,7 +37,7 @@ class RMemoise(Package):
 
     extends('R')
 
-    depends_on('r-digest')
+    depends_on('r-digest', type=nolink)
 
     def install(self, spec, prefix):
         R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
diff --git a/var/spack/repos/builtin/packages/r-mgcv/package.py b/var/spack/repos/builtin/packages/r-mgcv/package.py
new file mode 100644
index 0000000000..4c49462ba2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-mgcv/package.py
@@ -0,0 +1,47 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RMgcv(Package):
+    """GAMs, GAMMs and other generalized ridge regression with multiple
+    smoothing parameter estimation by GCV, REML or UBRE/AIC. Includes a gam()
+    function, a wide variety of smoothers, JAGS support and distributions
+    beyond the exponential family."""
+
+    homepage = "https://cran.r-project.org/package=mgcv"
+    url      = "https://cran.r-project.org/src/contrib/mgcv_1.8-13.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/mgcv"
+
+    version('1.8-13', '30607be3aaf44b13bd8c81fc32e8c984')
+
+    extends('R')
+
+    depends_on('r-nlme', type=nolink)
+    depends_on('r-matrix', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-mime/package.py b/var/spack/repos/builtin/packages/r-mime/package.py
index fb079f44c5..5e78889a76 100644
--- a/var/spack/repos/builtin/packages/r-mime/package.py
+++ b/var/spack/repos/builtin/packages/r-mime/package.py
@@ -30,9 +30,10 @@ class RMime(Package):
     from /etc/mime.types in UNIX-type systems."""
 
     homepage = "https://github.com/yihui/mime"
-    url      = "https://cran.r-project.org/src/contrib/mime_0.4.tar.gz"
+    url      = "https://cran.r-project.org/src/contrib/mime_0.5.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/mime"
 
+    version('0.5', '87e00b6d57b581465c19ae869a723c4d')
     version('0.4', '789cb33e41db2206c6fc7c3e9fbc2c02')
 
     extends('R')
diff --git a/var/spack/repos/builtin/packages/r-minqa/package.py b/var/spack/repos/builtin/packages/r-minqa/package.py
new file mode 100644
index 0000000000..16cff20b41
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-minqa/package.py
@@ -0,0 +1,44 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RMinqa(Package):
+    """Derivative-free optimization by quadratic approximation based on an
+    interface to Fortran implementations by M. J. D. Powell."""
+
+    homepage = "http://optimizer.r-forge.r-project.org/"
+    url      = "https://cran.r-project.org/src/contrib/minqa_1.2.4.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/minqa"
+
+    version('1.2.4', 'bcaae4fdba60a33528f2116e2fd51105')
+
+    extends('R')
+
+    depends_on('r-rcpp', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-multcomp/package.py b/var/spack/repos/builtin/packages/r-multcomp/package.py
new file mode 100644
index 0000000000..54416502d9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-multcomp/package.py
@@ -0,0 +1,51 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RMultcomp(Package):
+    """Simultaneous tests and confidence intervals for general linear
+    hypotheses in parametric models, including linear, generalized linear,
+    linear mixed effects, and survival models. The package includes demos
+    reproducing analyzes presented in the book "Multiple Comparisons Using R"
+    (Bretz, Hothorn, Westfall, 2010, CRC Press)."""
+
+    homepage = "http://multcomp.r-forge.r-project.org/"
+    url      = "https://cran.r-project.org/src/contrib/multcomp_1.4-6.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/multcomp"
+
+    version('1.4-6', 'f1353ede2ed78b23859a7f1f1f9ebe88')
+
+    extends('R')
+
+    depends_on('r-mvtnorm', type=nolink)
+    depends_on('r-survival', type=nolink)
+    depends_on('r-thdata', type=nolink)
+    depends_on('r-sandwich', type=nolink)
+    depends_on('r-codetools', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-munsell/package.py b/var/spack/repos/builtin/packages/r-munsell/package.py
index 3216c95e00..b96b90f9c7 100644
--- a/var/spack/repos/builtin/packages/r-munsell/package.py
+++ b/var/spack/repos/builtin/packages/r-munsell/package.py
@@ -40,7 +40,7 @@ class RMunsell(Package):
 
     extends('R')
 
-    depends_on('r-colorspace')
+    depends_on('r-colorspace', type=nolink)
 
     def install(self, spec, prefix):
         R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
diff --git a/var/spack/repos/builtin/packages/r-mvtnorm/package.py b/var/spack/repos/builtin/packages/r-mvtnorm/package.py
new file mode 100644
index 0000000000..b3f7db60c6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-mvtnorm/package.py
@@ -0,0 +1,42 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RMvtnorm(Package):
+    """Computes multivariate normal and t probabilities, quantiles, random
+    deviates and densities."""
+
+    homepage = "http://mvtnorm.r-forge.r-project.org/"
+    url      = "https://cran.r-project.org/src/contrib/mvtnorm_1.0-5.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/mvtnorm"
+
+    version('1.0-5', '5894dd3969bbfa26f4862c45f9a48a52')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-ncdf4/package.py b/var/spack/repos/builtin/packages/r-ncdf4/package.py
new file mode 100644
index 0000000000..11bf7abb38
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-ncdf4/package.py
@@ -0,0 +1,56 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RNcdf4(Package):
+    """Provides a high-level R interface to data files written using Unidata's
+    netCDF library (version 4 or earlier), which are binary data files that are
+    portable across platforms and include metadata information in addition to
+    the data sets. Using this package, netCDF files (either version 4 or
+    "classic" version 3) can be opened and data sets read in easily. It is also
+    easy to create new netCDF dimensions, variables, and files, in either
+    version 3 or 4 format, and manipulate existing netCDF files. This package
+    replaces the former ncdf package, which only worked with netcdf version 3
+    files. For various reasons the names of the functions have had to be
+    changed from the names in the ncdf package. The old ncdf package is still
+    available at the URL given below, if you need to have backward
+    compatibility. It should be possible to have both the ncdf and ncdf4
+    packages installed simultaneously without a problem. However, the ncdf
+    package does not provide an interface for netcdf version 4 files."""
+
+    homepage = "http://cirrus.ucsd.edu/~pierce/ncdf"
+    url      = "https://cran.r-project.org/src/contrib/ncdf4_1.15.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/ncdf4"
+
+    version('1.15', 'cd60dadbae3be31371e1ed40ddeb420a')
+
+    extends('R')
+
+    depends_on('netcdf')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-networkd3/package.py b/var/spack/repos/builtin/packages/r-networkd3/package.py
new file mode 100644
index 0000000000..8884f7cf1b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-networkd3/package.py
@@ -0,0 +1,46 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RNetworkd3(Package):
+    """Creates 'D3' 'JavaScript' network, tree, dendrogram, and Sankey graphs
+    from 'R'."""
+
+    homepage = "http://cran.r-project.org/package=networkD3"
+    url      = "https://cran.r-project.org/src/contrib/networkD3_0.2.12.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/networkD3"
+
+    version('0.2.12', '356fe4be59698e6fb052644bd9659d84')
+
+    extends('R')
+
+    depends_on('r-htmlwidgets', type=nolink)
+    depends_on('r-igraph', type=nolink)
+    depends_on('r-magrittr', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-nlme/package.py b/var/spack/repos/builtin/packages/r-nlme/package.py
new file mode 100644
index 0000000000..1b6bb114e1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-nlme/package.py
@@ -0,0 +1,43 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RNlme(Package):
+    """Fit and compare Gaussian linear and nonlinear mixed-effects models."""
+
+    homepage = "https://cran.r-project.org/package=nlme"
+    url      = "https://cran.r-project.org/src/contrib/nlme_3.1-128.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/nlme"
+
+    version('3.1-128', '3d75ae7380bf123761b95a073eb55008')
+
+    extends('R')
+
+    depends_on('r-lattice', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-nloptr/package.py b/var/spack/repos/builtin/packages/r-nloptr/package.py
new file mode 100644
index 0000000000..58cb585c49
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-nloptr/package.py
@@ -0,0 +1,47 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RNloptr(Package):
+    """nloptr is an R interface to NLopt. NLopt is a free/open-source library
+    for nonlinear optimization, providing a common interface for a number of
+    different free optimization routines available online as well as original
+    implementations of various other algorithms. See
+    http://ab-initio.mit.edu/wiki/index.php/NLopt_Introduction for more
+    information on the available algorithms. During installation on Unix the
+    NLopt code is downloaded and compiled from the NLopt website."""
+
+    homepage = "https://cran.r-project.org/package=nloptr"
+    url      = "https://cran.r-project.org/src/contrib/nloptr_1.0.4.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/nloptr"
+
+    version('1.0.4', '9af69a613349b236fd377d0a107f484c')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-nmf/package.py b/var/spack/repos/builtin/packages/r-nmf/package.py
new file mode 100644
index 0000000000..c30a1ac101
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-nmf/package.py
@@ -0,0 +1,60 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RNmf(Package):
+    """Provides a framework to perform Non-negative Matrix Factorization (NMF).
+    The package implements a set of already published algorithms and seeding
+    methods, and provides a framework to test, develop and plug new/custom
+    algorithms. Most of the built-in algorithms have been optimized in C++, and
+    the main interface function provides an easy way of performing parallel
+    computations on multicore machines.."""
+
+    homepage = "http://renozao.github.io/NMF"
+    url      = "https://cran.r-project.org/src/contrib/NMF_0.20.6.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/NMF"
+
+    version('0.20.6', '81df07b3bf710a611db5af24730ff3d0')
+
+    extends('R')
+
+    depends_on('r-pkgmaker', type=nolink)
+    depends_on('r-registry', type=nolink)
+    depends_on('r-rngtools', type=nolink)
+    depends_on('r-cluster', type=nolink)
+    depends_on('r-stringr', type=nolink)
+    depends_on('r-digest', type=nolink)
+    depends_on('r-gridbase', type=nolink)
+    depends_on('r-colorspace', type=nolink)
+    depends_on('r-rcolorbrewer', type=nolink)
+    depends_on('r-foreach', type=nolink)
+    depends_on('r-doparallel', type=nolink)
+    depends_on('r-ggplot2', type=nolink)
+    depends_on('r-reshape2', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-nnet/package.py b/var/spack/repos/builtin/packages/r-nnet/package.py
new file mode 100644
index 0000000000..be048f5ad0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-nnet/package.py
@@ -0,0 +1,42 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RNnet(Package):
+    """Software for feed-forward neural networks with a single hidden layer,
+    and for multinomial log-linear models."""
+
+    homepage = "http://www.stats.ox.ac.uk/pub/MASS4/"
+    url      = "https://cran.r-project.org/src/contrib/nnet_7.3-12.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/nnet"
+
+    version('7.3-12', 'dc7c6f0d0de53d8fc72b44554400a74e')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-np/package.py b/var/spack/repos/builtin/packages/r-np/package.py
new file mode 100644
index 0000000000..bff7d0f195
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-np/package.py
@@ -0,0 +1,50 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RNp(Package):
+    """This package provides a variety of nonparametric (and semiparametric)
+    kernel methods that seamlessly handle a mix of continuous, unordered, and
+    ordered factor data types. We would like to gratefully acknowledge support
+    from the Natural Sciences and Engineering Research Council of Canada
+    (NSERC:www.nserc.ca), the Social Sciences and Humanities Research Council
+    of Canada (SSHRC:www.sshrc.ca), and the Shared Hierarchical Academic
+    Research Computing Network (SHARCNET:www.sharcnet.ca)."""
+
+    homepage = "https://github.com/JeffreyRacine/R-Package-np/"
+    url      = "https://cran.r-project.org/src/contrib/np_0.60-2.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/np"
+
+    version('0.60-2', 'e094d52ddff7280272b41e6cb2c74389')
+
+    extends('R')
+
+    depends_on('r-boot', type=nolink)
+    depends_on('r-cubature', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-pbkrtest/package.py b/var/spack/repos/builtin/packages/r-pbkrtest/package.py
new file mode 100644
index 0000000000..40b6f96927
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-pbkrtest/package.py
@@ -0,0 +1,49 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RPbkrtest(Package):
+    """Test in mixed effects models. Attention is on mixed effects models as
+    implemented in the 'lme4' package. This package implements a parametric
+    bootstrap test and a Kenward Roger modification of F-tests for linear mixed
+    effects models and a parametric bootstrap test for generalized linear mixed
+    models."""
+
+    homepage = "http://people.math.aau.dk/~sorenh/software/pbkrtest/"
+    url      = "https://cran.r-project.org/src/contrib/pbkrtest_0.4-6.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/pbkrtest"
+
+    version('0.4-6', '0a7d9ff83b8d131af9b2335f35781ef9')
+
+    extends('R')
+
+    depends_on('r-lme4', type=nolink)
+    depends_on('r-matrix', type=nolink)
+    depends_on('r-mass', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-pkgmaker/package.py b/var/spack/repos/builtin/packages/r-pkgmaker/package.py
new file mode 100644
index 0000000000..87daec5ad0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-pkgmaker/package.py
@@ -0,0 +1,53 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RPkgmaker(Package):
+    """This package provides some low-level utilities to use for package
+    development. It currently provides managers for multiple package specific
+    options and registries, vignette, unit test and bibtex related utilities.
+    It serves as a base package for packages like NMF, RcppOctave, doRNG, and
+    as an incubator package for other general purposes utilities, that will
+    eventually be packaged separately. It is still under heavy development and
+    changes in the interface(s) are more than likely to happen."""
+
+    homepage = "https://renozao.github.io/pkgmaker"
+    url      = "https://cran.r-project.org/src/contrib/pkgmaker_0.22.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/pkgmaker"
+
+    version('0.22', '73a0c6d3e84c6dadf3de7582ef7e88a4')
+
+    extends('R')
+
+    depends_on('r-registry', type=nolink)
+    depends_on('r-codetools', type=nolink)
+    depends_on('r-digest', type=nolink)
+    depends_on('r-stringr', type=nolink)
+    depends_on('r-xtable', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-plotrix/package.py b/var/spack/repos/builtin/packages/r-plotrix/package.py
new file mode 100644
index 0000000000..d1d61dbc4d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-plotrix/package.py
@@ -0,0 +1,41 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RPlotrix(Package):
+    """Lots of plots, various labeling, axis and color scaling functions."""
+
+    homepage = "https://cran.r-project.org/package=plotrix"
+    url      = "https://cran.r-project.org/src/contrib/plotrix_3.6-3.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/plotrix"
+
+    version('3.6-3', '23e3e022a13a596e9b77b40afcb4a2ef')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-plyr/package.py b/var/spack/repos/builtin/packages/r-plyr/package.py
index 192e7e8b18..fe4512347a 100644
--- a/var/spack/repos/builtin/packages/r-plyr/package.py
+++ b/var/spack/repos/builtin/packages/r-plyr/package.py
@@ -42,7 +42,7 @@ class RPlyr(Package):
 
     extends('R')
 
-    depends_on('r-rcpp')
+    depends_on('r-rcpp', type=nolink)
 
     def install(self, spec, prefix):
         R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
diff --git a/var/spack/repos/builtin/packages/r-png/package.py b/var/spack/repos/builtin/packages/r-png/package.py
new file mode 100644
index 0000000000..d3a80a4e16
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-png/package.py
@@ -0,0 +1,45 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RPng(Package):
+    """This package provides an easy and simple way to read, write and display
+    bitmap images stored in the PNG format. It can read and write both files
+    and in-memory raw vectors."""
+
+    homepage = "http://www.rforge.net/png/"
+    url      = "https://cran.r-project.org/src/contrib/png_0.1-7.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/png"
+
+    version('0.1-7', '1ebc8b8aa5979b12c5ec2384b30d649f')
+
+    extends('R')
+
+    depends_on('libpng')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-praise/package.py b/var/spack/repos/builtin/packages/r-praise/package.py
new file mode 100644
index 0000000000..102d86d2fa
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-praise/package.py
@@ -0,0 +1,41 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RPraise(Package):
+    """Build friendly R packages that praise their users if they have done
+    something good, or they just need it to feel better."""
+
+    homepage = "https://github.com/gaborcsardi/praise"
+    url      = "https://cran.r-project.org/src/contrib/praise_1.0.0.tar.gz"
+
+    version('1.0.0', '9318724cec0454884b5f762bee2da6a1')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-proto/package.py b/var/spack/repos/builtin/packages/r-proto/package.py
new file mode 100644
index 0000000000..07ace3ad29
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-proto/package.py
@@ -0,0 +1,42 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RProto(Package):
+    """An object oriented system using object-based, also called
+    prototype-based, rather than class-based object oriented ideas."""
+
+    homepage = "http://r-proto.googlecode.com/"
+    url      = "https://cran.r-project.org/src/contrib/proto_0.3-10.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/proto"
+
+    version('0.3-10', 'd5523943a5be6ca2f0ab557c900f8212')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-quantmod/package.py b/var/spack/repos/builtin/packages/r-quantmod/package.py
new file mode 100644
index 0000000000..ecfbf49055
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-quantmod/package.py
@@ -0,0 +1,46 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RQuantmod(Package):
+    """Specify, build, trade, and analyse quantitative financial trading
+    strategies."""
+
+    homepage = "http://www.quantmod.com/"
+    url      = "https://cran.r-project.org/src/contrib/quantmod_0.4-5.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/quantmod"
+
+    version('0.4-5', 'cab3c409e4de3df98a20f1ded60f3631')
+
+    extends('R')
+
+    depends_on('r-xts', type=nolink)
+    depends_on('r-zoo', type=nolink)
+    depends_on('r-ttr', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-quantreg/package.py b/var/spack/repos/builtin/packages/r-quantreg/package.py
new file mode 100644
index 0000000000..89a26070ba
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-quantreg/package.py
@@ -0,0 +1,50 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RQuantreg(Package):
+    """Estimation and inference methods for models of conditional quantiles:
+        Linear and nonlinear parametric and non-parametric (total variation
+        penalized) models for conditional quantiles of a univariate response
+        and several methods for handling censored survival data. Portfolio
+        selection methods based on expected shortfall risk are also
+        included."""
+
+    homepage = "https://cran.r-project.org/package=quantreg"
+    url      = "https://cran.r-project.org/src/contrib/quantreg_5.26.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/quantreg"
+
+    version('5.26', '1d89ed932fb4d67ae2d5da0eb8c2989f')
+
+    extends('R')
+
+    depends_on('r-sparsem', type=nolink)
+    depends_on('r-matrix', type=nolink)
+    depends_on('r-matrixmodels', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-randomforest/package.py b/var/spack/repos/builtin/packages/r-randomforest/package.py
new file mode 100644
index 0000000000..1066c217f4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-randomforest/package.py
@@ -0,0 +1,42 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RRandomforest(Package):
+    """Classification and regression based on a forest of trees using random
+    inputs."""
+
+    homepage = "https://www.stat.berkeley.edu/~breiman/RandomForests/"
+    url      = "https://cran.r-project.org/src/contrib/randomForest_4.6-12.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/randomForest"
+
+    version('4.6-12', '071c03af974198e861f1475c5bab9e7a')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-raster/package.py b/var/spack/repos/builtin/packages/r-raster/package.py
new file mode 100644
index 0000000000..39f4256703
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-raster/package.py
@@ -0,0 +1,46 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RRaster(Package):
+    """Reading, writing, manipulating, analyzing and modeling of gridded
+    spatial data. The package implements basic and high-level functions.
+    Processing of very large files is supported."""
+
+    homepage = "http://cran.r-project.org/package=raster"
+    url      = "https://cran.r-project.org/src/contrib/raster_2.5-8.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/raster"
+
+    version('2.5-8', '2a7db931c74d50516e82d04687c0a577')
+
+    extends('R')
+
+    depends_on('r-sp', type=nolink)
+    depends_on('r-rcpp', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-rcpp/package.py b/var/spack/repos/builtin/packages/r-rcpp/package.py
index 2428f4af3b..94580a8700 100644
--- a/var/spack/repos/builtin/packages/r-rcpp/package.py
+++ b/var/spack/repos/builtin/packages/r-rcpp/package.py
@@ -37,9 +37,10 @@ class RRcpp(Package):
     last two."""
 
     homepage = "http://dirk.eddelbuettel.com/code/rcpp.html"
-    url      = "https://cran.r-project.org/src/contrib/Rcpp_0.12.5.tar.gz"
+    url      = "https://cran.r-project.org/src/contrib/Rcpp_0.12.6.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/Rcpp"
 
+    version('0.12.6', 'db4280fb0a79cd19be73a662c33b0a8b')
     version('0.12.5', 'f03ec05b4e391cc46e7ce330e82ff5e2')
 
     extends('R')
diff --git a/var/spack/repos/builtin/packages/r-rcppeigen/package.py b/var/spack/repos/builtin/packages/r-rcppeigen/package.py
index 3175628a73..ecf9256ab3 100644
--- a/var/spack/repos/builtin/packages/r-rcppeigen/package.py
+++ b/var/spack/repos/builtin/packages/r-rcppeigen/package.py
@@ -48,8 +48,8 @@ class RRcppeigen(Package):
 
     extends('R')
 
-    depends_on('r-matrix')
-    depends_on('r-rcpp')
+    depends_on('r-matrix', type=nolink)
+    depends_on('r-rcpp', type=nolink)
 
     def install(self, spec, prefix):
         R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
diff --git a/var/spack/repos/builtin/packages/r-registry/package.py b/var/spack/repos/builtin/packages/r-registry/package.py
new file mode 100644
index 0000000000..119a84718a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-registry/package.py
@@ -0,0 +1,41 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RRegistry(Package):
+    """Provides a generic infrastructure for creating and using registries."""
+
+    homepage = "https://cran.r-project.org/web/packages/registry/index.html"
+    url      = "https://cran.r-project.org/src/contrib/registry_0.3.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/registry"
+
+    version('0.3', '85345b334ec81eb3da6edcbb27c5f421')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-reshape2/package.py b/var/spack/repos/builtin/packages/r-reshape2/package.py
index a96a314008..769e82aff9 100644
--- a/var/spack/repos/builtin/packages/r-reshape2/package.py
+++ b/var/spack/repos/builtin/packages/r-reshape2/package.py
@@ -37,9 +37,9 @@ class RReshape2(Package):
 
     extends('R')
 
-    depends_on('r-plyr')
-    depends_on('r-stringr')
-    depends_on('r-rcpp')
+    depends_on('r-plyr', type=nolink)
+    depends_on('r-stringr', type=nolink)
+    depends_on('r-rcpp', type=nolink)
 
     def install(self, spec, prefix):
         R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
diff --git a/var/spack/repos/builtin/packages/r-rgooglemaps/package.py b/var/spack/repos/builtin/packages/r-rgooglemaps/package.py
new file mode 100644
index 0000000000..0d28b68b94
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rgooglemaps/package.py
@@ -0,0 +1,47 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RRgooglemaps(Package):
+    """This package serves two purposes: (i) Provide a comfortable R interface
+    to query the Google server for static maps, and (ii) Use the map as a
+    background image to overlay plots within R. This requires proper coordinate
+    scaling."""
+
+    homepage = "https://cran.r-project.org/package=RgoogleMaps"
+    url      = "https://cran.r-project.org/src/contrib/RgoogleMaps_1.2.0.7.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/RgoogleMaps"
+
+    version('1.2.0.7', '2e1df804f0331b4122d841105f0c7ea5')
+
+    extends('R')
+
+    depends_on('r-png', type=nolink)
+    depends_on('r-rjsonio', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-rjava/package.py b/var/spack/repos/builtin/packages/r-rjava/package.py
index 0ce0942602..47804bd7fc 100644
--- a/var/spack/repos/builtin/packages/r-rjava/package.py
+++ b/var/spack/repos/builtin/packages/r-rjava/package.py
@@ -37,6 +37,8 @@ class RRjava(Package):
 
     extends('R')
 
+    depends_on('jdk')
+
     def install(self, spec, prefix):
         R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
           self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-rjson/package.py b/var/spack/repos/builtin/packages/r-rjson/package.py
new file mode 100644
index 0000000000..94ca45f485
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rjson/package.py
@@ -0,0 +1,41 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RRjson(Package):
+    """Converts R object into JSON objects and vice-versa."""
+
+    homepage = "https://cran.r-project.org/package=rjson"
+    url      = "https://cran.r-project.org/src/contrib/rjson_0.2.15.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/rjson"
+
+    version('0.2.15', '87d0e29bc179c6aeaf312b138089f8e9')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-rjsonio/package.py b/var/spack/repos/builtin/packages/r-rjsonio/package.py
new file mode 100644
index 0000000000..b56dfbe21d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rjsonio/package.py
@@ -0,0 +1,55 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RRjsonio(Package):
+    """This is a package that allows conversion to and from data in Javascript
+    object notation (JSON) format. This allows R objects to be inserted into
+    Javascript/ECMAScript/ActionScript code and allows R programmers to read
+    and convert JSON content to R objects. This is an alternative to rjson
+    package. Originally, that was too slow for converting large R objects to
+    JSON and was not extensible. rjson's performance is now similar to this
+    package, and perhaps slightly faster in some cases. This package uses
+    methods and is readily extensible by defining methods for different
+    classes, vectorized operations, and C code and callbacks to R functions for
+    deserializing JSON objects to R. The two packages intentionally share the
+    same basic interface. This package (RJSONIO) has many additional options to
+    allow customizing the generation and processing of JSON content. This
+    package uses libjson rather than implementing yet another JSON parser. The
+    aim is to support other general projects by building on their work,
+    providing feedback and benefit from their ongoing development."""
+
+    homepage = "https://cran.r-project.org/package=RJSONIO"
+    url      = "https://cran.r-project.org/src/contrib/RJSONIO_1.3-0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/RJSONIO"
+
+    version('1.3-0', '72c395622ba8d1435ec43849fd32c830')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-rmysql/package.py b/var/spack/repos/builtin/packages/r-rmysql/package.py
index 774c166f8b..bc42c51ca9 100644
--- a/var/spack/repos/builtin/packages/r-rmysql/package.py
+++ b/var/spack/repos/builtin/packages/r-rmysql/package.py
@@ -36,7 +36,7 @@ class RRmysql(Package):
 
     extends('R')
 
-    depends_on('r-DBI')
+    depends_on('r-dbi', type=nolink)
     depends_on('mariadb')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/r-rngtools/package.py b/var/spack/repos/builtin/packages/r-rngtools/package.py
new file mode 100644
index 0000000000..2f33cd9f88
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rngtools/package.py
@@ -0,0 +1,49 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RRngtools(Package):
+    """This package contains a set of functions for working with Random Number
+    Generators (RNGs). In particular, it defines a generic S4 framework for
+    getting/setting the current RNG, or RNG data that are embedded into objects
+    for reproducibility. Notably, convenient default methods greatly facilitate
+    the way current RNG settings can be changed."""
+
+    homepage = "https://renozao.github.io/rngtools"
+    url      = "https://cran.r-project.org/src/contrib/rngtools_1.2.4.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/rngtools"
+
+    version('1.2.4', '715967f8b3af2848a76593a7c718c1cd')
+
+    extends('R')
+
+    depends_on('r-pkgmaker', type=nolink)
+    depends_on('r-stringr', type=nolink)
+    depends_on('r-digest', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-rodbc/package.py b/var/spack/repos/builtin/packages/r-rodbc/package.py
index 9cc9aebd9a..11fe0ace56 100644
--- a/var/spack/repos/builtin/packages/r-rodbc/package.py
+++ b/var/spack/repos/builtin/packages/r-rodbc/package.py
@@ -36,7 +36,7 @@ class RRodbc(Package):
 
     extends('R')
 
-    depends_on('unixODBC')
+    depends_on('unixodbc')
 
     def install(self, spec, prefix):
         R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
diff --git a/var/spack/repos/builtin/packages/r-roxygen2/package.py b/var/spack/repos/builtin/packages/r-roxygen2/package.py
new file mode 100644
index 0000000000..4f4b8dcafa
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-roxygen2/package.py
@@ -0,0 +1,48 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RRoxygen2(Package):
+    """A 'Doxygen'-like in-source documentation system for Rd, collation, and
+    'NAMESPACE' files."""
+
+    homepage = "https://github.com/klutometis/roxygen"
+    url      = "https://cran.r-project.org/src/contrib/roxygen2_5.0.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/roxygen2"
+
+    version('5.0.1', 'df5bdbc12fda372e427710ef1cd92ed7')
+
+    extends('R')
+
+    depends_on('r-stringr', type=nolink)
+    depends_on('r-stringi', type=nolink)
+    depends_on('r-brew', type=nolink)
+    depends_on('r-digest', type=nolink)
+    depends_on('r-rcpp', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-rpostgresql/package.py b/var/spack/repos/builtin/packages/r-rpostgresql/package.py
index 83c9b85525..999fb4a1b9 100644
--- a/var/spack/repos/builtin/packages/r-rpostgresql/package.py
+++ b/var/spack/repos/builtin/packages/r-rpostgresql/package.py
@@ -44,7 +44,7 @@ class RRpostgresql(Package):
 
     extends('R')
 
-    depends_on('r-DBI')
+    depends_on('r-dbi', type=nolink)
     depends_on('postgresql')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/r-rsqlite/package.py b/var/spack/repos/builtin/packages/r-rsqlite/package.py
index 9602f6d927..c7d41f0fb3 100644
--- a/var/spack/repos/builtin/packages/r-rsqlite/package.py
+++ b/var/spack/repos/builtin/packages/r-rsqlite/package.py
@@ -38,7 +38,7 @@ class RRsqlite(Package):
 
     extends('R')
 
-    depends_on('r-DBI')
+    depends_on('r-dbi', type=nolink)
 
     def install(self, spec, prefix):
         R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
diff --git a/var/spack/repos/builtin/packages/r-rstan/package.py b/var/spack/repos/builtin/packages/r-rstan/package.py
index 00fd5116d9..1d0052563b 100644
--- a/var/spack/repos/builtin/packages/r-rstan/package.py
+++ b/var/spack/repos/builtin/packages/r-rstan/package.py
@@ -44,13 +44,13 @@ class RRstan(Package):
 
     extends('R')
 
-    depends_on('r-ggplot2')
-    depends_on('r-stanheaders')
-    depends_on('r-inline')
-    depends_on('r-gridextra')
-    depends_on('r-rcpp')
-    depends_on('r-rcppeigen')
-    depends_on('r-bh')
+    depends_on('r-ggplot2', type=nolink)
+    depends_on('r-stanheaders', type=nolink)
+    depends_on('r-inline', type=nolink)
+    depends_on('r-gridextra', type=nolink)
+    depends_on('r-rcpp', type=nolink)
+    depends_on('r-rcppeigen', type=nolink)
+    depends_on('r-bh', type=nolink)
 
     def install(self, spec, prefix):
         R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
diff --git a/var/spack/repos/builtin/packages/r-rstudioapi/package.py b/var/spack/repos/builtin/packages/r-rstudioapi/package.py
index 0ef2d9b987..bf9b35fe5b 100644
--- a/var/spack/repos/builtin/packages/r-rstudioapi/package.py
+++ b/var/spack/repos/builtin/packages/r-rstudioapi/package.py
@@ -33,6 +33,7 @@ class RRstudioapi(Package):
     url      = "https://cran.r-project.org/src/contrib/rstudioapi_0.5.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/rstudioapi"
 
+    version('0.6', 'fdb13bf46aab02421557e713fceab66b')
     version('0.5', '6ce1191da74e7bcbf06b61339486b3ba')
 
     extends('R')
diff --git a/var/spack/repos/builtin/packages/r-sandwich/package.py b/var/spack/repos/builtin/packages/r-sandwich/package.py
new file mode 100644
index 0000000000..ffd62b1b14
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-sandwich/package.py
@@ -0,0 +1,44 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RSandwich(Package):
+    """Model-robust standard error estimators for cross-sectional, time series,
+    and longitudinal data."""
+
+    homepage = "https://cran.r-project.org/package=sandwich"
+    url      = "https://cran.r-project.org/src/contrib/sandwich_2.3-4.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/sandwich"
+
+    version('2.3-4', 'a621dbd8a57b6e1e036496642aadc2e5')
+
+    extends('R')
+
+    depends_on('r-zoo', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-scales/package.py b/var/spack/repos/builtin/packages/r-scales/package.py
index 046a05d48e..44bd5a5a2a 100644
--- a/var/spack/repos/builtin/packages/r-scales/package.py
+++ b/var/spack/repos/builtin/packages/r-scales/package.py
@@ -37,12 +37,12 @@ class RScales(Package):
 
     extends('R')
 
-    depends_on('r-rcolorbrewer')
-    depends_on('r-dichromat')
-    depends_on('r-plyr')
-    depends_on('r-munsell')
-    depends_on('r-labeling')
-    depends_on('r-rcpp')
+    depends_on('r-rcolorbrewer', type=nolink)
+    depends_on('r-dichromat', type=nolink)
+    depends_on('r-plyr', type=nolink)
+    depends_on('r-munsell', type=nolink)
+    depends_on('r-labeling', type=nolink)
+    depends_on('r-rcpp', type=nolink)
 
     def install(self, spec, prefix):
         R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
diff --git a/var/spack/repos/builtin/packages/r-shiny/package.py b/var/spack/repos/builtin/packages/r-shiny/package.py
index a9a9532910..a80860f4a5 100644
--- a/var/spack/repos/builtin/packages/r-shiny/package.py
+++ b/var/spack/repos/builtin/packages/r-shiny/package.py
@@ -39,13 +39,13 @@ class RShiny(Package):
 
     extends('R')
 
-    depends_on('r-httpuv')
-    depends_on('r-mime')
-    depends_on('r-jsonlite')
-    depends_on('r-xtable')
-    depends_on('r-digest')
-    depends_on('r-htmltools')
-    depends_on('r-R6')
+    depends_on('r-httpuv', type=nolink)
+    depends_on('r-mime', type=nolink)
+    depends_on('r-jsonlite', type=nolink)
+    depends_on('r-xtable', type=nolink)
+    depends_on('r-digest', type=nolink)
+    depends_on('r-htmltools', type=nolink)
+    depends_on('r-R6', type=nolink)
 
     def install(self, spec, prefix):
         R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
diff --git a/var/spack/repos/builtin/packages/r-sp/package.py b/var/spack/repos/builtin/packages/r-sp/package.py
new file mode 100644
index 0000000000..bb7589d490
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-sp/package.py
@@ -0,0 +1,46 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RSp(Package):
+    """Classes and methods for spatial data; the classes document where the
+    spatial location information resides, for 2D or 3D data. Utility functions
+    are provided, e.g. for plotting data as maps, spatial selection, as well as
+    methods for retrieving coordinates, for subsetting, print, summary, etc."""
+
+    homepage = "https://github.com/edzer/sp/"
+    url      = "https://cran.r-project.org/src/contrib/sp_1.2-3.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/sp"
+
+    version('1.2-3', 'f0e24d993dec128642ee66b6b47b10c1')
+
+    extends('R')
+
+    depends_on('r-lattice', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-sparsem/package.py b/var/spack/repos/builtin/packages/r-sparsem/package.py
new file mode 100644
index 0000000000..c4dabf5c15
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-sparsem/package.py
@@ -0,0 +1,43 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RSparsem(Package):
+    """Some basic linear algebra functionality for sparse matrices is provided:
+        including Cholesky decomposition and backsolving as well as standard R
+        subsetting and Kronecker products."""
+
+    homepage = "http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html"
+    url      = "https://cran.r-project.org/src/contrib/SparseM_1.7.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/SparseM"
+
+    version('1.7', '7b5b0ab166a0929ef6dcfe1d97643601')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-stringr/package.py b/var/spack/repos/builtin/packages/r-stringr/package.py
index 01fd969522..08ded95833 100644
--- a/var/spack/repos/builtin/packages/r-stringr/package.py
+++ b/var/spack/repos/builtin/packages/r-stringr/package.py
@@ -40,8 +40,8 @@ class RStringr(Package):
 
     extends('R')
 
-    depends_on('r-stringi')
-    depends_on('r-magrittr')
+    depends_on('r-stringi', type=nolink)
+    depends_on('r-magrittr', type=nolink)
 
     def install(self, spec, prefix):
         R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
diff --git a/var/spack/repos/builtin/packages/r-survey/package.py b/var/spack/repos/builtin/packages/r-survey/package.py
new file mode 100644
index 0000000000..646793f7a4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-survey/package.py
@@ -0,0 +1,47 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RSurvey(Package):
+    """Summary statistics, two-sample tests, rank tests, generalised linear
+    models, cumulative link models, Cox models, loglinear models, and general
+    maximum pseudolikelihood estimation for multistage stratified,
+    cluster-sampled, unequally weighted survey samples. Variances by Taylor
+    series linearisation or replicate weights. Post-stratification,
+    calibration, and raking. Two-phase subsampling designs. Graphics. PPS
+    sampling without replacement. Principal components, factor analysis."""
+
+    homepage = "http://r-survey.r-forge.r-project.org/survey/"
+    url      = "https://cran.r-project.org/src/contrib/survey_3.30-3.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/survey"
+
+    version('3.30-3', 'c70cdae9cb43d35abddd11173d64cad0')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-survival/package.py b/var/spack/repos/builtin/packages/r-survival/package.py
new file mode 100644
index 0000000000..cfba9298fe
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-survival/package.py
@@ -0,0 +1,45 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RSurvival(Package):
+    """Contains the core survival analysis routines, including definition of
+    Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox
+    models, and parametric accelerated failure time models."""
+
+    homepage = "https://cran.r-project.org/package=survival"
+    url      = "https://cran.r-project.org/src/contrib/survival_2.39-5.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/survival"
+
+    version('2.39-5', 'a3cc6b5762e8c5c0bb9e64a276710be2')
+
+    extends('R')
+
+    depends_on('r-matrix', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-tarifx/package.py b/var/spack/repos/builtin/packages/r-tarifx/package.py
new file mode 100644
index 0000000000..a85aa8baef
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-tarifx/package.py
@@ -0,0 +1,44 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RTarifx(Package):
+    """A collection of various utility and convenience functions."""
+
+    homepage = "https://cran.r-project.org/package=taRifx"
+    url      = "https://cran.r-project.org/src/contrib/taRifx_1.0.6.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/taRifx"
+
+    version('1.0.6', '7e782e04bd69d929b29f91553382e6a2')
+
+    extends('R')
+
+    depends_on('r-reshape2', type=nolink)
+    depends_on('r-plyr', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-testthat/package.py b/var/spack/repos/builtin/packages/r-testthat/package.py
new file mode 100644
index 0000000000..60dfd2afcd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-testthat/package.py
@@ -0,0 +1,48 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RTestthat(Package):
+    """A unit testing system designed to be fun, flexible and easy to set
+    up."""
+
+    homepage = "https://github.com/hadley/testthat"
+    url      = "https://cran.r-project.org/src/contrib/testthat_1.0.2.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/testthat"
+
+    version('1.0.2', '6c6a90c8db860292df5784a70e07b8dc')
+
+    extends('R')
+
+    depends_on('r-digest', type=nolink)
+    depends_on('r-crayon', type=nolink)
+    depends_on('r-praise', type=nolink)
+    depends_on('r-magrittr', type=nolink)
+    depends_on('r-R6', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-thdata/package.py b/var/spack/repos/builtin/packages/r-thdata/package.py
new file mode 100644
index 0000000000..e1cf050181
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-thdata/package.py
@@ -0,0 +1,44 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RThdata(Package):
+    """Contains data sets used in other packages Torsten Hothorn maintains."""
+
+    homepage = "https://cran.r-project.org/package=TH.data"
+    url      = "https://cran.r-project.org/src/contrib/TH.data_1.0-7.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/TH.data"
+
+    version('1.0-7', '3e8b6b1a4699544f175215aed7039a94')
+
+    extends('R')
+
+    depends_on('r-survival', type=nolink)
+    depends_on('r-mass', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-threejs/package.py b/var/spack/repos/builtin/packages/r-threejs/package.py
new file mode 100644
index 0000000000..89ecce8bfc
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-threejs/package.py
@@ -0,0 +1,47 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RThreejs(Package):
+    """Create interactive 3D scatter plots, network plots, and globes using the
+    'three.js' visualization library ("http://threejs.org")."""
+
+    homepage = "http://bwlewis.github.io/rthreejs"
+    url      = "https://cran.r-project.org/src/contrib/threejs_0.2.2.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/threejs"
+
+    version('0.2.2', '35c179b10813c5e4bd3e7827fae6627b')
+
+    extends('R')
+
+    depends_on('r-htmlwidgets', type=nolink)
+    depends_on('r-base64enc', type=nolink)
+    depends_on('r-matrix', type=nolink)
+    depends_on('r-jsonlite', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-tibble/package.py b/var/spack/repos/builtin/packages/r-tibble/package.py
index 837c3df603..c601de3c88 100644
--- a/var/spack/repos/builtin/packages/r-tibble/package.py
+++ b/var/spack/repos/builtin/packages/r-tibble/package.py
@@ -37,9 +37,9 @@ class RTibble(Package):
 
     extends('R')
 
-    depends_on('r-assertthat')
-    depends_on('r-lazyeval')
-    depends_on('r-rcpp')
+    depends_on('r-assertthat', type=nolink)
+    depends_on('r-lazyeval', type=nolink)
+    depends_on('r-rcpp', type=nolink)
 
     def install(self, spec, prefix):
         R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
diff --git a/var/spack/repos/builtin/packages/r-tidyr/package.py b/var/spack/repos/builtin/packages/r-tidyr/package.py
index 2db7b174c2..d82ae278fe 100644
--- a/var/spack/repos/builtin/packages/r-tidyr/package.py
+++ b/var/spack/repos/builtin/packages/r-tidyr/package.py
@@ -37,12 +37,12 @@ class RTidyr(Package):
     version('0.5.1', '3cadc869510c054ed93d374ab44120bd')
 
     extends('R')
-    depends_on('r-tibble')
-    depends_on('r-dplyr')
-    depends_on('r-stringi')
-    depends_on('r-lazyeval')
-    depends_on('r-magrittr')
-    depends_on('r-rcpp')
+    depends_on('r-tibble', type=nolink)
+    depends_on('r-dplyr', type=nolink)
+    depends_on('r-stringi', type=nolink)
+    depends_on('r-lazyeval', type=nolink)
+    depends_on('r-magrittr', type=nolink)
+    depends_on('r-rcpp', type=nolink)
 
     def install(self, spec, prefix):
         R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
diff --git a/var/spack/repos/builtin/packages/r-ttr/package.py b/var/spack/repos/builtin/packages/r-ttr/package.py
new file mode 100644
index 0000000000..c9b40a8262
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-ttr/package.py
@@ -0,0 +1,44 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RTtr(Package):
+    """Functions and data to construct technical trading rules with R."""
+
+    homepage = "https://github.com/joshuaulrich/TTR"
+    url      = "https://cran.r-project.org/src/contrib/TTR_0.23-1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/TTR"
+
+    version('0.23-1', '35f693ac0d97e8ec742ebea2da222986')
+
+    extends('R')
+
+    depends_on('r-xts', type=nolink)
+    depends_on('r-zoo', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-vcd/package.py b/var/spack/repos/builtin/packages/r-vcd/package.py
new file mode 100644
index 0000000000..06e609b1ef
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-vcd/package.py
@@ -0,0 +1,50 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RVcd(Package):
+    """Visualization techniques, data sets, summary and inference procedures
+    aimed particularly at categorical data. Special emphasis is given to highly
+    extensible grid graphics. The package was package was originally inspired
+    by the book "Visualizing Categorical Data" by Michael Friendly and is now
+    the main support package for a new book, "Discrete Data Analysis with R" by
+    Michael Friendly and David Meyer (2015)."""
+
+    homepage = "https://cran.r-project.org/package=vcd"
+    url      = "https://cran.r-project.org/src/contrib/vcd_1.4-1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/vcd"
+
+    version('1.4-1', '7db150a77f173f85b69a1f86f73f8f02')
+
+    extends('R')
+
+    depends_on('r-mass', type=nolink)
+    depends_on('r-colorspace', type=nolink)
+    depends_on('r-lmtest', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-visnetwork/package.py b/var/spack/repos/builtin/packages/r-visnetwork/package.py
new file mode 100644
index 0000000000..90d55bbb2f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-visnetwork/package.py
@@ -0,0 +1,47 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RVisnetwork(Package):
+    """Provides an R interface to the 'vis.js' JavaScript charting library. It
+    allows an interactive visualization of networks."""
+
+    homepage = "https://github.com/datastorm-open/visNetwork"
+    url      = "https://cran.r-project.org/src/contrib/visNetwork_1.0.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/visNetwork"
+
+    version('1.0.1', 'dfc9664a5165134d8dbdcd949ad73cf7')
+
+    extends('R')
+
+    depends_on('r-htmlwidgets', type=nolink)
+    depends_on('r-htmltools', type=nolink)
+    depends_on('r-jsonlite', type=nolink)
+    depends_on('r-magrittr', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-xlconnect/package.py b/var/spack/repos/builtin/packages/r-xlconnect/package.py
index 919291a023..332c80fb92 100644
--- a/var/spack/repos/builtin/packages/r-xlconnect/package.py
+++ b/var/spack/repos/builtin/packages/r-xlconnect/package.py
@@ -33,12 +33,13 @@ class RXlconnect(Package):
     url      = "https://cran.r-project.org/src/contrib/XLConnect_0.2-11.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/XLConnect"
 
+    version('0.2-12', '3340d05d259f0a41262eab4ed32617ad')
     version('0.2-11', '9d1769a103cda05665df399cc335017d')
 
     extends('R')
 
-    depends_on('r-XLConnectJars')
-    depends_on('r-rJava')
+    depends_on('r-xlconnectjars', type=nolink)
+    depends_on('r-rjava', type=nolink)
 
     def install(self, spec, prefix):
         R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
diff --git a/var/spack/repos/builtin/packages/r-xlconnectjars/package.py b/var/spack/repos/builtin/packages/r-xlconnectjars/package.py
index 15d08cc5af..26e822d2b7 100644
--- a/var/spack/repos/builtin/packages/r-xlconnectjars/package.py
+++ b/var/spack/repos/builtin/packages/r-xlconnectjars/package.py
@@ -32,11 +32,12 @@ class RXlconnectjars(Package):
     url      = "https://cran.r-project.org/src/contrib/XLConnectJars_0.2-9.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/XLConnectJars"
 
+    version('0.2-12', '6984e5140cd1c887c017ef6f88cbba81')
     version('0.2-9', 'e6d6b1acfede26acaa616ee421bd30fb')
 
     extends('R')
 
-    depends_on('r-rJava')
+    depends_on('r-rjava', type=nolink)
 
     def install(self, spec, prefix):
         R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
diff --git a/var/spack/repos/builtin/packages/r-xlsx/package.py b/var/spack/repos/builtin/packages/r-xlsx/package.py
index 0aac6cdd1f..6fed09296d 100644
--- a/var/spack/repos/builtin/packages/r-xlsx/package.py
+++ b/var/spack/repos/builtin/packages/r-xlsx/package.py
@@ -37,8 +37,8 @@ class RXlsx(Package):
 
     extends('R')
 
-    depends_on('r-rJava')
-    depends_on('r-xlsxjars')
+    depends_on('r-rjava', type=nolink)
+    depends_on('r-xlsxjars', type=nolink)
 
     def install(self, spec, prefix):
         R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
diff --git a/var/spack/repos/builtin/packages/r-xlsxjars/package.py b/var/spack/repos/builtin/packages/r-xlsxjars/package.py
index cff6e7427e..19f0006ce9 100644
--- a/var/spack/repos/builtin/packages/r-xlsxjars/package.py
+++ b/var/spack/repos/builtin/packages/r-xlsxjars/package.py
@@ -37,7 +37,7 @@ class RXlsxjars(Package):
 
     extends('R')
 
-    depends_on('r-rJava')
+    depends_on('r-rjava', type=nolink)
 
     def install(self, spec, prefix):
         R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
diff --git a/var/spack/repos/builtin/packages/r-xml/package.py b/var/spack/repos/builtin/packages/r-xml/package.py
new file mode 100644
index 0000000000..591c887f32
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-xml/package.py
@@ -0,0 +1,45 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RXml(Package):
+    """Many approaches for both reading and creating XML (and HTML) documents
+    (including DTDs), both local and accessible via HTTP or FTP. Also offers
+    access to an 'XPath' "interpreter"."""
+
+    homepage = "http://www.omegahat.net/RSXML"
+    url      = "https://cran.r-project.org/src/contrib/XML_3.98-1.4.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/XML"
+
+    version('3.98-1', '1a7f3ce6f264eeb109bfa57bedb26c14')
+
+    extends('R')
+
+    depends_on('libxml2')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-xts/package.py b/var/spack/repos/builtin/packages/r-xts/package.py
new file mode 100644
index 0000000000..d8a4b62d27
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-xts/package.py
@@ -0,0 +1,46 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RXts(Package):
+    """Provide for uniform handling of R's different time-based data classes by
+    extending zoo, maximizing native format information preservation and
+    allowing for user level customization and extension, while simplifying
+    cross-class interoperability."""
+
+    homepage = "http://r-forge.r-project.org/projects/xts/"
+    url      = "https://cran.r-project.org/src/contrib/xts_0.9-7.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/xts"
+
+    version('0.9-7', 'a232e94aebfa654653a7d88a0503537b')
+
+    extends('R')
+
+    depends_on('r-zoo', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-yaml/package.py b/var/spack/repos/builtin/packages/r-yaml/package.py
new file mode 100644
index 0000000000..b68f26e9b8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-yaml/package.py
@@ -0,0 +1,42 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RYaml(Package):
+    """This package implements the libyaml YAML 1.1 parser and emitter
+    (http://pyyaml.org/wiki/LibYAML) for R."""
+
+    homepage = "https://cran.r-project.org/web/packages/yaml/index.html"
+    url      = "https://cran.r-project.org/src/contrib/yaml_2.1.13.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/yaml"
+
+    version('2.1.13', 'f2203ea395adaff6bd09134666191d9a')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-zoo/package.py b/var/spack/repos/builtin/packages/r-zoo/package.py
new file mode 100644
index 0000000000..d889cacbee
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-zoo/package.py
@@ -0,0 +1,47 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RZoo(Package):
+    """An S3 class with methods for totally ordered indexed observations. It is
+    particularly aimed at irregular time series of numeric vectors/matrices and
+    factors. zoo's key design goals are independence of a particular
+    index/date/time class and consistency with ts and base R by providing
+    methods to extend standard generics."""
+
+    homepage = "http://zoo.r-forge.r-project.org/"
+    url      = "https://cran.r-project.org/src/contrib/zoo_1.7-13.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/zoo"
+
+    version('1.7-13', '99521dfa4c668e692720cefcc5a1bf30')
+
+    extends('R')
+
+    depends_on('r-lattice', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/raja/package.py b/var/spack/repos/builtin/packages/raja/package.py
index b6300a1dfa..e9db4b4fc8 100644
--- a/var/spack/repos/builtin/packages/raja/package.py
+++ b/var/spack/repos/builtin/packages/raja/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Raja(Package):
     """RAJA Parallel Framework."""
     homepage = "http://software.llnl.gov/RAJA/"
@@ -31,6 +32,6 @@ class Raja(Package):
     version('git', git='https://github.com/LLNL/RAJA.git', branch="master")
 
     def install(self, spec, prefix):
-            cmake('.',*std_cmake_args)
-            make()
-            make('install')
+        cmake('.', *std_cmake_args)
+        make()
+        make('install')
diff --git a/var/spack/repos/builtin/packages/ravel/package.py b/var/spack/repos/builtin/packages/ravel/package.py
index 96692ac7c1..4f4f2b2e10 100644
--- a/var/spack/repos/builtin/packages/ravel/package.py
+++ b/var/spack/repos/builtin/packages/ravel/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Ravel(Package):
     """Ravel is a parallel communication trace visualization tool that
        orders events according to logical time."""
diff --git a/var/spack/repos/builtin/packages/readline/package.py b/var/spack/repos/builtin/packages/readline/package.py
index 039bf725eb..abb6ba04ce 100644
--- a/var/spack/repos/builtin/packages/readline/package.py
+++ b/var/spack/repos/builtin/packages/readline/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Readline(Package):
     """The GNU Readline library provides a set of functions for use by
        applications that allow users to edit command lines as they
diff --git a/var/spack/repos/builtin/packages/rose/package.py b/var/spack/repos/builtin/packages/rose/package.py
index bcd317eb8f..02b09f0126 100644
--- a/var/spack/repos/builtin/packages/rose/package.py
+++ b/var/spack/repos/builtin/packages/rose/package.py
@@ -22,12 +22,13 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-#------------------------------------------------------------------------------
+# -----------------------------------------------------------------------------
 # Author: Justin Too <too1@llnl.gov>
-#------------------------------------------------------------------------------
+# -----------------------------------------------------------------------------
 
 from spack import *
 
+
 class Rose(Package):
     """A compiler infrastructure to build source-to-source program
        transformation and analysis tools.
@@ -36,7 +37,8 @@ class Rose(Package):
     homepage = "http://rosecompiler.org/"
     url      = "https://github.com/rose-compiler/edg4x-rose"
 
-    version('master', branch='master', git='https://github.com/rose-compiler/edg4x-rose.git')
+    version('master', branch='master',
+            git='https://github.com/rose-compiler/edg4x-rose.git')
 
     patch('add_spack_compiler_recognition.patch')
 
@@ -60,4 +62,3 @@ class Rose(Package):
                       "--with-boost=" + boost.prefix,
                       "--disable-boost-version-check")
             make("install-core")
-
diff --git a/var/spack/repos/builtin/packages/rsync/package.py b/var/spack/repos/builtin/packages/rsync/package.py
index a9f8d4cfda..4e741b255f 100644
--- a/var/spack/repos/builtin/packages/rsync/package.py
+++ b/var/spack/repos/builtin/packages/rsync/package.py
@@ -24,8 +24,9 @@
 ##############################################################################
 from spack import *
 
+
 class Rsync(Package):
-    """rsync is an open source utility that provides fast incremental file transfer."""
+    """An open source utility that provides fast incremental file transfer."""
     homepage = "https://rsync.samba.org"
     url      = "https://download.samba.org/pub/rsync/rsync-3.1.1.tar.gz"
 
diff --git a/var/spack/repos/builtin/packages/rust/package.py b/var/spack/repos/builtin/packages/rust/package.py
index 65f81ce534..629dfb4649 100644
--- a/var/spack/repos/builtin/packages/rust/package.py
+++ b/var/spack/repos/builtin/packages/rust/package.py
@@ -6,6 +6,7 @@ def get_submodules():
     git = which('git')
     git('submodule', 'update', '--init', '--recursive')
 
+
 class Rust(Package):
     """The rust programming language toolchain"""
     homepage = "http://www.rust-lang.org"
diff --git a/var/spack/repos/builtin/packages/samtools/package.py b/var/spack/repos/builtin/packages/samtools/package.py
index f5c7f4431f..6b0b224785 100644
--- a/var/spack/repos/builtin/packages/samtools/package.py
+++ b/var/spack/repos/builtin/packages/samtools/package.py
@@ -24,19 +24,27 @@
 ##############################################################################
 from spack import *
 
+
 class Samtools(Package):
-    """SAM Tools provide various utilities for manipulating alignments in the SAM format, 
-       including sorting, merging, indexing and generating
+    """SAM Tools provide various utilities for manipulating alignments in
+       the SAM format, including sorting, merging, indexing and generating
        alignments in a per-position format"""
 
     homepage = "www.htslib.org"
-    version('1.2','988ec4c3058a6ceda36503eebecd4122',url = "https://github.com/samtools/samtools/releases/download/1.2/samtools-1.2.tar.bz2")
+    url = "https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2"
 
-    depends_on("zlib")
-    depends_on("mpc")
-    parallel=False
-    patch("samtools1.2.patch",level=0)
+    version('1.3.1', 'a7471aa5a1eb7fc9cc4c6491d73c2d88')
+    version('1.2', '988ec4c3058a6ceda36503eebecd4122')
 
-    def install(self, spec, prefix):
-        make("prefix=%s" % prefix, "install")
+    depends_on("ncurses")
+    depends_on("htslib", when='@1.3.1:')  # htslib became standalone
+    depends_on('zlib', when='@1.2')       # needed for builtin htslib
 
+    def install(self, spec, prefix):
+        if self.spec.version >= Version('1.3.1'):
+            configure('--prefix={0}'.format(prefix), '--with-ncurses')
+            make()
+            make('install')
+        else:
+            make("prefix=%s" % prefix)
+            make("prefix=%s" % prefix, "install")
diff --git a/var/spack/repos/builtin/packages/samtools/samtools1.2.patch b/var/spack/repos/builtin/packages/samtools/samtools1.2.patch
deleted file mode 100644
index ead3ab4e2c..0000000000
--- a/var/spack/repos/builtin/packages/samtools/samtools1.2.patch
+++ /dev/null
@@ -1,20 +0,0 @@
---- Makefile	2015-02-03 08:27:34.000000000 -0800
-+++ Makefile.new	2015-07-21 10:38:27.881406892 -0700
-@@ -26,7 +26,7 @@
- CFLAGS   = -g -Wall -O2
- LDFLAGS  =
- LDLIBS   =
--DFLAGS=     -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1
-+DFLAGS=     -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0
- LOBJS=      bam_aux.o bam.o bam_import.o sam.o \
-             sam_header.o bam_plbuf.o
- AOBJS=      bam_index.o bam_plcmd.o sam_view.o \
-@@ -37,7 +37,7 @@
-             faidx.o stats.o stats_isize.o bam_flags.o bam_split.o \
-             bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o
- INCLUDES=   -I. -I$(HTSDIR)
--LIBCURSES=  -lcurses # -lXCurses
-+#LIBCURSES=  -lcurses # -lXCurses
- 
- prefix      = /usr/local
- exec_prefix = $(prefix)
diff --git a/var/spack/repos/builtin/packages/scalasca/package.py b/var/spack/repos/builtin/packages/scalasca/package.py
index 98e43ee75a..228d814aed 100644
--- a/var/spack/repos/builtin/packages/scalasca/package.py
+++ b/var/spack/repos/builtin/packages/scalasca/package.py
@@ -27,10 +27,12 @@ from spack import *
 
 
 class Scalasca(Package):
-    """
-    Scalasca is a software tool that supports the performance optimization of parallel programs by measuring and
-    analyzing their runtime behavior. The analysis identifies potential performance bottlenecks - in particular those
-    concerning communication and synchronization - and offers guidance in exploring their causes.
+    """Scalasca is a software tool that supports the performance optimization
+       of parallel programs by measuring and analyzing their runtime
+       behavior. The analysis identifies potential performance
+       bottlenecks - in particular those concerning communication and
+       synchronization - and offers guidance in exploring their causes.
+
     """
 
     homepage = "http://www.scalasca.org"
@@ -44,7 +46,8 @@ class Scalasca(Package):
 
     depends_on("mpi")
     ##########
-    # Hard-code dependencies for Scalasca according to what stated in the release page
+    # Hard-code dependencies for Scalasca according to what stated in the
+    # release page
     # The OTF2 library path should be detected automatically from SCOREP
     # SCALASCA 2.2.2
     depends_on("scorep@1.4:", when='@2.2.2')
@@ -60,4 +63,4 @@ class Scalasca(Package):
                           "--enable-shared"]
         configure(*configure_args)
         make()
-        make("install")
\ No newline at end of file
+        make("install")
diff --git a/var/spack/repos/builtin/packages/scons/package.py b/var/spack/repos/builtin/packages/scons/package.py
index 40ae4176dd..2c32bde4a1 100644
--- a/var/spack/repos/builtin/packages/scons/package.py
+++ b/var/spack/repos/builtin/packages/scons/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Scons(Package):
     """SCons is a software construction tool"""
     homepage = "http://scons.org"
diff --git a/var/spack/repos/builtin/packages/scorep/package.py b/var/spack/repos/builtin/packages/scorep/package.py
index 633511a15a..d40e08740f 100644
--- a/var/spack/repos/builtin/packages/scorep/package.py
+++ b/var/spack/repos/builtin/packages/scorep/package.py
@@ -28,20 +28,28 @@ from spack import *
 
 class Scorep(Package):
     """
-    The Score-P measurement infrastructure is a highly scalable and easy-to-use tool suite for profiling, event
-    tracing, and online analysis of HPC applications.
+    The Score-P measurement infrastructure is a highly scalable and easy-to-use
+    tool suite for profiling, event tracing, and online analysis of HPC
+    applications.
     """
 
     homepage = "http://www.vi-hps.org/projects/score-p"
     url      = "http://www.vi-hps.org/upload/packages/scorep/scorep-1.2.3.tar.gz"
 
+    version('2.0.2', '8f00e79e1b5b96e511c5ebecd10b2888',
+            url='http://www.vi-hps.org/upload/packages/scorep/scorep-2.0.2.tar.gz')
     version('1.4.2', '3b9a042b13bdd5836452354e6567f71e',
             url='http://www.vi-hps.org/upload/packages/scorep/scorep-1.4.2.tar.gz')
     version('1.3', '9db6f957b7f51fa01377a9537867a55c',
             url='http://www.vi-hps.org/upload/packages/scorep/scorep-1.3.tar.gz')
 
     ##########
-    # Dependencies for SCORE-P are quite tight. See the homepage for more information.
+    # Dependencies for SCORE-P are quite tight. See the homepage for more
+    # information.
+    # SCOREP 2.0.2
+    depends_on('otf2@2.0', when='@2.0.2')
+    depends_on('opari2@2.0', when='@2.0.2')
+    depends_on('cube@4.3:4.4', when='@2.0.2')
     # SCOREP 1.4.2
     depends_on('otf2@1.5:1.6', when='@1.4.2')
     depends_on('opari2@1.1.4', when='@1.4.2')
@@ -56,17 +64,18 @@ class Scorep(Package):
     depends_on("papi")
 
     def install(self, spec, prefix):
-        configure = Executable( join_path(self.stage.source_path, 'configure') )
+        configure = Executable(join_path(self.stage.source_path, 'configure'))
         with working_dir('spack-build', create=True):
-            configure_args = ["--prefix=%s" % prefix,
-                              "--with-otf2=%s" % spec['otf2'].prefix.bin,
-                              "--with-opari2=%s" % spec['opari2'].prefix.bin,
-                              "--with-cube=%s" % spec['cube'].prefix.bin,
-                              "--with-papi-header=%s" % spec['papi'].prefix.include,
-                              "--with-papi-lib=%s" % spec['papi'].prefix.lib,
-                              "--enable-shared",
-                              "CFLAGS=-fPIC",
-                              "CXXFLAGS=-fPIC"]
+            configure_args = [
+                "--prefix=%s" % prefix,
+                "--with-otf2=%s" % spec['otf2'].prefix.bin,
+                "--with-opari2=%s" % spec['opari2'].prefix.bin,
+                "--with-cube=%s" % spec['cube'].prefix.bin,
+                "--with-papi-header=%s" % spec['papi'].prefix.include,
+                "--with-papi-lib=%s" % spec['papi'].prefix.lib,
+                "--enable-shared",
+                "CFLAGS=-fPIC",
+                "CXXFLAGS=-fPIC"]
             configure(*configure_args)
             make()
             make("install")
diff --git a/var/spack/repos/builtin/packages/scotch/package.py b/var/spack/repos/builtin/packages/scotch/package.py
index c2bad20c2f..94a323ce90 100644
--- a/var/spack/repos/builtin/packages/scotch/package.py
+++ b/var/spack/repos/builtin/packages/scotch/package.py
@@ -39,11 +39,16 @@ class Scotch(Package):
     version('6.0.0', 'c50d6187462ba801f9a82133ee666e8e')
     version('5.1.10b', 'f587201d6cf5cf63527182fbfba70753')
 
-    variant('mpi', default=False, description='Activate the compilation of parallel libraries')
-    variant('compression', default=True, description='Activate the posibility to use compressed files')
-    variant('esmumps', default=False, description='Activate the compilation of esmumps needed by mumps')
-    variant('shared', default=True, description='Build a shared version of the library')
-    variant('metis', default=True, description='Build metis and parmetis wrapper libraries')
+    variant('mpi', default=False,
+            description='Activate the compilation of parallel libraries')
+    variant('compression', default=True,
+            description='Activate the posibility to use compressed files')
+    variant('esmumps', default=False,
+            description='Activate the compilation of esmumps needed by mumps')
+    variant('shared', default=True,
+            description='Build a shared version of the library')
+    variant('metis', default=True,
+            description='Build metis and parmetis wrapper libraries')
 
     depends_on('flex', type='build')
     depends_on('bison', type='build')
diff --git a/var/spack/repos/builtin/packages/scr/package.py b/var/spack/repos/builtin/packages/scr/package.py
index b638688e7b..2b01c60b3e 100644
--- a/var/spack/repos/builtin/packages/scr/package.py
+++ b/var/spack/repos/builtin/packages/scr/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Scr(Package):
     """SCR caches checkpoint data in storage on the compute nodes of a
        Linux cluster to provide a fast, scalable checkpoint/restart
@@ -34,8 +35,10 @@ class Scr(Package):
     depends_on("mpi")
 #    depends_on("dtcmp")
 
-    version('1.1-7', 'a5930e9ab27d1b7049447c2fd7734ebd', url='http://downloads.sourceforge.net/project/scalablecr/releases/scr-1.1-7.tar.gz')
-    version('1.1.8', '6a0f11ad18e27fcfc00a271ff587b06e', url='https://github.com/hpc/scr/releases/download/v1.1.8/scr-1.1.8.tar.gz')
+    version('1.1-7', 'a5930e9ab27d1b7049447c2fd7734ebd',
+            url='http://downloads.sourceforge.net/project/scalablecr/releases/scr-1.1-7.tar.gz')
+    version('1.1.8', '6a0f11ad18e27fcfc00a271ff587b06e',
+            url='https://github.com/hpc/scr/releases/download/v1.1.8/scr-1.1.8.tar.gz')
 
     def install(self, spec, prefix):
         configure("--prefix=" + prefix,
diff --git a/var/spack/repos/builtin/packages/screen/package.py b/var/spack/repos/builtin/packages/screen/package.py
new file mode 100644
index 0000000000..17335603e6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/screen/package.py
@@ -0,0 +1,59 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Screen(Package):
+    """
+    Screen is a full-screen window manager that multiplexes a physical
+    terminal between several processes, typically interactive shells.
+    """
+
+    homepage = "https://www.gnu.org/software/screen/"
+    url      = "http://ftp.gnu.org/gnu/screen/screen-4.3.1.tar.gz"
+
+    version('4.3.1', '5bb3b0ff2674e29378c31ad3411170ad')
+    version('4.3.0', 'f76d28eadc4caaf6cdff00685ae6ad46')
+    version('4.2.1', '419a0594e2b25039239af8b90eda7d92')
+    version('4.2.0', 'e5199156a8ac863bbf92495a7638b612')
+    version('4.0.3', '8506fd205028a96c741e4037de6e3c42')
+    version('4.0.2', 'ed68ea9b43d9fba0972cb017a24940a1')
+    version('3.9.15', '0dff6fdc3fbbceabf25a43710fbfe75f')
+    version('3.9.11', '19572f92404995e7b2dea8117204dd67')
+    version('3.9.10', 'bbe271715d1dee038b3cd72d6d2f05fb')
+    version('3.9.9', '9a8b1d6c7438c64b884c4f7d7662afdc')
+    version('3.9.8', '8ddfebe32c2d45410ce89ea9779bb1cf')
+    version('3.9.4', '7de72cd18f7adcdf993ecc6764d0478a')
+    version('3.7.6', '9a353b828d79c3c143109265cae663a7')
+    version('3.7.4', 'c5ab40b068968075e41e25607dfce543')
+    version('3.7.2', '2d6db5de7fb0cf849cc5a6f94203f029')
+    version('3.7.1', '27cdd29318446561ef7c966041cbd2c9')
+
+    depends_on('ncurses')
+
+    def install(self, spec, prefix):
+        configure('--prefix=%s' % prefix)
+        make()
+        make("install")
diff --git a/var/spack/repos/builtin/packages/seqtk/package.py b/var/spack/repos/builtin/packages/seqtk/package.py
new file mode 100644
index 0000000000..ca168c176c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/seqtk/package.py
@@ -0,0 +1,43 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Seqtk(Package):
+    """Toolkit for processing sequences in FASTA/Q formats."""
+
+    homepage = "https://github.com/lh3/seqtk"
+    url      = "https://github.com/lh3/seqtk/archive/v1.1.tar.gz"
+
+    version('1.2', '255ffe05bf2f073dc57abcff97f11a37')
+    version('1.1', 'ebf5cc57698a217150c2250494e039a2')
+
+    depends_on('zlib')
+
+    def install(self, spec, prefix):
+        make()
+        mkdirp(prefix.bin)
+        install('seqtk', prefix.bin)
+        set_executable(join_path(prefix.bin, 'seqtk'))
diff --git a/var/spack/repos/builtin/packages/silo/package.py b/var/spack/repos/builtin/packages/silo/package.py
index 017a09977a..5113c88bdf 100644
--- a/var/spack/repos/builtin/packages/silo/package.py
+++ b/var/spack/repos/builtin/packages/silo/package.py
@@ -38,7 +38,8 @@ class Silo(Package):
 
     variant('fortran', default=True, description='Enable Fortran support')
     variant('shared', default=True, description='Build shared libraries')
-    variant('silex', default=False, description='Builds Silex, a GUI for viewing Silo files')
+    variant('silex', default=False,
+            description='Builds Silex, a GUI for viewing Silo files')
 
     depends_on('hdf5')
     depends_on('qt', when='+silex')
@@ -55,8 +56,10 @@ class Silo(Package):
 
         configure(
             '--prefix=%s' % prefix,
-            '--with-hdf5=%s,%s' % (spec['hdf5'].prefix.include, spec['hdf5'].prefix.lib),
-            '--with-zlib=%s,%s' % (spec['zlib'].prefix.include, spec['zlib'].prefix.lib),
+            '--with-hdf5=%s,%s' % (spec['hdf5'].prefix.include,
+                                   spec['hdf5'].prefix.lib),
+            '--with-zlib=%s,%s' % (spec['zlib'].prefix.include,
+                                   spec['zlib'].prefix.lib),
             '--enable-install-lite-headers',
             *config_args)
 
diff --git a/var/spack/repos/builtin/packages/snappy/package.py b/var/spack/repos/builtin/packages/snappy/package.py
index 836063f933..1e94980c92 100644
--- a/var/spack/repos/builtin/packages/snappy/package.py
+++ b/var/spack/repos/builtin/packages/snappy/package.py
@@ -22,9 +22,9 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import os
 from spack import *
 
+
 class Snappy(Package):
     """A fast compressor/decompressor: https://code.google.com/p/snappy"""
 
diff --git a/var/spack/repos/builtin/packages/sparsehash/package.py b/var/spack/repos/builtin/packages/sparsehash/package.py
index a72a5ce105..e5abd42ae6 100644
--- a/var/spack/repos/builtin/packages/sparsehash/package.py
+++ b/var/spack/repos/builtin/packages/sparsehash/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Sparsehash(Package):
     """Sparse and dense hash-tables for C++ by Google"""
     homepage = "https://github.com/sparsehash/sparsehash"
diff --git a/var/spack/repos/builtin/packages/spindle/package.py b/var/spack/repos/builtin/packages/spindle/package.py
index bcdc7543a3..213d41e970 100644
--- a/var/spack/repos/builtin/packages/spindle/package.py
+++ b/var/spack/repos/builtin/packages/spindle/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Spindle(Package):
     """Spindle improves the library-loading performance of dynamically
        linked HPC applications.  Without Spindle large MPI jobs can
diff --git a/var/spack/repos/builtin/packages/spot/package.py b/var/spack/repos/builtin/packages/spot/package.py
index 21bb6f03a7..096aa24c02 100644
--- a/var/spack/repos/builtin/packages/spot/package.py
+++ b/var/spack/repos/builtin/packages/spot/package.py
@@ -23,16 +23,17 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
-import os
+
 
 class Spot(Package):
-    """Spot is a C++11 library for omega-automata manipulation and model checking."""
+    """Spot is a C++11 library for omega-automata manipulation and model
+       checking."""
     homepage = "https://spot.lrde.epita.fr/index.html"
     url      = "http://www.lrde.epita.fr/dload/spot/spot-1.99.3.tar.gz"
 
     version('1.99.3', 'd53adcb2d0fe7c69f45d4e595a58254e')
 
-    #depends_on("gcc@4.8:", type='build')
+    # depends_on("gcc@4.8:", type='build')
     depends_on("python@3.2:")
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/sqlite/package.py b/var/spack/repos/builtin/packages/sqlite/package.py
index 5e7ae4fb8b..513f8ec6d4 100644
--- a/var/spack/repos/builtin/packages/sqlite/package.py
+++ b/var/spack/repos/builtin/packages/sqlite/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Sqlite(Package):
     """SQLite3 is an SQL database engine in a C library. Programs that
        link the SQLite3 library can have SQL database access without
diff --git a/var/spack/repos/builtin/packages/stat/package.py b/var/spack/repos/builtin/packages/stat/package.py
index a03713397b..ec2fae5e9b 100644
--- a/var/spack/repos/builtin/packages/stat/package.py
+++ b/var/spack/repos/builtin/packages/stat/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Stat(Package):
     """Library to create, manipulate, and export graphs Graphlib."""
     homepage = "http://paradyn.org/STAT/STAT.html"
@@ -49,13 +50,14 @@ class Stat(Package):
         configure_args = [
             "--enable-gui",
             "--prefix=%s" % prefix,
-            "--disable-examples", # Examples require MPI: avoid this dependency.
+            # Examples require MPI: avoid this dependency.
+            "--disable-examples",
             "--with-launchmon=%s"   % spec['launchmon'].prefix,
             "--with-mrnet=%s"       % spec['mrnet'].prefix,
             "--with-graphlib=%s"    % spec['graphlib'].prefix,
             "--with-stackwalker=%s" % spec['dyninst'].prefix,
             "--with-libdwarf=%s"    % spec['libdwarf'].prefix
-            ]
+        ]
         if '+dysect' in spec:
             configure_args.append('--enable-dysectapi')
         configure(*configure_args)
diff --git a/var/spack/repos/builtin/packages/subversion/package.py b/var/spack/repos/builtin/packages/subversion/package.py
index 68ee397857..26d143e4aa 100644
--- a/var/spack/repos/builtin/packages/subversion/package.py
+++ b/var/spack/repos/builtin/packages/subversion/package.py
@@ -23,7 +23,7 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
-#import os
+
 
 class Subversion(Package):
     """Apache Subversion - an open source version control system."""
@@ -41,39 +41,40 @@ class Subversion(Package):
 
     # Optional: We need swig if we want the Perl, Python or Ruby
     # bindings.
-    #depends_on('swig')
-    #depends_on('python')
-    #depends_on('perl')
-    #depends_on('ruby')
+    # depends_on('swig')
+    # depends_on('python')
+    # depends_on('perl')
+    # depends_on('ruby')
 
     def install(self, spec, prefix):
 
         # configure, build, install:
-        # Ref: http://www.linuxfromscratch.org/blfs/view/svn/general/subversion.html
+        # Ref:
+        # http://www.linuxfromscratch.org/blfs/view/svn/general/subversion.html
         options = ['--prefix=%s' % prefix]
         options.append('--with-apr=%s' % spec['apr'].prefix)
         options.append('--with-apr-util=%s' % spec['apr-util'].prefix)
         options.append('--with-zlib=%s' % spec['zlib'].prefix)
         options.append('--with-sqlite=%s' % spec['sqlite'].prefix)
         options.append('--with-serf=%s' % spec['serf'].prefix)
-        #options.append('--with-swig=%s' % spec['swig'].prefix)
+        # options.append('--with-swig=%s' % spec['swig'].prefix)
 
         configure(*options)
         make()
         make('install')
 
         # python bindings
-        #make('swig-py',
+        # make('swig-py',
         #     'swig-pydir=/usr/lib/python2.7/site-packages/libsvn',
         #     'swig_pydir_extra=/usr/lib/python2.7/site-packages/svn')
-        #make('install-swig-py',
+        # make('install-swig-py',
         #     'swig-pydir=/usr/lib/python2.7/site-packages/libsvn',
         #     'swig_pydir_extra=/usr/lib/python2.7/site-packages/svn')
 
         # perl bindings
-        #make('swig-pl')
-        #make('install-swig-pl')
+        # make('swig-pl')
+        # make('install-swig-pl')
 
         # ruby bindings
-        #make('swig-rb')
-        #make('isntall-swig-rb')
+        # make('swig-rb')
+        # make('isntall-swig-rb')
diff --git a/var/spack/repos/builtin/packages/sundials/package.py b/var/spack/repos/builtin/packages/sundials/package.py
index e52b90eb8a..7582954ab1 100644
--- a/var/spack/repos/builtin/packages/sundials/package.py
+++ b/var/spack/repos/builtin/packages/sundials/package.py
@@ -36,11 +36,15 @@ class Sundials(Package):
     version('2.6.2', '3deeb0ede9f514184c6bd83ecab77d95')
 
     variant('mpi',     default=True,  description='Enable MPI support')
-    variant('lapack',  default=True,  description='Build with external BLAS/LAPACK libraries')
-    variant('klu',     default=False, description='Build with SuiteSparse KLU libraries')
-    variant('superlu', default=False, description='Build with SuperLU_MT libraries')
+    variant('lapack',  default=True,
+            description='Build with external BLAS/LAPACK libraries')
+    variant('klu',     default=False,
+            description='Build with SuiteSparse KLU libraries')
+    variant('superlu', default=False,
+            description='Build with SuperLU_MT libraries')
     variant('openmp',  default=False, description='Enable OpenMP support')
-    variant('pthread', default=True,  description='Enable POSIX threads support')
+    variant('pthread', default=True,
+            description='Enable POSIX threads support')
 
     depends_on('cmake', type='build')
     depends_on('mpi',                when='+mpi')
diff --git a/var/spack/repos/builtin/packages/superlu-dist/package.py b/var/spack/repos/builtin/packages/superlu-dist/package.py
index e51d7224d9..4b3354e379 100644
--- a/var/spack/repos/builtin/packages/superlu-dist/package.py
+++ b/var/spack/repos/builtin/packages/superlu-dist/package.py
@@ -57,7 +57,7 @@ class SuperluDist(Package):
             'METISLIB     = -L%s -lmetis' % spec['metis'].prefix.lib,
             'PARMETISLIB  = -L%s -lparmetis' % spec['parmetis'].prefix.lib,
             'FLIBS        =',
-            'LIBS         = $(DSUPERLULIB) $(BLASLIB) $(PARMETISLIB) $(METISLIB)',  # NOQA: ignore=E501
+            'LIBS         = $(DSUPERLULIB) $(BLASLIB) $(PARMETISLIB) $(METISLIB)',  # noqa
             'ARCH         = ar',
             'ARCHFLAGS    = cr',
             'RANLIB       = true',
diff --git a/var/spack/repos/builtin/packages/superlu-mt/package.py b/var/spack/repos/builtin/packages/superlu-mt/package.py
index 5a9429d6e5..e849273e08 100644
--- a/var/spack/repos/builtin/packages/superlu-mt/package.py
+++ b/var/spack/repos/builtin/packages/superlu-mt/package.py
@@ -37,11 +37,13 @@ class SuperluMt(Package):
 
     version('3.1', '06ac62f1b4b7d17123fffa0d0c315e91')
 
-    variant('blas',    default=True,  description='Build with external BLAS library')
+    variant('blas',    default=True,
+            description='Build with external BLAS library')
 
     # Must choose one or the other
     variant('openmp',  default=False, description='Build with OpenMP support')
-    variant('pthread', default=True,  description='Build with POSIX threads support')
+    variant('pthread', default=True,
+            description='Build with POSIX threads support')
 
     # NOTE: must link with a single-threaded BLAS library
     depends_on('blas', when='+blas')
diff --git a/var/spack/repos/builtin/packages/swiftsim/package.py b/var/spack/repos/builtin/packages/swiftsim/package.py
index e65e723869..ae33445377 100644
--- a/var/spack/repos/builtin/packages/swiftsim/package.py
+++ b/var/spack/repos/builtin/packages/swiftsim/package.py
@@ -38,9 +38,11 @@ class Swiftsim(AutotoolsPackage):
     homepage = 'http://icc.dur.ac.uk/swift/'
     url = 'http://gitlab.cosma.dur.ac.uk/swift/swiftsim/repository/archive.tar.gz?ref=v0.3.0'
 
-    version('0.3.0', git='https://gitlab.cosma.dur.ac.uk/swift/swiftsim.git', commit='254cc1b563b2f88ddcf437b1f71da123bb9db733')
+    version('0.3.0', git='https://gitlab.cosma.dur.ac.uk/swift/swiftsim.git',
+            commit='254cc1b563b2f88ddcf437b1f71da123bb9db733')
 
-    variant('mpi', default=True, description='Enable distributed memory parallelism')
+    variant('mpi', default=True,
+            description='Enable distributed memory parallelism')
 
     # Build dependencies
     depends_on('autoconf', type='build')
diff --git a/var/spack/repos/builtin/packages/swig/package.py b/var/spack/repos/builtin/packages/swig/package.py
index f552621821..b43246dcee 100644
--- a/var/spack/repos/builtin/packages/swig/package.py
+++ b/var/spack/repos/builtin/packages/swig/package.py
@@ -22,9 +22,9 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-
 from spack import *
 
+
 class Swig(Package):
     """SWIG is an interface compiler that connects programs written in
        C and C++ with scripting languages such as Perl, Python, Ruby,
@@ -38,6 +38,7 @@ class Swig(Package):
     homepage = "http://www.swig.org"
     url      = "http://prdownloads.sourceforge.net/swig/swig-3.0.8.tar.gz"
 
+    version('3.0.10', 'bb4ab8047159469add7d00910e203124')
     version('3.0.8', 'c96a1d5ecb13d38604d7e92148c73c97')
     version('3.0.2', '62f9b0d010cef36a13a010dc530d0d41')
     version('2.0.12', 'c3fb0b2d710cc82ed0154b91e43085a4')
diff --git a/var/spack/repos/builtin/packages/tar/gnutar-configure-xattrs.patch b/var/spack/repos/builtin/packages/tar/gnutar-configure-xattrs.patch
new file mode 100644
index 0000000000..e5c183b720
--- /dev/null
+++ b/var/spack/repos/builtin/packages/tar/gnutar-configure-xattrs.patch
@@ -0,0 +1,482 @@
+diff --git a/Makefile.in b/Makefile.in
+index f9f1d1d..b403e46 100644
+--- a/Makefile.in
++++ b/Makefile.in
+@@ -1,4 +1,4 @@
+-# Makefile.in generated by automake 1.14 from Makefile.am.
++# Makefile.in generated by automake 1.14.1 from Makefile.am.
+ # @configure_input@
+ 
+ # Copyright (C) 1994-2013 Free Software Foundation, Inc.
+@@ -1583,9 +1583,10 @@ distcheck: dist
+ 	  && dc_destdir="$${TMPDIR-/tmp}/am-dc-$$$$/" \
+ 	  && am__cwd=`pwd` \
+ 	  && $(am__cd) $(distdir)/_build \
+-	  && ../configure --srcdir=.. --prefix="$$dc_install_base" \
++	  && ../configure \
+ 	    $(AM_DISTCHECK_CONFIGURE_FLAGS) \
+ 	    $(DISTCHECK_CONFIGURE_FLAGS) \
++	    --srcdir=.. --prefix="$$dc_install_base" \
+ 	  && $(MAKE) $(AM_MAKEFLAGS) \
+ 	  && $(MAKE) $(AM_MAKEFLAGS) dvi \
+ 	  && $(MAKE) $(AM_MAKEFLAGS) check \
+diff --git a/aclocal.m4 b/aclocal.m4
+index 0e09589..804c0b3 100644
+--- a/aclocal.m4
++++ b/aclocal.m4
+@@ -1,4 +1,4 @@
+-# generated automatically by aclocal 1.14 -*- Autoconf -*-
++# generated automatically by aclocal 1.14.1 -*- Autoconf -*-
+ 
+ # Copyright (C) 1996-2013 Free Software Foundation, Inc.
+ 
+@@ -35,7 +35,7 @@ AC_DEFUN([AM_AUTOMAKE_VERSION],
+ [am__api_version='1.14'
+ dnl Some users find AM_AUTOMAKE_VERSION and mistake it for a way to
+ dnl require some minimum version.  Point them to the right macro.
+-m4_if([$1], [1.14], [],
++m4_if([$1], [1.14.1], [],
+       [AC_FATAL([Do not call $0, use AM_INIT_AUTOMAKE([$1]).])])dnl
+ ])
+ 
+@@ -51,7 +51,7 @@ m4_define([_AM_AUTOCONF_VERSION], [])
+ # Call AM_AUTOMAKE_VERSION and AM_AUTOMAKE_VERSION so they can be traced.
+ # This function is AC_REQUIREd by AM_INIT_AUTOMAKE.
+ AC_DEFUN([AM_SET_CURRENT_AUTOMAKE_VERSION],
+-[AM_AUTOMAKE_VERSION([1.14])dnl
++[AM_AUTOMAKE_VERSION([1.14.1])dnl
+ m4_ifndef([AC_AUTOCONF_VERSION],
+   [m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl
+ _AM_AUTOCONF_VERSION(m4_defn([AC_AUTOCONF_VERSION]))])
+diff --git a/config.h.in b/config.h.in
+index 6646ea5..8571ef4 100644
+--- a/config.h.in
++++ b/config.h.in
+@@ -617,7 +617,7 @@
+    */
+ #undef HAVE_ALLOCA_H
+ 
+-/* define to 1 if we have <attr/xattr.h> header */
++/* Define to 1 if you have the <attr/xattr.h> header file. */
+ #undef HAVE_ATTR_XATTR_H
+ 
+ /* Define to 1 if you have the <bp-sym.h> header file. */
+@@ -924,21 +924,12 @@
+ /* Define to 1 if you have the <features.h> header file. */
+ #undef HAVE_FEATURES_H
+ 
+-/* Define to 1 if you have the `fgetxattr' function. */
+-#undef HAVE_FGETXATTR
+-
+-/* Define to 1 if you have the `flistxattr' function. */
+-#undef HAVE_FLISTXATTR
+-
+ /* Define to 1 if you have the `flockfile' function. */
+ #undef HAVE_FLOCKFILE
+ 
+ /* Define to 1 if fseeko (and presumably ftello) exists and is declared. */
+ #undef HAVE_FSEEKO
+ 
+-/* Define to 1 if you have the `fsetxattr' function. */
+-#undef HAVE_FSETXATTR
+-
+ /* Define to 1 if you have the `fstatat' function. */
+ #undef HAVE_FSTATAT
+ 
+@@ -990,9 +981,6 @@
+ /* Define to 1 if you have the `gettimeofday' function. */
+ #undef HAVE_GETTIMEOFDAY
+ 
+-/* Define to 1 if you have the `getxattr' function. */
+-#undef HAVE_GETXATTR
+-
+ /* Define to 1 if you have the `grantpt' function. */
+ #undef HAVE_GRANTPT
+ 
+@@ -1045,12 +1033,6 @@
+ /* Define to 1 if you have the `lchown' function. */
+ #undef HAVE_LCHOWN
+ 
+-/* Define to 1 if you have the `lgetxattr' function. */
+-#undef HAVE_LGETXATTR
+-
+-/* Define to 1 if you have the `attr' library (-lattr). */
+-#undef HAVE_LIBATTR
+-
+ /* Define to 1 if you have the <libgen.h> header file. */
+ #undef HAVE_LIBGEN_H
+ 
+@@ -1069,12 +1051,6 @@
+ /* Define to 1 if you have the <linux/fd.h> header file. */
+ #undef HAVE_LINUX_FD_H
+ 
+-/* Define to 1 if you have the `listxattr' function. */
+-#undef HAVE_LISTXATTR
+-
+-/* Define to 1 if you have the `llistxattr' function. */
+-#undef HAVE_LLISTXATTR
+-
+ /* Define to 1 if you have the <locale.h> header file. */
+ #undef HAVE_LOCALE_H
+ 
+@@ -1087,9 +1063,6 @@
+ /* Define to 1 if the system has the type 'long long int'. */
+ #undef HAVE_LONG_LONG_INT
+ 
+-/* Define to 1 if you have the `lsetxattr' function. */
+-#undef HAVE_LSETXATTR
+-
+ /* Define to 1 if you have the `lstat' function. */
+ #undef HAVE_LSTAT
+ 
+@@ -1867,9 +1840,6 @@
+ /* Define to 1 if you have the `setlocale' function. */
+ #undef HAVE_SETLOCALE
+ 
+-/* Define to 1 if you have the `setxattr' function. */
+-#undef HAVE_SETXATTR
+-
+ /* Define to 1 if you have the <sgtty.h> header file. */
+ #undef HAVE_SGTTY_H
+ 
+@@ -2074,7 +2044,7 @@
+ /* Define to 1 if you have the <sys/wait.h> header file. */
+ #undef HAVE_SYS_WAIT_H
+ 
+-/* define to 1 if we have <sys/xattr.h> header */
++/* Define to 1 if you have the <sys/xattr.h> header file. */
+ #undef HAVE_SYS_XATTR_H
+ 
+ /* Define if struct tm has the tm_gmtoff member. */
+diff --git a/configure b/configure
+index cfdd721..8cf6e91 100755
+--- a/configure
++++ b/configure
+@@ -663,8 +663,6 @@ RSH
+ LIBOBJS
+ TAR_COND_GRANTPT_FALSE
+ TAR_COND_GRANTPT_TRUE
+-TAR_LIB_ATTR_FALSE
+-TAR_LIB_ATTR_TRUE
+ TAR_COND_XATTR_H_FALSE
+ TAR_COND_XATTR_H_TRUE
+ GNULIB_TEST_WARN_CFLAGS
+@@ -34994,41 +34992,6 @@ else
+   TAR_COND_XATTR_H_FALSE=
+ fi
+ 
+-   if false; then
+-  TAR_LIB_ATTR_TRUE=
+-  TAR_LIB_ATTR_FALSE='#'
+-else
+-  TAR_LIB_ATTR_TRUE='#'
+-  TAR_LIB_ATTR_FALSE=
+-fi
+-
+-  if test "$ac_cv_header_sys_xattr_h" = yes; then
+-    for ac_func in getxattr  fgetxattr  lgetxattr \
+-                   setxattr  fsetxattr  lsetxattr \
+-                   listxattr flistxattr llistxattr
+-do :
+-  as_ac_var=`$as_echo "ac_cv_func_$ac_func" | $as_tr_sh`
+-ac_fn_c_check_func "$LINENO" "$ac_func" "$as_ac_var"
+-if eval test \"x\$"$as_ac_var"\" = x"yes"; then :
+-  cat >>confdefs.h <<_ACEOF
+-#define `$as_echo "HAVE_$ac_func" | $as_tr_cpp` 1
+-_ACEOF
+- # only when functions are present
+-
+-$as_echo "#define HAVE_SYS_XATTR_H 1" >>confdefs.h
+-
+-        if test "$with_xattrs" != no; then
+-
+-$as_echo "#define HAVE_XATTRS /**/" >>confdefs.h
+-
+-        fi
+-
+-fi
+-done
+-
+-  fi
+-
+-  # If <sys/xattr.h> is not found, then check for <attr/xattr.h>
+   if test "$ac_cv_header_sys_xattr_h" != yes; then
+     for ac_header in attr/xattr.h
+ do :
+@@ -35050,13 +35013,20 @@ else
+   TAR_COND_XATTR_H_FALSE=
+ fi
+ 
+-    { $as_echo "$as_me:${as_lineno-$LINENO}: checking for fgetxattr in -lattr" >&5
+-$as_echo_n "checking for fgetxattr in -lattr... " >&6; }
+-if ${ac_cv_lib_attr_fgetxattr+:} false; then :
++  fi
++
++  if test "$with_xattrs" != no; then
++    for i in getxattr  fgetxattr  lgetxattr \
++             setxattr  fsetxattr  lsetxattr \
++             listxattr flistxattr llistxattr
++    do
++      as_ac_Search=`$as_echo "ac_cv_search_$i" | $as_tr_sh`
++{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing $i" >&5
++$as_echo_n "checking for library containing $i... " >&6; }
++if eval \${$as_ac_Search+:} false; then :
+   $as_echo_n "(cached) " >&6
+ else
+-  ac_check_lib_save_LIBS=$LIBS
+-LIBS="-lattr  $LIBS"
++  ac_func_search_save_LIBS=$LIBS
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+ /* end confdefs.h.  */
+ 
+@@ -35066,67 +35036,56 @@ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+ #ifdef __cplusplus
+ extern "C"
+ #endif
+-char fgetxattr ();
++char $i ();
+ int
+ main ()
+ {
+-return fgetxattr ();
++return $i ();
+   ;
+   return 0;
+ }
+ _ACEOF
+-if ac_fn_c_try_link "$LINENO"; then :
+-  ac_cv_lib_attr_fgetxattr=yes
+-else
+-  ac_cv_lib_attr_fgetxattr=no
++for ac_lib in '' attr; do
++  if test -z "$ac_lib"; then
++    ac_res="none required"
++  else
++    ac_res=-l$ac_lib
++    LIBS="-l$ac_lib  $ac_func_search_save_LIBS"
++  fi
++  if ac_fn_c_try_link "$LINENO"; then :
++  eval "$as_ac_Search=\$ac_res"
+ fi
+ rm -f core conftest.err conftest.$ac_objext \
+-    conftest$ac_exeext conftest.$ac_ext
+-LIBS=$ac_check_lib_save_LIBS
+-fi
+-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_attr_fgetxattr" >&5
+-$as_echo "$ac_cv_lib_attr_fgetxattr" >&6; }
+-if test "x$ac_cv_lib_attr_fgetxattr" = xyes; then :
+-  cat >>confdefs.h <<_ACEOF
+-#define HAVE_LIBATTR 1
+-_ACEOF
+-
+-  LIBS="-lattr $LIBS"
+-
++    conftest$ac_exeext
++  if eval \${$as_ac_Search+:} false; then :
++  break
+ fi
++done
++if eval \${$as_ac_Search+:} false; then :
+ 
+-     if test "$ac_cv_lib_attr_fgetxattr" = yes; then
+-  TAR_LIB_ATTR_TRUE=
+-  TAR_LIB_ATTR_FALSE='#'
+ else
+-  TAR_LIB_ATTR_TRUE='#'
+-  TAR_LIB_ATTR_FALSE=
++  eval "$as_ac_Search=no"
++fi
++rm conftest.$ac_ext
++LIBS=$ac_func_search_save_LIBS
+ fi
++eval ac_res=\$$as_ac_Search
++	       { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
++$as_echo "$ac_res" >&6; }
++eval ac_res=\$$as_ac_Search
++if test "$ac_res" != no; then :
++  test "$ac_res" = "none required" || LIBS="$ac_res $LIBS"
+ 
+-    if test "$ac_cv_header_attr_xattr_h" = yes; then
+-      for ac_func in getxattr  fgetxattr  lgetxattr \
+-                     setxattr  fsetxattr  lsetxattr \
+-                     listxattr flistxattr llistxattr
+-do :
+-  as_ac_var=`$as_echo "ac_cv_func_$ac_func" | $as_tr_sh`
+-ac_fn_c_check_func "$LINENO" "$ac_func" "$as_ac_var"
+-if eval test \"x\$"$as_ac_var"\" = x"yes"; then :
+-  cat >>confdefs.h <<_ACEOF
+-#define `$as_echo "HAVE_$ac_func" | $as_tr_cpp` 1
+-_ACEOF
+- # only when functions are present
++fi
+ 
+-$as_echo "#define HAVE_ATTR_XATTR_H 1" >>confdefs.h
++      eval found=\$ac_cv_search_$i
++      test "$found" = "no" && break
++    done
+ 
+-          if test "$with_xattrs" != no; then
++    if test "$found" != no; then
+ 
+ $as_echo "#define HAVE_XATTRS /**/" >>confdefs.h
+ 
+-          fi
+-
+-fi
+-done
+-
+     fi
+   fi
+ 
+@@ -38187,18 +38146,10 @@ if test -z "${TAR_COND_XATTR_H_TRUE}" && test -z "${TAR_COND_XATTR_H_FALSE}"; th
+   as_fn_error $? "conditional \"TAR_COND_XATTR_H\" was never defined.
+ Usually this means the macro was only invoked conditionally." "$LINENO" 5
+ fi
+-if test -z "${TAR_LIB_ATTR_TRUE}" && test -z "${TAR_LIB_ATTR_FALSE}"; then
+-  as_fn_error $? "conditional \"TAR_LIB_ATTR\" was never defined.
+-Usually this means the macro was only invoked conditionally." "$LINENO" 5
+-fi
+ if test -z "${TAR_COND_XATTR_H_TRUE}" && test -z "${TAR_COND_XATTR_H_FALSE}"; then
+   as_fn_error $? "conditional \"TAR_COND_XATTR_H\" was never defined.
+ Usually this means the macro was only invoked conditionally." "$LINENO" 5
+ fi
+-if test -z "${TAR_LIB_ATTR_TRUE}" && test -z "${TAR_LIB_ATTR_FALSE}"; then
+-  as_fn_error $? "conditional \"TAR_LIB_ATTR\" was never defined.
+-Usually this means the macro was only invoked conditionally." "$LINENO" 5
+-fi
+ if test -z "${TAR_COND_GRANTPT_TRUE}" && test -z "${TAR_COND_GRANTPT_FALSE}"; then
+   as_fn_error $? "conditional \"TAR_COND_GRANTPT\" was never defined.
+ Usually this means the macro was only invoked conditionally." "$LINENO" 5
+diff --git a/doc/Makefile.in b/doc/Makefile.in
+index ca44f1a..42a06b3 100644
+--- a/doc/Makefile.in
++++ b/doc/Makefile.in
+@@ -1,4 +1,4 @@
+-# Makefile.in generated by automake 1.14 from Makefile.am.
++# Makefile.in generated by automake 1.14.1 from Makefile.am.
+ # @configure_input@
+ 
+ # Copyright (C) 1994-2013 Free Software Foundation, Inc.
+diff --git a/gnu/Makefile.in b/gnu/Makefile.in
+index 03eed58..d908a03 100644
+--- a/gnu/Makefile.in
++++ b/gnu/Makefile.in
+@@ -1,4 +1,4 @@
+-# Makefile.in generated by automake 1.14 from Makefile.am.
++# Makefile.in generated by automake 1.14.1 from Makefile.am.
+ # @configure_input@
+ 
+ # Copyright (C) 1994-2013 Free Software Foundation, Inc.
+diff --git a/lib/Makefile.in b/lib/Makefile.in
+index 41a9aca..1254b8f 100644
+--- a/lib/Makefile.in
++++ b/lib/Makefile.in
+@@ -1,4 +1,4 @@
+-# Makefile.in generated by automake 1.14 from Makefile.am.
++# Makefile.in generated by automake 1.14.1 from Makefile.am.
+ # @configure_input@
+ 
+ # Copyright (C) 1994-2013 Free Software Foundation, Inc.
+diff --git a/rmt/Makefile.in b/rmt/Makefile.in
+index c3f2509..0f3dca4 100644
+--- a/rmt/Makefile.in
++++ b/rmt/Makefile.in
+@@ -1,4 +1,4 @@
+-# Makefile.in generated by automake 1.14 from Makefile.am.
++# Makefile.in generated by automake 1.14.1 from Makefile.am.
+ # @configure_input@
+ 
+ # Copyright (C) 1994-2013 Free Software Foundation, Inc.
+diff --git a/scripts/Makefile.in b/scripts/Makefile.in
+index 57c0d0d..bf344ed 100644
+--- a/scripts/Makefile.in
++++ b/scripts/Makefile.in
+@@ -1,4 +1,4 @@
+-# Makefile.in generated by automake 1.14 from Makefile.am.
++# Makefile.in generated by automake 1.14.1 from Makefile.am.
+ # @configure_input@
+ 
+ # Copyright (C) 1994-2013 Free Software Foundation, Inc.
+diff --git a/src/Makefile.in b/src/Makefile.in
+index 6f9a592..fc6fc87 100644
+--- a/src/Makefile.in
++++ b/src/Makefile.in
+@@ -1,4 +1,4 @@
+-# Makefile.in generated by automake 1.14 from Makefile.am.
++# Makefile.in generated by automake 1.14.1 from Makefile.am.
+ # @configure_input@
+ 
+ # Copyright (C) 1994-2013 Free Software Foundation, Inc.
+@@ -99,7 +99,6 @@ POST_UNINSTALL = :
+ build_triplet = @build@
+ host_triplet = @host@
+ bin_PROGRAMS = tar$(EXEEXT)
+-@TAR_LIB_ATTR_TRUE@am__append_1 = -lattr
+ subdir = src
+ DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/Makefile.am \
+ 	$(top_srcdir)/build-aux/depcomp $(noinst_HEADERS)
+@@ -254,7 +253,7 @@ am__DEPENDENCIES_2 = ../lib/libtar.a ../gnu/libgnu.a \
+ 	$(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1)
+ tar_DEPENDENCIES = $(am__DEPENDENCIES_1) $(am__DEPENDENCIES_2) \
+ 	$(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1) \
+-	$(am__DEPENDENCIES_1) $(am__DEPENDENCIES_1)
++	$(am__DEPENDENCIES_1)
+ AM_V_P = $(am__v_P_@AM_V@)
+ am__v_P_ = $(am__v_P_@AM_DEFAULT_V@)
+ am__v_P_0 = false
+@@ -1225,8 +1224,7 @@ tar_SOURCES = \
+ AM_CPPFLAGS = -I$(top_srcdir)/gnu -I../ -I../gnu -I$(top_srcdir)/lib -I../lib
+ AM_CFLAGS = $(WARN_CFLAGS) $(WERROR_CFLAGS)
+ LDADD = ../lib/libtar.a ../gnu/libgnu.a $(LIBINTL) $(LIBICONV)
+-tar_LDADD = $(LIBS) $(LDADD) $(LIB_CLOCK_GETTIME) $(LIB_EACCESS) \
+-	$(LIB_SELINUX) $(am__append_1)
++tar_LDADD = $(LIBS) $(LDADD) $(LIB_CLOCK_GETTIME) $(LIB_EACCESS) $(LIB_SELINUX)
+ all: all-am
+ 
+ .SUFFIXES:
+diff --git a/tests/Makefile.in b/tests/Makefile.in
+index 6807509..50d7689 100644
+--- a/tests/Makefile.in
++++ b/tests/Makefile.in
+@@ -1,4 +1,4 @@
+-# Makefile.in generated by automake 1.14 from Makefile.am.
++# Makefile.in generated by automake 1.14.1 from Makefile.am.
+ # @configure_input@
+ 
+ # Copyright (C) 1994-2013 Free Software Foundation, Inc.
+diff --git a/lib/xattr-at.c b/lib/xattr-at.c
+index 443ccae..009bde5 100644
+--- a/lib/xattr-at.c
++++ b/lib/xattr-at.c
+@@ -18,6 +18,11 @@
+
+ #include <config.h>
+
++/* Temporarily don't build.  We are unable to build on (probably not only)
++   darwin due to lack of l*xattr callbacks (XATTR_NOFOLLOW is alternative) and
++   different function definitions. */
++#ifdef HAVE_XATTRS
++
+ #include "xattr-at.h"
+ #include "openat.h"
+
+@@ -108,3 +113,5 @@
+ #undef AT_FUNC_RESULT
+ #undef AT_FUNC_POST_FILE_PARAM_DECLS
+ #undef AT_FUNC_POST_FILE_ARGS
++
++#endif
+diff --git a/src/Makefile.am b/src/Makefile.am
+index 82b2d46..42daaef 100644
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -52,7 +52,3 @@ AM_CFLAGS = $(WARN_CFLAGS) $(WERROR_CFLAGS)
+ LDADD = ../lib/libtar.a ../gnu/libgnu.a $(LIBINTL) $(LIBICONV)
+
+ tar_LDADD = $(LIBS) $(LDADD) $(LIB_CLOCK_GETTIME) $(LIB_EACCESS) $(LIB_SELINUX)
+-
+-if TAR_LIB_ATTR
+-tar_LDADD += -lattr
+-endif
+--
+1.9.3
\ No newline at end of file
diff --git a/var/spack/repos/builtin/packages/tar/package.py b/var/spack/repos/builtin/packages/tar/package.py
index c55b5165bf..f5995cb007 100644
--- a/var/spack/repos/builtin/packages/tar/package.py
+++ b/var/spack/repos/builtin/packages/tar/package.py
@@ -24,13 +24,21 @@
 ##############################################################################
 from spack import *
 
+
 class Tar(Package):
-    """GNU Tar provides the ability to create tar archives, as well as various other kinds of manipulation."""
+    """GNU Tar provides the ability to create tar archives, as well as various
+    other kinds of manipulation."""
     homepage = "https://www.gnu.org/software/tar/"
-    url      = "http://ftp.gnu.org/gnu/tar/tar-1.28.tar.gz"
+    url      = "https://ftp.gnu.org/gnu/tar/tar-1.28.tar.gz"
 
+    version('1.29', 'cae466e6e58c7292355e7080248f244db3a4cf755f33f4fa25ca7f9a7ed09af0')
     version('1.28', '6ea3dbea1f2b0409b234048e021a9fd7')
 
+    # see http://lists.gnu.org/archive/html/bug-tar/2014-08/msg00001.html and
+    # https://github.com/Homebrew/homebrew-core/commit/aef9a1792de4648d0322b4b04d32287532f046bb
+    # TODO: when=sys.platform=='darwin' ?
+    patch('gnutar-configure-xattrs.patch', when='@1.28')
+
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
         make()
diff --git a/var/spack/repos/builtin/packages/task/package.py b/var/spack/repos/builtin/packages/task/package.py
index 8c3b412f48..785023fd03 100644
--- a/var/spack/repos/builtin/packages/task/package.py
+++ b/var/spack/repos/builtin/packages/task/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Task(Package):
     """Feature-rich console based todo list manager"""
     homepage = "http://www.taskwarrior.org"
diff --git a/var/spack/repos/builtin/packages/taskd/package.py b/var/spack/repos/builtin/packages/taskd/package.py
index 1d7f9ed49e..d13f480374 100644
--- a/var/spack/repos/builtin/packages/taskd/package.py
+++ b/var/spack/repos/builtin/packages/taskd/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Taskd(Package):
     """TaskWarrior task synchronization daemon"""
     # FIXME: add a proper url for your package's homepage here.
diff --git a/var/spack/repos/builtin/packages/tau/package.py b/var/spack/repos/builtin/packages/tau/package.py
index 3b181f3fa4..a77df8d37c 100644
--- a/var/spack/repos/builtin/packages/tau/package.py
+++ b/var/spack/repos/builtin/packages/tau/package.py
@@ -30,6 +30,7 @@ import os.path
 
 from llnl.util.filesystem import join_path
 
+
 class Tau(Package):
     """
     A portable profiling and tracing toolkit for performance
@@ -45,15 +46,20 @@ class Tau(Package):
     version('2.23.1', '6593b47ae1e7a838e632652f0426fe72')
 
     # TODO : shmem variant missing
-    variant('download', default=False, description='Downloads and builds various dependencies')
+    variant('download', default=False,
+            description='Downloads and builds various dependencies')
     variant('scorep', default=False, description='Activates SCOREP support')
     variant('openmp', default=True, description='Use OpenMP threads')
-    variant('mpi', default=True, description='Specify use of TAU MPI wrapper library')
+    variant('mpi', default=True,
+            description='Specify use of TAU MPI wrapper library')
     variant('phase', default=True, description='Generate phase based profiles')
-    variant('comm', default=True, description=' Generate profiles with MPI communicator info')
+    variant('comm', default=True,
+            description=' Generate profiles with MPI communicator info')
 
-    # TODO : Try to build direct OTF2 support? Some parts of the OTF support library in TAU are non-conformant,
-    # TODO : and fail at compile-time. Further, SCOREP is compiled with OTF2 support.
+    # TODO : Try to build direct OTF2 support? Some parts of the OTF support
+    # TODO : library in TAU are non-conformant,
+    # TODO : and fail at compile-time. Further, SCOREP is compiled with OTF2
+    # support.
     depends_on('pdt')  # Required for TAU instrumentation
     depends_on('scorep', when='+scorep')
     depends_on('binutils', when='~download')
@@ -65,13 +71,17 @@ class Tau(Package):
 
         ##########
         # Selecting a compiler with TAU configure is quite tricky:
-        # 1 - compilers are mapped to a given set of strings (and spack cc, cxx, etc. wrappers are not among them)
+        # 1 - compilers are mapped to a given set of strings
+        #     (and spack cc, cxx, etc. wrappers are not among them)
         # 2 - absolute paths are not allowed
-        # 3 - the usual environment variables seems not to be checked ('CC', 'CXX' and 'FC')
-        # 4 - if no -cc=<compiler> -cxx=<compiler> is passed tau is built with system compiler silently
+        # 3 - the usual environment variables seems not to be checked
+        #     ('CC', 'CXX' and 'FC')
+        # 4 - if no -cc=<compiler> -cxx=<compiler> is passed tau is built with
+        #     system compiler silently
         # (regardless of what %<compiler> is used in the spec)
         #
-        # In the following we give TAU what he expects and put compilers into PATH
+        # In the following we give TAU what he expects and put compilers into
+        # PATH
         compiler_path = os.path.dirname(self.compiler.cc)
         os.environ['PATH'] = ':'.join([compiler_path, os.environ['PATH']])
         compiler_options = ['-c++=%s' % self.compiler.cxx_names[0],
@@ -80,7 +90,8 @@ class Tau(Package):
             compiler_options.append('-fortran=%s' % self.compiler.fc_names[0])
         ##########
 
-        # Construct the string of custom compiler flags and append it to compiler related options
+        # Construct the string of custom compiler flags and append it to
+        # compiler related options
         useropt = ' '.join(useropt)
         useropt = "-useropt=%s" % useropt
         compiler_options.append(useropt)
@@ -92,8 +103,9 @@ class Tau(Package):
         change_sed_delimiter('@', ';', 'utils/FixMakefile')
         change_sed_delimiter('@', ';', 'utils/FixMakefile.sed.default')
 
-        # TAU configure, despite the name , seems to be a manually written script (nothing related to autotools).
-        # As such it has a few #peculiarities# that make this build quite hackish.
+        # TAU configure, despite the name , seems to be a manually
+        # written script (nothing related to autotools).  As such it has
+        # a few #peculiarities# that make this build quite hackish.
         options = ["-prefix=%s" % prefix,
                    "-iowrapper",
                    "-pdt=%s" % spec['pdt'].prefix]
diff --git a/var/spack/repos/builtin/packages/tbb/package.py b/var/spack/repos/builtin/packages/tbb/package.py
index c88b170816..d13579b44d 100644
--- a/var/spack/repos/builtin/packages/tbb/package.py
+++ b/var/spack/repos/builtin/packages/tbb/package.py
@@ -35,8 +35,10 @@ class Tbb(Package):
     homepage = "http://www.threadingbuildingblocks.org/"
 
     # Only version-specific URL's work for TBB
-    version('4.4.4', 'd4cee5e4ca75cab5181834877738619c56afeb71', url='https://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb44_20160413oss_src.tgz')    # NOQA: ignore=E501
-    version('4.4.3', '80707e277f69d9b20eeebdd7a5f5331137868ce1', url='https://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb44_20160128oss_src_0.tgz')  # NOQA: ignore=E501
+    version('4.4.4', 'd4cee5e4ca75cab5181834877738619c56afeb71',
+            url='https://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb44_20160413oss_src.tgz')
+    version('4.4.3', '80707e277f69d9b20eeebdd7a5f5331137868ce1',
+            url='https://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb44_20160128oss_src_0.tgz')
 
     def coerce_to_spack(self, tbb_build_subdir):
         for compiler in ["icc", "gcc", "clang"]:
diff --git a/var/spack/repos/builtin/packages/tcl/package.py b/var/spack/repos/builtin/packages/tcl/package.py
index ef922314d8..16d896acc6 100644
--- a/var/spack/repos/builtin/packages/tcl/package.py
+++ b/var/spack/repos/builtin/packages/tcl/package.py
@@ -57,3 +57,5 @@ class Tcl(Package):
             configure("--prefix={0}".format(prefix))
             make()
             make("install")
+        with working_dir(prefix.bin):
+            symlink('tclsh{0}'.format(self.version.up_to(2)), 'tclsh')
diff --git a/var/spack/repos/builtin/packages/tetgen/package.py b/var/spack/repos/builtin/packages/tetgen/package.py
index 97aa68be65..7ac55a6785 100644
--- a/var/spack/repos/builtin/packages/tetgen/package.py
+++ b/var/spack/repos/builtin/packages/tetgen/package.py
@@ -36,7 +36,8 @@ class Tetgen(Package):
     url      = "http://www.tetgen.org/files/tetgen1.4.3.tar.gz"
 
     version('1.4.3', 'd6a4bcdde2ac804f7ec66c29dcb63c18')
-    version('1.5.0', '3b9fd9cdec121e52527b0308f7aad5c1', url='http://www.tetgen.org/1.5/src/tetgen1.5.0.tar.gz')
+    version('1.5.0', '3b9fd9cdec121e52527b0308f7aad5c1',
+            url='http://www.tetgen.org/1.5/src/tetgen1.5.0.tar.gz')
 
     depends_on('cmake@2.8.7:', when='@1.5.0:', type='build')
 
diff --git a/var/spack/repos/builtin/packages/texinfo/package.py b/var/spack/repos/builtin/packages/texinfo/package.py
index 5c6fef0db6..ddb23e5d6f 100644
--- a/var/spack/repos/builtin/packages/texinfo/package.py
+++ b/var/spack/repos/builtin/packages/texinfo/package.py
@@ -27,10 +27,13 @@ from spack import *
 
 
 class Texinfo(Package):
-    """
-    Texinfo is the official documentation format of the GNU project. It was invented by Richard Stallman and Bob
-    Chassell many years ago, loosely based on Brian Reid's Scribe and other formatting languages of the time. It is
-    used by many non-GNU projects as well.FIXME: put a proper description of your package here.
+    """Texinfo is the official documentation format of the GNU project.
+
+    It was invented by Richard Stallman and Bob Chassell many years ago,
+    loosely based on Brian Reid's Scribe and other formatting languages
+    of the time. It is used by many non-GNU projects as well.FIXME: put a
+    proper description of your package here.
+
     """
     homepage = "https://www.gnu.org/software/texinfo/"
     url      = "http://ftp.gnu.org/gnu/texinfo/texinfo-6.0.tar.gz"
diff --git a/var/spack/repos/builtin/packages/texlive/package.py b/var/spack/repos/builtin/packages/texlive/package.py
new file mode 100644
index 0000000000..64158e74cb
--- /dev/null
+++ b/var/spack/repos/builtin/packages/texlive/package.py
@@ -0,0 +1,58 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+import os
+
+
+class Texlive(Package):
+    """TeX Live is a free software distribution for the TeX typesetting
+       system"""
+
+    homepage = "http://www.tug.org/texlive"
+
+    version('live', 'e671eea7f142c438959493cc42a2a59b',
+            url="http://mirror.ctan.org/systems/texlive/tlnet/install-tl-unx.tar.gz")
+
+    # There does not seem to be a complete list of schemes.
+    # Examples include:
+    #   full scheme (everything)
+    #   medium scheme (small + more packages and languages)
+    #   small scheme (basic + xetex, metapost, a few languages)
+    #   basic scheme (plain and latex)
+    #   minimal scheme (plain only)
+    # See:
+    # https://www.tug.org/texlive/doc/texlive-en/texlive-en.html#x1-25025r6
+    variant('scheme',  default="small",
+            description='Package subset to install (e.g. full, small, basic)')
+
+    depends_on('perl')
+
+    def install(self, spec, prefix):
+        env = os.environ
+        env['TEXLIVE_INSTALL_PREFIX'] = prefix
+        perl = which('perl')
+        scheme = spec.variants['scheme'].value
+        perl('./install-tl', '-scheme', scheme,
+             '-portable', '-profile', '/dev/null')
diff --git a/var/spack/repos/builtin/packages/thrift/package.py b/var/spack/repos/builtin/packages/thrift/package.py
index 025ee2b885..755f7a80b9 100644
--- a/var/spack/repos/builtin/packages/thrift/package.py
+++ b/var/spack/repos/builtin/packages/thrift/package.py
@@ -24,12 +24,16 @@
 ##############################################################################
 from spack import *
 
+
 class Thrift(Package):
-    """The Apache Thrift software framework, for scalable cross-language services
-    development, combines a software stack with a code generation engine to build
-    services that work efficiently and seamlessly between C++, Java, Python, PHP,
-    Ruby, Erlang, Perl, Haskell, C#, Cocoa, JavaScript, Node.js, Smalltalk, OCaml
-     and Delphi and other languages."""
+    """Software framework for scalable cross-language services development.
+
+    Thrift combines a software stack with a code generation engine to
+    build services that work efficiently and seamlessly between C++,
+    Java, Python, PHP, Ruby, Erlang, Perl, Haskell, C#, Cocoa,
+    JavaScript, Node.js, Smalltalk, OCaml and Delphi and other languages.
+
+    """
 
     homepage = "http://thrift.apache.org"
     url      = "http://apache.mirrors.ionfish.org/thrift/0.9.2/thrift-0.9.2.tar.gz"
@@ -37,8 +41,10 @@ class Thrift(Package):
     version('0.9.2', '89f63cc4d0100912f4a1f8a9dee63678')
 
     # Currently only support for c-family and python
-    variant('c', default=True, description="Build support for C-family languages")
-    variant('python', default=True, description="Build support for python")
+    variant('c', default=True,
+            description="Build support for C-family languages")
+    variant('python', default=True,
+            description="Build support for python")
 
     depends_on('jdk')
     depends_on('autoconf', type='build')
@@ -66,7 +72,8 @@ class Thrift(Package):
         options.append('--enable-tests=no')
 
         options.append('--with-c=%s' % ('yes' if '+c' in spec else 'no'))
-        options.append('--with-python=%s' % ('yes' if '+python' in spec else 'no'))
+        options.append('--with-python=%s' %
+                       ('yes' if '+python' in spec else 'no'))
         options.append('--with-java=%s' % ('yes' if '+java' in spec else 'no'))
         options.append('--with-go=%s' % ('yes' if '+go' in spec else 'no'))
         options.append('--with-lua=%s' % ('yes' if '+lua' in spec else 'no'))
diff --git a/var/spack/repos/builtin/packages/tmuxinator/package.py b/var/spack/repos/builtin/packages/tmuxinator/package.py
index b9c92ea4db..66da4006f2 100644
--- a/var/spack/repos/builtin/packages/tmuxinator/package.py
+++ b/var/spack/repos/builtin/packages/tmuxinator/package.py
@@ -24,17 +24,18 @@
 ##############################################################################
 from spack import *
 
+
 class Tmuxinator(Package):
     """A session configuration creator and manager for tmux"""
     homepage = "https://github.com/tmuxinator/tmuxinator"
     url      = "https://github.com/tmuxinator/tmuxinator"
 
     version('0.6.11',
-        git='https://github.com/tmuxinator/tmuxinator',
-        tag='v0.6.11')
+            git='https://github.com/tmuxinator/tmuxinator',
+            tag='v0.6.11')
 
     extends('ruby')
 
     def install(self, spec, prefix):
-      gem('build', 'tmuxinator.gemspec')
-      gem('install', 'tmuxinator-{0}.gem'.format(self.version))
+        gem('build', 'tmuxinator.gemspec')
+        gem('install', 'tmuxinator-{0}.gem'.format(self.version))
diff --git a/var/spack/repos/builtin/packages/tree/package.py b/var/spack/repos/builtin/packages/tree/package.py
new file mode 100644
index 0000000000..8e0e176c4c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/tree/package.py
@@ -0,0 +1,46 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Tree(Package):
+    """Tree is a recursive directory listing command that produces a depth
+       indented listing of files, which is colorized ala dircolors if
+       the LS_COLORS environment variable is set and output is to
+       tty. Tree has been ported and reported to work under the
+       following operating systems: Linux, FreeBSD, OS X, Solaris,
+       HP/UX, Cygwin, HP Nonstop and OS/2."""
+
+    homepage = "http://mama.indstate.edu/users/ice/tree/"
+    url      = "http://mama.indstate.edu/users/ice/tree/src/tree-1.7.0.tgz"
+
+    version('1.7.0', 'abe3e03e469c542d8e157cdd93f4d8a6')
+
+    def install(self, spec, prefix):
+        filter_file(r'^prefix =.*', 'prefix = %s' % prefix, 'Makefile')
+        filter_file(r'^CFLAGS', '# use spack settings instead... CFLAGS',
+                    'Makefile')
+        make()
+        make('install')
diff --git a/var/spack/repos/builtin/packages/triangle/package.py b/var/spack/repos/builtin/packages/triangle/package.py
index bc8b0ec639..f4ee9ca1c9 100644
--- a/var/spack/repos/builtin/packages/triangle/package.py
+++ b/var/spack/repos/builtin/packages/triangle/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Triangle(Package):
     """Triangle is a two-dimensional mesh generator and Delaunay
        triangulator. Triangle generates exact Delaunay triangulations,
diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 77589bb8f9..d39e45f054 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -45,6 +45,7 @@ class Trilinos(Package):
     homepage = "https://trilinos.org/"
     url = "http://trilinos.csbsju.edu/download/files/trilinos-12.2.1-Source.tar.gz"
 
+    version('12.6.4', 'db25056617c688f6f25092376a03200f')
     version('12.6.3', '960f5f4d3f7c3da818e5a5fb4684559eff7e0c25f959ef576561b8a52f0e4d1e')
     version('12.6.2', '0c076090508170ddee5efeed317745027f9418319720dc40a072e478775279f9')
     version('12.6.1', 'adcf2d3aab74cdda98f88fee19cd1442604199b0515ee3da4d80cbe8f37d00e4')
@@ -55,17 +56,24 @@ class Trilinos(Package):
     version('11.14.2', 'a43590cf896c677890d75bfe75bc6254')
     version('11.14.1', '40febc57f76668be8b6a77b7607bb67f')
 
-    variant('metis',        default=True,  description='Compile with METIS and ParMETIS')
-    variant('mumps',        default=True,  description='Compile with support for MUMPS solvers')
-    variant('superlu-dist', default=True,  description='Compile with SuperluDist solvers')
-    variant('hypre',        default=True,  description='Compile with Hypre preconditioner')
+    variant('metis',        default=True,
+            description='Compile with METIS and ParMETIS')
+    variant('mumps',        default=True,
+            description='Compile with support for MUMPS solvers')
+    variant('superlu-dist', default=True,
+            description='Compile with SuperluDist solvers')
+    variant('hypre',        default=True,
+            description='Compile with Hypre preconditioner')
     variant('hdf5',         default=True,  description='Compile with HDF5')
-    variant('suite-sparse', default=True,  description='Compile with SuiteSparse solvers')
+    variant('suite-sparse', default=True,
+            description='Compile with SuiteSparse solvers')
     # not everyone has py-numpy activated, keep it disabled by default to avoid
     # configure errors
     variant('python',       default=False, description='Build python wrappers')
-    variant('shared',       default=True,  description='Enables the build of shared libraries')
-    variant('debug',        default=False, description='Builds a debug version of the libraries')
+    variant('shared',       default=True,
+            description='Enables the build of shared libraries')
+    variant('debug',        default=False,
+            description='Builds a debug version of the libraries')
     variant('boost',        default=True, description='Compile with Boost')
 
     depends_on('cmake', type='build')
@@ -138,16 +146,23 @@ class Trilinos(Package):
             '-DTPL_ENABLE_LAPACK=ON',
             '-DLAPACK_LIBRARY_NAMES=%s' % to_lib_name(
                 spec['lapack'].lapack_shared_lib),
-            '-DLAPACK_LIBRARY_DIRS=%s' % spec['lapack'].prefix,
+            '-DLAPACK_LIBRARY_DIRS=%s' % spec['lapack'].prefix.lib,
             '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON',
             '-DTrilinos_ENABLE_CXX11:BOOL=ON',
             '-DTPL_ENABLE_Netcdf:BOOL=ON',
             '-DTPL_ENABLE_HYPRE:BOOL=%s' % (
-                'ON' if '+hypre' in spec else 'OFF'),
-            '-DTPL_ENABLE_HDF5:BOOL=%s' % (
-                'ON' if '+hdf5' in spec else 'OFF'),
+                'ON' if '+hypre' in spec else 'OFF')
         ])
 
+        if '+hdf5' in spec:
+            options.extend([
+                '-DTPL_ENABLE_HDF5:BOOL=ON',
+                '-DHDF5_INCLUDE_DIRS:PATH=%s' % spec['hdf5'].prefix.include,
+                '-DHDF5_LIBRARY_DIRS:PATH=%s' % spec['hdf5'].prefix.lib
+            ])
+        else:
+            options.extend(['-DTPL_ENABLE_HDF5:BOOL=OFF'])
+
         if '+boost' in spec:
             options.extend([
                 '-DTPL_ENABLE_Boost:BOOL=ON',
diff --git a/var/spack/repos/builtin/packages/udunits2/package.py b/var/spack/repos/builtin/packages/udunits2/package.py
index aed39668fd..bae6414c5b 100644
--- a/var/spack/repos/builtin/packages/udunits2/package.py
+++ b/var/spack/repos/builtin/packages/udunits2/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Udunits2(Package):
     """Automated units conversion"""
 
diff --git a/var/spack/repos/builtin/packages/uncrustify/package.py b/var/spack/repos/builtin/packages/uncrustify/package.py
index db96bc301e..c3182d0dc8 100644
--- a/var/spack/repos/builtin/packages/uncrustify/package.py
+++ b/var/spack/repos/builtin/packages/uncrustify/package.py
@@ -24,8 +24,9 @@
 ##############################################################################
 from spack import *
 
+
 class Uncrustify(Package):
-    """Source Code Beautifier for C, C++, C#, ObjectiveC, D, Java, Pawn and VALA"""
+    """Source Code Beautifier for C, C++, C#, ObjectiveC, Java, and others."""
 
     homepage = "http://uncrustify.sourceforge.net/"
     url      = "http://downloads.sourceforge.net/project/uncrustify/uncrustify/uncrustify-0.61/uncrustify-0.61.tar.gz"
diff --git a/var/spack/repos/builtin/packages/unibilium/package.py b/var/spack/repos/builtin/packages/unibilium/package.py
index d9e0ad6bcb..943e4737e1 100644
--- a/var/spack/repos/builtin/packages/unibilium/package.py
+++ b/var/spack/repos/builtin/packages/unibilium/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Unibilium(Package):
     """A terminfo parsing library"""
     homepage = "https://github.com/mauke/unibilium"
@@ -32,5 +33,5 @@ class Unibilium(Package):
     version('1.2.0', '9b1c97839a880a373da6c097443b43c4')
 
     def install(self, spec, prefix):
-        make("PREFIX="+prefix)
-        make("install", "PREFIX="+prefix)
+        make("PREFIX=" + prefix)
+        make("install", "PREFIX=" + prefix)
diff --git a/var/spack/repos/builtin/packages/unison/package.py b/var/spack/repos/builtin/packages/unison/package.py
new file mode 100644
index 0000000000..181e1e6410
--- /dev/null
+++ b/var/spack/repos/builtin/packages/unison/package.py
@@ -0,0 +1,51 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Unison(Package):
+    """Unison is a file-synchronization tool for OSX, Unix, and
+       Windows. It allows two replicas of a collection of files and
+       directories to be stored on different hosts (or different disks
+       on the same host), modified separately, and then brought up to
+       date by propagating the changes in each replica to the
+       other."""
+
+    homepage = "https://www.cis.upenn.edu/~bcpierce/unison/"
+    url      = "https://www.seas.upenn.edu/~bcpierce/unison//download/releases/stable/unison-2.48.3.tar.gz"
+
+    version('2.48.4', '5334b78c7e68169df7de95f4c6c4b60f')
+
+    depends_on('ocaml', type='build')
+
+    parallel = False
+
+    def install(self, spec, prefix):
+        make('./mkProjectInfo')
+        make('UISTYLE=text')
+
+        mkdirp(prefix.bin)
+        install('unison', prefix.bin)
+        set_executable(join_path(prefix.bin, 'unison'))
diff --git a/var/spack/repos/builtin/packages/util-linux/package.py b/var/spack/repos/builtin/packages/util-linux/package.py
index bf6972683d..99af170ca1 100644
--- a/var/spack/repos/builtin/packages/util-linux/package.py
+++ b/var/spack/repos/builtin/packages/util-linux/package.py
@@ -23,7 +23,7 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
-import os
+
 
 class UtilLinux(Package):
     """Util-linux is a suite of essential utilities for any Linux system."""
@@ -36,9 +36,9 @@ class UtilLinux(Package):
     depends_on("python@2.7:")
 
     def install(self, spec, prefix):
-        configure("--prefix=%s" % prefix, 
-                "PKG_CONFIG_PATH=%s/pkgconfig" % spec['python'].prefix.lib,
-                "--disable-use-tty-group")
+        configure("--prefix=%s" % prefix,
+                  "PKG_CONFIG_PATH=%s/pkgconfig" % spec['python'].prefix.lib,
+                  "--disable-use-tty-group")
 
         make()
         make("install")
diff --git a/var/spack/repos/builtin/packages/valgrind/package.py b/var/spack/repos/builtin/packages/valgrind/package.py
index afd4cc6ad0..e7ae227c27 100644
--- a/var/spack/repos/builtin/packages/valgrind/package.py
+++ b/var/spack/repos/builtin/packages/valgrind/package.py
@@ -27,12 +27,15 @@ from spack import *
 
 
 class Valgrind(Package):
-    """
-    Valgrind is an instrumentation framework for building dynamic analysis tools. There are Valgrind tools that can
-    automatically detect many memory management and threading bugs, and profile your programs in detail. You can also
-    use Valgrind to build new tools.
+    """An instrumentation framework for building dynamic analysis.
+
+    There are Valgrind tools that can automatically detect many memory
+    management and threading bugs, and profile your programs in
+    detail. You can also use Valgrind to build new tools.
+
+    Valgrind is Open Source / Free Software, and is freely available
+    under the GNU General Public License, version 2.
 
-    Valgrind is Open Source / Free Software, and is freely available under the GNU General Public License, version 2.
     """
     homepage = "http://valgrind.org/"
     url = "http://valgrind.org/downloads/valgrind-3.11.0.tar.bz2"
@@ -42,7 +45,8 @@ class Valgrind(Package):
     version('3.10.0', '7c311a72a20388aceced1aa5573ce970')
 
     variant('mpi', default=True, description='Activates MPI support for valgrind')
-    variant('boost', default=True, description='Activates boost support for valgrind')
+    variant('boost', default=True,
+            description='Activates boost support for valgrind')
 
     depends_on('mpi', when='+mpi')
     depends_on('boost', when='+boost')
diff --git a/var/spack/repos/builtin/packages/vim/package.py b/var/spack/repos/builtin/packages/vim/package.py
index e0dfb64879..01eccfab57 100644
--- a/var/spack/repos/builtin/packages/vim/package.py
+++ b/var/spack/repos/builtin/packages/vim/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Vim(Package):
     """Vim is a highly configurable text editor built to enable efficient text
     editing. It is an improved version of the vi editor distributed with most
@@ -51,7 +52,7 @@ class Vim(Package):
 
     feature_sets = ('huge', 'big', 'normal', 'small', 'tiny')
     for fs in feature_sets:
-      variant(fs, default=False, description="Use '%s' feature set" % fs)
+        variant(fs, default=False, description="Use '%s' feature set" % fs)
 
     variant('python', default=False, description="build with Python")
     depends_on('python', when='+python')
@@ -66,42 +67,44 @@ class Vim(Package):
     # virtual dependency?
 
     def install(self, spec, prefix):
-      feature_set = None
-      for fs in self.feature_sets:
-        if "+" + fs in spec:
-          if feature_set is not None:
-            tty.error("Only one feature set allowed, both %s and %s specified"
-                      % (feature_set, fs))
-          feature_set = fs
-      if '+gui' in spec:
-        if feature_set is not None:
-          if feature_set is not 'huge':
-            tty.error("+gui variant requires 'huge' feature set, %s was specified"
-                      % feature_set)
-        feature_set = 'huge'
-      if feature_set is None:
-        feature_set = 'normal'
-
-      configure_args = []
-      configure_args.append("--with-features=" + feature_set)
-
-      if '+python' in spec:
-        configure_args.append("--enable-pythoninterp=yes")
-      else:
-        configure_args.append("--enable-pythoninterp=dynamic")
-
-      if '+ruby' in spec:
-        configure_args.append("--enable-rubyinterp=yes")
-      else:
-        configure_args.append("--enable-rubyinterp=dynamic")
-
-      if '+gui' in spec:
-        configure_args.append("--enable-gui=auto")
-
-      if '+cscope' in spec:
-        configure_args.append("--enable-cscope")
-
-      configure("--prefix=%s" % prefix, *configure_args)
-
-      make()
-      make("install")
+        feature_set = None
+        for fs in self.feature_sets:
+            if "+" + fs in spec:
+                if feature_set is not None:
+                    tty.error(
+                        "Only one feature set allowed, specified %s and %s"
+                        % (feature_set, fs))
+                feature_set = fs
+        if '+gui' in spec:
+            if feature_set is not None:
+                if feature_set is not 'huge':
+                    tty.error(
+                        "+gui variant requires 'huge' feature set, "
+                        "%s was specified" % feature_set)
+            feature_set = 'huge'
+        if feature_set is None:
+            feature_set = 'normal'
+
+        configure_args = []
+        configure_args.append("--with-features=" + feature_set)
+
+        if '+python' in spec:
+            configure_args.append("--enable-pythoninterp=yes")
+        else:
+            configure_args.append("--enable-pythoninterp=dynamic")
+
+        if '+ruby' in spec:
+            configure_args.append("--enable-rubyinterp=yes")
+        else:
+            configure_args.append("--enable-rubyinterp=dynamic")
+
+        if '+gui' in spec:
+            configure_args.append("--enable-gui=auto")
+
+        if '+cscope' in spec:
+            configure_args.append("--enable-cscope")
+
+        configure("--prefix=%s" % prefix, *configure_args)
+
+        make()
+        make("install")
diff --git a/var/spack/repos/builtin/packages/visit/package.py b/var/spack/repos/builtin/packages/visit/package.py
index ae19fd0450..d88caeb00a 100644
--- a/var/spack/repos/builtin/packages/visit/package.py
+++ b/var/spack/repos/builtin/packages/visit/package.py
@@ -26,7 +26,8 @@ from spack import *
 
 
 class Visit(Package):
-    """VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool."""
+    """VisIt is an Open Source, interactive, scalable, visualization,
+       animation and analysis tool."""
     homepage = "https://wci.llnl.gov/simulation/computer-codes/visit/"
     url = "http://portal.nersc.gov/project/visit/releases/2.10.1/visit2.10.1.tar.gz"
 
@@ -42,12 +43,15 @@ class Visit(Package):
         with working_dir('spack-build', create=True):
 
             feature_args = std_cmake_args[:]
-            feature_args.extend(["-DVTK_MAJOR_VERSION=6",
-                                 "-DVTK_MINOR_VERSION=1",
-                                 "-DVISIT_LOC_QMAKE_EXE:FILEPATH=%s/qmake-qt4" % spec['qt'].prefix.bin,
-                                 "-DPYTHON_EXECUTABLE:FILEPATH=%s/python" % spec['python'].prefix.bin,
-                                 "-DVISIT_SILO_DIR:PATH=%s" % spec['silo'].prefix,
-                                 "-DVISIT_HDF5_DIR:PATH=%s" % spec['hdf5'].prefix])
+            feature_args.extend([
+                "-DVTK_MAJOR_VERSION=6",
+                "-DVTK_MINOR_VERSION=1",
+                "-DVISIT_LOC_QMAKE_EXE:FILEPATH=%s/qmake-qt4" % spec[
+                    'qt'].prefix.bin,
+                "-DPYTHON_EXECUTABLE:FILEPATH=%s/python" % spec[
+                    'python'].prefix.bin,
+                "-DVISIT_SILO_DIR:PATH=%s" % spec['silo'].prefix,
+                "-DVISIT_HDF5_DIR:PATH=%s" % spec['hdf5'].prefix])
 
             cmake('../src', *feature_args)
 
diff --git a/var/spack/repos/builtin/packages/vtk/package.py b/var/spack/repos/builtin/packages/vtk/package.py
index 5c196b5ea8..087c0e93eb 100644
--- a/var/spack/repos/builtin/packages/vtk/package.py
+++ b/var/spack/repos/builtin/packages/vtk/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Vtk(Package):
     """The Visualization Toolkit (VTK) is an open-source, freely
     available software system for 3D computer graphics, image
@@ -31,9 +32,11 @@ class Vtk(Package):
     homepage = "http://www.vtk.org"
     url      = "http://www.vtk.org/files/release/6.1/VTK-6.1.0.tar.gz"
 
-    version("7.0.0", "5fe35312db5fb2341139b8e4955c367d", url="http://www.vtk.org/files/release/7.0/VTK-7.0.0.tar.gz")
+    version("7.0.0", "5fe35312db5fb2341139b8e4955c367d",
+            url="http://www.vtk.org/files/release/7.0/VTK-7.0.0.tar.gz")
 
-    version("6.3.0", '0231ca4840408e9dd60af48b314c5b6d', url="http://www.vtk.org/files/release/6.3/VTK-6.3.0.tar.gz")
+    version("6.3.0", '0231ca4840408e9dd60af48b314c5b6d',
+            url="http://www.vtk.org/files/release/6.3/VTK-6.3.0.tar.gz")
 
     version('6.1.0', '25e4dfb3bad778722dcaec80cd5dab7d')
 
@@ -41,7 +44,8 @@ class Vtk(Package):
     depends_on("qt")
 
     # VTK7 defaults to OpenGL2 rendering backend
-    variant('opengl2', default=True, description='Build with OpenGL instead of OpenGL2 as rendering backend')
+    variant('opengl2', default=True,
+            description='Build with OpenGL instead of OpenGL2 backend')
 
     def install(self, spec, prefix):
         def feature_to_bool(feature, on='ON', off='OFF'):
@@ -67,7 +71,7 @@ class Vtk(Package):
                 "-DVTK_Group_Qt=OFF",
                 "-DModule_vtkGUISupportQt:BOOL=ON",
                 "-DModule_vtkGUISupportQtOpenGL:BOOL=ON"
-                ])
+            ])
 
             if spec['qt'].satisfies('@5'):
                 cmake_args.append("-DVTK_QT_VERSION:STRING=5")
@@ -76,7 +80,8 @@ class Vtk(Package):
                 cmake_args.append("-DCMAKE_C_FLAGS=-DGLX_GLXEXT_LEGACY")
                 cmake_args.append("-DCMAKE_CXX_FLAGS=-DGLX_GLXEXT_LEGACY")
 
-            cmake_args.append('-DVTK_RENDERING_BACKEND:STRING=%s' % feature_to_bool('+opengl2', 'OpenGL2', 'OpenGL'))
+            cmake_args.append('-DVTK_RENDERING_BACKEND:STRING=%s' %
+                              feature_to_bool('+opengl2', 'OpenGL2', 'OpenGL'))
 
             cmake(*cmake_args)
             make()
diff --git a/var/spack/repos/builtin/packages/wget/package.py b/var/spack/repos/builtin/packages/wget/package.py
index 532cf332e9..aff771b723 100644
--- a/var/spack/repos/builtin/packages/wget/package.py
+++ b/var/spack/repos/builtin/packages/wget/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Wget(Package):
     """GNU Wget is a free software package for retrieving files using
        HTTP, HTTPS and FTP, the most widely-used Internet protocols. It
@@ -40,9 +41,11 @@ class Wget(Package):
     depends_on("openssl")
 
     def install(self, spec, prefix):
-        configure("--prefix=%s" % prefix,
-                  "--with-ssl=openssl",
-                  "OPENSSL_CFLAGS=-I%s" % spec['openssl'].prefix.include,
-                  "OPENSSL_LIBS=-L%s -lssl -lcrypto -lz" % spec['openssl'].prefix.lib)
+        configure(
+            "--prefix=%s" % prefix,
+            "--with-ssl=openssl",
+            "OPENSSL_CFLAGS=-I%s" % spec['openssl'].prefix.include,
+            "OPENSSL_LIBS=-L%s -lssl -lcrypto -lz" % spec[
+                'openssl'].prefix.lib)
         make()
         make("install")
diff --git a/var/spack/repos/builtin/packages/wx/package.py b/var/spack/repos/builtin/packages/wx/package.py
index c000824803..5a80ca1c1f 100644
--- a/var/spack/repos/builtin/packages/wx/package.py
+++ b/var/spack/repos/builtin/packages/wx/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Wx(Package):
     """wxWidgets is a C++ library that lets developers create
        applications for Windows, Mac OS X, Linux and other platforms
@@ -43,8 +44,8 @@ class Wx(Package):
     depends_on('gtkplus')
 
     def install(self, spec, prefix):
-        configure("--prefix=%s" % prefix, "--enable-unicode", "--disable-precomp-headers")
+        configure("--prefix=%s" % prefix, "--enable-unicode",
+                  "--disable-precomp-headers")
 
         make(parallel=False)
         make("install")
-
diff --git a/var/spack/repos/builtin/packages/wxpropgrid/package.py b/var/spack/repos/builtin/packages/wxpropgrid/package.py
index 2283e1acf1..cc9ff445d6 100644
--- a/var/spack/repos/builtin/packages/wxpropgrid/package.py
+++ b/var/spack/repos/builtin/packages/wxpropgrid/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Wxpropgrid(Package):
     """wxPropertyGrid is a property sheet control for wxWidgets. In
        other words, it is a specialized two-column grid for editing
@@ -37,8 +38,8 @@ class Wxpropgrid(Package):
     depends_on("wx")
 
     def install(self, spec, prefix):
-        configure("--prefix=%s" % prefix, "--with-wxdir=%s" % spec['wx'].prefix.bin, "--enable-unicode")
+        configure("--prefix=%s" % prefix, "--with-wxdir=%s" %
+                  spec['wx'].prefix.bin, "--enable-unicode")
 
         make()
         make("install")
-
diff --git a/var/spack/repos/builtin/packages/xcb-proto/package.py b/var/spack/repos/builtin/packages/xcb-proto/package.py
index efcbdf0aea..587983f6bd 100644
--- a/var/spack/repos/builtin/packages/xcb-proto/package.py
+++ b/var/spack/repos/builtin/packages/xcb-proto/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class XcbProto(Package):
     """Protocol for libxcb"""
 
diff --git a/var/spack/repos/builtin/packages/xerces-c/package.py b/var/spack/repos/builtin/packages/xerces-c/package.py
index 2efccc3c08..d0c2d3d497 100644
--- a/var/spack/repos/builtin/packages/xerces-c/package.py
+++ b/var/spack/repos/builtin/packages/xerces-c/package.py
@@ -24,16 +24,18 @@
 ##############################################################################
 from spack import *
 
+
 class XercesC(Package):
     """ Xerces-C++ is a validating XML parser written in a portable subset of C++.
     Xerces-C++ makes it easy to give your application the ability to read and
     write XML data. A shared library is provided for parsing, generating,
-    manipulating, and validating XML documents using the DOM, SAX, and SAX2 APIs.
+    manipulating, and validating XML documents using the DOM, SAX, and SAX2
+    APIs.
     """
 
     homepage = "https://xerces.apache.org/xerces-c"
-    url      = "https://www.apache.org/dist/xerces/c/3/sources/xerces-c-3.1.3.tar.bz2"
-    version('3.1.3', '5e333b55cb43e6b025ddf0e5d0f0fb0d')
+    url      = "https://www.apache.org/dist/xerces/c/3/sources/xerces-c-3.1.4.tar.bz2"
+    version('3.1.4', 'd04ae9d8b2dee2157c6db95fa908abfd')
 
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix,
@@ -41,4 +43,3 @@ class XercesC(Package):
         make("clean")
         make()
         make("install")
-
diff --git a/var/spack/repos/builtin/packages/xorg-util-macros/package.py b/var/spack/repos/builtin/packages/xorg-util-macros/package.py
index 963d93442f..cd50d46826 100644
--- a/var/spack/repos/builtin/packages/xorg-util-macros/package.py
+++ b/var/spack/repos/builtin/packages/xorg-util-macros/package.py
@@ -24,11 +24,12 @@
 ##############################################################################
 from spack import *
 
+
 class XorgUtilMacros(Package):
-    """The util-macros package contains the m4 macros used by all of the Xorg packages."""
+    """The m4 macros used by all of the Xorg packages."""
 
     homepage = "http://www.example.com"
-    url      = "http://ftp.x.org/pub/individual/util/util-macros-1.19.0.tar.bz2"
+    url = "http://ftp.x.org/pub/individual/util/util-macros-1.19.0.tar.bz2"
 
     version('1.19.0', '1cf984125e75f8204938d998a8b6c1e1')
 
diff --git a/var/spack/repos/builtin/packages/xproto/package.py b/var/spack/repos/builtin/packages/xproto/package.py
index 7be6defb83..dbceaa1575 100644
--- a/var/spack/repos/builtin/packages/xproto/package.py
+++ b/var/spack/repos/builtin/packages/xproto/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Xproto(Package):
     """The Xorg protocol headers provide the header files required to
        build the system, and to allow other applications to build against
diff --git a/var/spack/repos/builtin/packages/xz/package.py b/var/spack/repos/builtin/packages/xz/package.py
index b3ef7808aa..a8ab959a62 100644
--- a/var/spack/repos/builtin/packages/xz/package.py
+++ b/var/spack/repos/builtin/packages/xz/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Xz(Package):
     """XZ Utils is free general-purpose data compression software with
        high compression ratio. XZ Utils were written for POSIX-like
@@ -39,4 +40,3 @@ class Xz(Package):
         configure("--prefix=%s" % prefix)
         make()
         make("install")
-
diff --git a/var/spack/repos/builtin/packages/yasm/package.py b/var/spack/repos/builtin/packages/yasm/package.py
index e05160c8ea..f14bdbcee7 100644
--- a/var/spack/repos/builtin/packages/yasm/package.py
+++ b/var/spack/repos/builtin/packages/yasm/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Yasm(Package):
     """Yasm is a complete rewrite of the NASM-2.11.06 assembler. It
        supports the x86 and AMD64 instruction sets, accepts NASM and
diff --git a/var/spack/repos/builtin/packages/zeromq/package.py b/var/spack/repos/builtin/packages/zeromq/package.py
index 9bdd5861e0..6a657dc39c 100644
--- a/var/spack/repos/builtin/packages/zeromq/package.py
+++ b/var/spack/repos/builtin/packages/zeromq/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Zeromq(Package):
     """ The ZMQ networking/concurrency library and core API """
     homepage = "http://zguide.zeromq.org/"
@@ -38,7 +39,7 @@ class Zeromq(Package):
     depends_on("libsodium")
 
     def install(self, spec, prefix):
-        configure("--with-libsodium","--prefix=%s" % prefix)
+        configure("--with-libsodium", "--prefix=%s" % prefix)
 
         make()
         make("install")
diff --git a/var/spack/repos/builtin/packages/zfp/package.py b/var/spack/repos/builtin/packages/zfp/package.py
index 878b65118f..a898ab03d3 100644
--- a/var/spack/repos/builtin/packages/zfp/package.py
+++ b/var/spack/repos/builtin/packages/zfp/package.py
@@ -24,12 +24,15 @@
 ##############################################################################
 from spack import *
 
+
 class Zfp(Package):
-    """zfp is an open source C library for compressed floating-point arrays that supports
-       very high throughput read and write random acces, target error bounds or bit rates.
-       Although bit-for-bit lossless compression is not always possible, zfp is usually
-       accurate to within machine epsilon in near-lossless mode, and is often orders of
-       magnitude more accurate than other lossy compressors.
+    """zfp is an open source C library for compressed floating-point arrays
+       that supports very high throughput read and write random acces,
+       target error bounds or bit rates.  Although bit-for-bit lossless
+       compression is not always possible, zfp is usually accurate to
+       within machine epsilon in near-lossless mode, and is often orders
+       of magnitude more accurate than other lossy compressors.
+
     """
 
     homepage = "http://computation.llnl.gov/projects/floating-point-compression"
diff --git a/var/spack/repos/builtin/packages/zlib/package.py b/var/spack/repos/builtin/packages/zlib/package.py
index e1cbdc7e28..6d799fb05a 100644
--- a/var/spack/repos/builtin/packages/zlib/package.py
+++ b/var/spack/repos/builtin/packages/zlib/package.py
@@ -24,11 +24,10 @@
 ##############################################################################
 from spack import *
 
+
 class Zlib(Package):
-    """zlib is designed to be a free, general-purpose, legally unencumbered --
-       that is, not covered by any patents -- lossless data-compression library for
-       use on virtually any computer hardware and operating system.
-    """
+    """A free, general-purpose, legally unencumbered lossless
+       data-compression library."""
 
     homepage = "http://zlib.net"
     url      = "http://zlib.net/zlib-1.2.8.tar.gz"
diff --git a/var/spack/repos/builtin/packages/zoltan/package.py b/var/spack/repos/builtin/packages/zoltan/package.py
index 841ff3f4a2..0094395968 100644
--- a/var/spack/repos/builtin/packages/zoltan/package.py
+++ b/var/spack/repos/builtin/packages/zoltan/package.py
@@ -22,16 +22,22 @@
 # License along with this program; if not, write to the Free Software
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
-import re, os, glob
+import re
+import os
+import glob
 from spack import *
 
+
 class Zoltan(Package):
-    """The Zoltan library is a toolkit of parallel combinatorial algorithms for
-       parallel, unstructured, and/or adaptive scientific applications.  Zoltan's
-       largest component is a suite of dynamic load-balancing and paritioning
-       algorithms that increase applications' parallel performance by reducing
-       idle time.  Zoltan also has graph coloring and graph ordering algorithms,
-       which are useful in task schedulers and parallel preconditioners."""
+    """The Zoltan library is a toolkit of parallel combinatorial algorithms
+       for parallel, unstructured, and/or adaptive scientific
+       applications.  Zoltan's largest component is a suite of dynamic
+       load-balancing and paritioning algorithms that increase
+       applications' parallel performance by reducing idle time.  Zoltan
+       also has graph coloring and graph ordering algorithms, which are
+       useful in task schedulers and parallel preconditioners.
+
+    """
 
     homepage = "http://www.cs.sandia.gov/zoltan"
     base_url = "http://www.cs.sandia.gov/~kddevin/Zoltan_Distributions"
@@ -41,8 +47,10 @@ class Zoltan(Package):
     version('3.6', '9cce794f7241ecd8dbea36c3d7a880f9')
     version('3.3', '5eb8f00bda634b25ceefa0122bd18d65')
 
-    variant('debug', default=False, description='Builds a debug version of the library')
-    variant('shared', default=True, description='Builds a shared version of the library')
+    variant('debug', default=False,
+            description='Builds a debug version of the library')
+    variant('shared', default=True,
+            description='Builds a shared version of the library')
 
     variant('fortran', default=True, description='Enable Fortran support')
     variant('mpi', default=False, description='Enable MPI support')
@@ -51,8 +59,11 @@ class Zoltan(Package):
 
     def install(self, spec, prefix):
         config_args = [
-            '--enable-f90interface' if '+fortan' in spec else '--disable-f90interface',
-            '--enable-mpi' if '+mpi' in spec else '--disable-mpi',
+            '--enable-f90interface'
+            if '+fortan' in spec else '--disable-f90interface',
+
+            '--enable-mpi'
+            if '+mpi' in spec else '--disable-mpi',
         ]
         config_cflags = [
             '-O0' if '+debug' in spec else '-O3',
@@ -68,7 +79,8 @@ class Zoltan(Package):
             config_args.append('CC=%s/mpicc' % spec['mpi'].prefix.bin)
             config_args.append('CXX=%s/mpicxx' % spec['mpi'].prefix.bin)
             config_args.append('--with-mpi=%s' % spec['mpi'].prefix)
-            config_args.append('--with-mpi-compilers=%s' % spec['mpi'].prefix.bin)
+            config_args.append('--with-mpi-compilers=%s' %
+                               spec['mpi'].prefix.bin)
 
         # NOTE: Early versions of Zoltan come packaged with a few embedded
         # library packages (e.g. ParMETIS, Scotch), which messes with Spack's
@@ -89,13 +101,15 @@ class Zoltan(Package):
         make()
         make('install')
 
-        # NOTE: Unfortunately, Zoltan doesn't provide any configuration options for
-        # the extension of the output library files, so this script must change these
-        # extensions as a post-processing step.
+        # NOTE: Unfortunately, Zoltan doesn't provide any configuration
+        # options for the extension of the output library files, so this
+        # script must change these extensions as a post-processing step.
         if '+shared' in spec:
             for libpath in glob.glob('lib/*.a'):
-                libdir, libname = (os.path.dirname(libpath), os.path.basename(libpath))
-                move(libpath, os.path.join(libdir, re.sub(r'\.a$', '.so', libname)))
+                libdir, libname = (os.path.dirname(libpath),
+                                   os.path.basename(libpath))
+                move(libpath, os.path.join(
+                    libdir, re.sub(r'\.a$', '.so', libname)))
 
         mkdirp(prefix)
         move('include', prefix)
diff --git a/var/spack/repos/builtin/packages/zsh/package.py b/var/spack/repos/builtin/packages/zsh/package.py
index 2c9ed4c6e7..4c27cd3ec2 100644
--- a/var/spack/repos/builtin/packages/zsh/package.py
+++ b/var/spack/repos/builtin/packages/zsh/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class Zsh(Package):
     """
     Zsh is a shell designed for interactive use, although it is also a powerful