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author <kellyt@MENE.localdomain>2016-08-01 20:50:28 -0600
committer <kellyt@MENE.localdomain>2016-08-01 20:50:28 -0600
commitba11f19efcec5b5581bb804fb91768205c5488af (patch)
treef0c4162eb3a2f4481fc13ccec1eff97bf56b1346
parent6c80b152208e8f2154db6c658475fe18a9c9f8bc (diff)
parentbb5dd49206e98f066d211b6a0f5a408b209ef2aa (diff)
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Merge remote-tracking branch 'upstream/develop' into gktplus3-deps
-rw-r--r--.travis.yml25
-rw-r--r--lib/spack/llnl/util/filesystem.py18
-rw-r--r--lib/spack/spack/concretize.py12
-rw-r--r--lib/spack/spack/config.py13
-rw-r--r--lib/spack/spack/operating_systems/cnl.py24
-rw-r--r--lib/spack/spack/platforms/cray.py105
-rw-r--r--lib/spack/spack/platforms/cray_xc.py72
-rw-r--r--lib/spack/spack/stage.py112
-rw-r--r--lib/spack/spack/test/architecture.py4
-rwxr-xr-xshare/spack/qa/run-unit-tests20
-rw-r--r--var/spack/repos/builtin/packages/R/package.py44
-rw-r--r--var/spack/repos/builtin/packages/cask/package.py53
-rw-r--r--var/spack/repos/builtin/packages/cp2k/package.py161
-rw-r--r--var/spack/repos/builtin/packages/hypre/package.py4
-rw-r--r--var/spack/repos/builtin/packages/jdk/package.py2
-rw-r--r--var/spack/repos/builtin/packages/libhio/package.py45
-rw-r--r--var/spack/repos/builtin/packages/libxsmm/package.py66
-rw-r--r--var/spack/repos/builtin/packages/mkl/package.py12
-rw-r--r--var/spack/repos/builtin/packages/opencv/package.py177
-rw-r--r--var/spack/repos/builtin/packages/pgi/package.py1
-rw-r--r--var/spack/repos/builtin/packages/r-boot/package.py43
-rw-r--r--var/spack/repos/builtin/packages/r-brew/package.py43
-rw-r--r--var/spack/repos/builtin/packages/r-car/package.py48
-rw-r--r--var/spack/repos/builtin/packages/r-caret/package.py50
-rw-r--r--var/spack/repos/builtin/packages/r-chron/package.py41
-rw-r--r--var/spack/repos/builtin/packages/r-class/package.py44
-rw-r--r--var/spack/repos/builtin/packages/r-crayon/package.py45
-rw-r--r--var/spack/repos/builtin/packages/r-cubature/package.py41
-rw-r--r--var/spack/repos/builtin/packages/r-curl/package.py3
-rw-r--r--var/spack/repos/builtin/packages/r-datatable/package.py46
-rw-r--r--var/spack/repos/builtin/packages/r-e1071/package.py45
-rw-r--r--var/spack/repos/builtin/packages/r-gdata/package.py59
-rw-r--r--var/spack/repos/builtin/packages/r-geosphere/package.py45
-rw-r--r--var/spack/repos/builtin/packages/r-ggmap/package.py57
-rw-r--r--var/spack/repos/builtin/packages/r-glmnet/package.py49
-rw-r--r--var/spack/repos/builtin/packages/r-gtools/package.py60
-rw-r--r--var/spack/repos/builtin/packages/r-jpeg/package.py45
-rw-r--r--var/spack/repos/builtin/packages/r-lme4/package.py53
-rw-r--r--var/spack/repos/builtin/packages/r-lmtest/package.py45
-rw-r--r--var/spack/repos/builtin/packages/r-mapproj/package.py43
-rw-r--r--var/spack/repos/builtin/packages/r-maps/package.py42
-rw-r--r--var/spack/repos/builtin/packages/r-maptools/package.py49
-rw-r--r--var/spack/repos/builtin/packages/r-matrixmodels/package.py44
-rw-r--r--var/spack/repos/builtin/packages/r-mgcv/package.py47
-rw-r--r--var/spack/repos/builtin/packages/r-minqa/package.py44
-rw-r--r--var/spack/repos/builtin/packages/r-multcomp/package.py51
-rw-r--r--var/spack/repos/builtin/packages/r-mvtnorm/package.py42
-rw-r--r--var/spack/repos/builtin/packages/r-ncdf4/package.py56
-rw-r--r--var/spack/repos/builtin/packages/r-nlme/package.py43
-rw-r--r--var/spack/repos/builtin/packages/r-nloptr/package.py47
-rw-r--r--var/spack/repos/builtin/packages/r-nnet/package.py42
-rw-r--r--var/spack/repos/builtin/packages/r-np/package.py50
-rw-r--r--var/spack/repos/builtin/packages/r-pbkrtest/package.py49
-rw-r--r--var/spack/repos/builtin/packages/r-plotrix/package.py41
-rw-r--r--var/spack/repos/builtin/packages/r-praise/package.py41
-rw-r--r--var/spack/repos/builtin/packages/r-proto/package.py42
-rw-r--r--var/spack/repos/builtin/packages/r-quantmod/package.py46
-rw-r--r--var/spack/repos/builtin/packages/r-quantreg/package.py50
-rw-r--r--var/spack/repos/builtin/packages/r-randomforest/package.py42
-rw-r--r--var/spack/repos/builtin/packages/r-rgooglemaps/package.py47
-rw-r--r--var/spack/repos/builtin/packages/r-rjson/package.py41
-rw-r--r--var/spack/repos/builtin/packages/r-rjsonio/package.py55
-rw-r--r--var/spack/repos/builtin/packages/r-roxygen2/package.py48
-rw-r--r--var/spack/repos/builtin/packages/r-sandwich/package.py44
-rw-r--r--var/spack/repos/builtin/packages/r-sparsem/package.py43
-rw-r--r--var/spack/repos/builtin/packages/r-survey/package.py47
-rw-r--r--var/spack/repos/builtin/packages/r-survival/package.py45
-rw-r--r--var/spack/repos/builtin/packages/r-tarifx/package.py44
-rw-r--r--var/spack/repos/builtin/packages/r-testthat/package.py48
-rw-r--r--var/spack/repos/builtin/packages/r-thdata/package.py44
-rw-r--r--var/spack/repos/builtin/packages/r-ttr/package.py44
-rw-r--r--var/spack/repos/builtin/packages/r-vcd/package.py50
-rw-r--r--var/spack/repos/builtin/packages/r-xml/package.py45
-rw-r--r--var/spack/repos/builtin/packages/tree/package.py46
-rw-r--r--var/spack/repos/builtin/packages/trilinos/package.py15
75 files changed, 3256 insertions, 193 deletions
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/lib/spack/llnl/util/filesystem.py b/lib/spack/llnl/util/filesystem.py
index 6e4cd338fe..2478f5c159 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()))
except:
# clean up the original file on failure.
shutil.move(backup_filename, filename)
@@ -189,7 +191,7 @@ 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)
diff --git a/lib/spack/spack/concretize.py b/lib/spack/spack/concretize.py
index 5180f3cf04..eced9917c9 100644
--- a/lib/spack/spack/concretize.py
+++ b/lib/spack/spack/concretize.py
@@ -336,14 +336,18 @@ class DefaultConcretizer(object):
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.
@@ -489,9 +493,9 @@ 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, # NOQA: ignore=E501
"Run 'spack compilers' to see available compiler Options.")
diff --git a/lib/spack/spack/config.py b/lib/spack/spack/config.py
index e2e7dbc0ee..31f0eb3a56 100644
--- a/lib/spack/spack/config.py
+++ b/lib/spack/spack/config.py
@@ -266,6 +266,19 @@ section_schemas = {
], },
},},},},},},
+ 'targets': {
+ '$schema': 'http://json-schema.org/schema#',
+ 'title': 'Spack target configuration file schema',
+ 'type': 'object',
+ 'additionalProperties': False,
+ 'patternProperties': {
+ r'targets:?': {
+ 'type': 'object',
+ 'default': {},
+ 'additionalProperties': False,
+ 'patternProperties': {
+ r'\w[\w-]*': { # target name
+ 'type': 'string' ,},},},},},
'modules': {
'$schema': 'http://json-schema.org/schema#',
'title': 'Spack module file configuration file schema',
diff --git a/lib/spack/spack/operating_systems/cnl.py b/lib/spack/spack/operating_systems/cnl.py
index c160a60be8..dbd2775861 100644
--- a/lib/spack/spack/operating_systems/cnl.py
+++ b/lib/spack/spack/operating_systems/cnl.py
@@ -7,11 +7,12 @@ 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):
@@ -19,17 +20,19 @@ class Cnl(OperatingSystem):
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 +48,16 @@ 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/platforms/cray.py b/lib/spack/spack/platforms/cray.py
new file mode 100644
index 0000000000..2a3b81cf9c
--- /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_PATHS', 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 03d0383cc5..0000000000
--- a/lib/spack/spack/platforms/cray_xc.py
+++ /dev/null
@@ -1,72 +0,0 @@
-import os
-import spack
-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
-from llnl.util.filesystem import join_path
-
-
-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 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_PATHS', cray_wrapper_names)
-
- @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/stage.py b/lib/spack/spack/stage.py
index b08cce43b8..1a8b1a169a 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:
@@ -306,6 +317,19 @@ class Stage(object):
fetchers.insert(0, fs.URLFetchStrategy(url, digest))
fetchers.insert(0, spack.cache.fetcher(self.mirror_path, digest))
+ # Look for the archive in list_url
+ archive_version = spack.url.parse_version(self.default_fetcher.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:
+ 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)
+
for fetcher in fetchers:
try:
fetcher.set_stage(self)
@@ -321,11 +345,11 @@ 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 +359,13 @@ class Stage(object):
else:
self.fetcher.check()
-
def cache_local(self):
spack.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 +407,8 @@ 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 +430,7 @@ 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 +440,15 @@ 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 +462,23 @@ 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 +523,11 @@ 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/architecture.py b/lib/spack/spack/test/architecture.py
index 09bdb021af..42dd9f4c04 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
@@ -76,7 +76,7 @@ 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():
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/var/spack/repos/builtin/packages/R/package.py b/var/spack/repos/builtin/packages/R/package.py
index ad06c2ca48..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
@@ -125,15 +132,21 @@ 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):
@@ -147,13 +160,14 @@ class R(Package):
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/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/cp2k/package.py b/var/spack/repos/builtin/packages/cp2k/package.py
new file mode 100644
index 0000000000..8fdd1e0ca3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cp2k/package.py
@@ -0,0 +1,161 @@
+##############################################################################
+# 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')
+
+ depends_on('python') # Build dependency
+
+ depends_on('lapack')
+ depends_on('blas')
+ depends_on('fftw')
+
+ depends_on('mpi', when='+mpi')
+ depends_on('scalapack', when='+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 plumed
+ # 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:
+ 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))
+ # 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 = []
+ # 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/hypre/package.py b/var/spack/repos/builtin/packages/hypre/package.py
index 65fef57559..b339e068bf 100644
--- a/var/spack/repos/builtin/packages/hypre/package.py
+++ b/var/spack/repos/builtin/packages/hypre/package.py
@@ -62,10 +62,10 @@ 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/jdk/package.py b/var/spack/repos/builtin/packages/jdk/package.py
index 593a6d8340..794966f1c3 100644
--- a/var/spack/repos/builtin/packages/jdk/package.py
+++ b/var/spack/repos/builtin/packages/jdk/package.py
@@ -25,7 +25,7 @@
#
# Author: Justin Too <too1@llnl.gov>
#
-import distutils
+import distutils.dir_util
import spack
from spack import *
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/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/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/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/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/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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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/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/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 77589bb8f9..4d1d27e74a 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -138,16 +138,23 @@ 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',