hlrs-software-stack/spack
7
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity

Merge remote-tracking branch 'upstream/develop' into gktplus3-deps

Browse source
This commit is contained in:
2016-08-01 20:50:28 -06:00
commit ba11f19efc
75 changed files with 3256 additions and 193 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

25
.travis.yml
View file

@ -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:

18
lib/spack/llnl/util/filesystem.py
View file

@ -29,8 +29,9 @@
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 groupid_to_group(x):
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)

12
lib/spack/spack/concretize.py
View file

@ -336,14 +336,18 @@ def _proper_compiler_style(cspec, arch):
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.")

13
lib/spack/spack/config.py
View file

@ -266,6 +266,19 @@
], },
},},},},},},
'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',

24
lib/spack/spack/operating_systems/cnl.py
View file

@ -7,11 +7,12 @@
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 @@ def __init__(self):
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 @@ def find_compiler(self, cmp_cls, *paths):
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)

105
lib/spack/spack/platforms/cray.py Normal file
View file

@ -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

72
lib/spack/spack/platforms/cray_xc.py
View file

@ -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

112
lib/spack/spack/stage.py
View file

@ -37,6 +37,7 @@
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 @@ def __init__(self, url_or_fetch_strategy,
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 @@ def __init__(self, url_or_fetch_strategy,
# 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 @@ def __enter__(self):
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 @@ def __exit__(self, exc_type, exc_val, exc_tb):
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 @@ def _need_to_create_path(self):
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 @@ def _need_to_create_path(self):
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 @@ def expected_archive_files(self):
"""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 @@ def archive_file(self):
"""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 @@ def source_path(self):
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 @@ def fetch(self, mirror_only=False):
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 @@ def fetch(self, mirror_only=False):
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 @@ def check(self):
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 @@ def create(self):
# 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 @@ def destroy(self):
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 @@ def expand_archive(self):
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 @@ def expand_archive(self):
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 @@ def chdir(self):
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()

4
lib/spack/spack/test/architecture.py
View file

@ -31,7 +31,7 @@
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 @@ def test_dict_functions_for_architecture(self):
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():

20
share/spack/qa/run-unit-tests Executable file
View file

@ -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

44
var/spack/repos/builtin/packages/R/package.py
View file

@ -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 @@ def install(self, spec, prefix):
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 @@ def filter_compilers(self, spec, prefix):
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 @@ def filter_compilers(self, spec, prefix):
@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 @@ def setup_dependent_environment(self, spack_env, run_env, extension_spec):
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 @@ def setup_environment(self, spack_env, run_env):
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.

53
var/spack/repos/builtin/packages/cask/package.py Normal file
View file

@ -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"))

161
var/spack/repos/builtin/packages/cp2k/package.py Normal file
View file

@ -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)

4
var/spack/repos/builtin/packages/hypre/package.py
View file

@ -62,10 +62,10 @@ def install(self, spec, prefix):
'--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:

2
var/spack/repos/builtin/packages/jdk/package.py
View file

@ -25,7 +25,7 @@
#
# Author: Justin Too <too1@llnl.gov>
#
import distutils
import distutils.dir_util
import spack
from spack import *

45
var/spack/repos/builtin/packages/libhio/package.py Normal file
View file

@ -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")

66
var/spack/repos/builtin/packages/libxsmm/package.py Normal file
View file

@ -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)

12
var/spack/repos/builtin/packages/mkl/package.py
View file

@ -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 @@ def install(self, spec, prefix):
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 @@ def setup_dependent_package(self, module, dspec):
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

177
var/spack/repos/builtin/packages/opencv/package.py
View file

@ -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)

1
var/spack/repos/builtin/packages/pgi/package.py
View file

@ -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,

43
var/spack/repos/builtin/packages/r-boot/package.py Normal file
View file

@ -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)

43
var/spack/repos/builtin/packages/r-brew/package.py Normal file
View file

@ -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)

48
var/spack/repos/builtin/packages/r-car/package.py Normal file
View file

@ -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)

50
var/spack/repos/builtin/packages/r-caret/package.py Normal file
View file

@ -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)

41
var/spack/repos/builtin/packages/r-chron/package.py Normal file
View file

@ -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)

44
var/spack/repos/builtin/packages/r-class/package.py Normal file
View file

@ -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)

45
var/spack/repos/builtin/packages/r-crayon/package.py Normal file
View file

@ -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)

41
var/spack/repos/builtin/packages/r-cubature/package.py Normal file
View file

@ -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)

3
var/spack/repos/builtin/packages/r-curl/package.py
View file

@ -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')

46
var/spack/repos/builtin/packages/r-datatable/package.py Normal file
View file

@ -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)

45
var/spack/repos/builtin/packages/r-e1071/package.py Normal file
View file

@ -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)

59
var/spack/repos/builtin/packages/r-gdata/package.py Normal file
View file

@ -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)

45
var/spack/repos/builtin/packages/r-geosphere/package.py Normal file
View file

@ -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)

57
var/spack/repos/builtin/packages/r-ggmap/package.py Normal file
View file

@ -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)

49
var/spack/repos/builtin/packages/r-glmnet/package.py Normal file
View file

@ -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)

60
var/spack/repos/builtin/packages/r-gtools/package.py Normal file
View file

@ -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)

45
var/spack/repos/builtin/packages/r-jpeg/package.py Normal file
View file

@ -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)

53
var/spack/repos/builtin/packages/r-lme4/package.py Normal file
View file

@ -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)

45
var/spack/repos/builtin/packages/r-lmtest/package.py Normal file
View file

@ -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)

43
var/spack/repos/builtin/packages/r-mapproj/package.py Normal file
View file

@ -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)

42
var/spack/repos/builtin/packages/r-maps/package.py Normal file
View file

@ -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)

49
var/spack/repos/builtin/packages/r-maptools/package.py Normal file
View file

@ -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)

44
var/spack/repos/builtin/packages/r-matrixmodels/package.py Normal file
View file

@ -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)

47
var/spack/repos/builtin/packages/r-mgcv/package.py Normal file
View file

@ -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)

44
var/spack/repos/builtin/packages/r-minqa/package.py Normal file
View file

@ -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)

51
var/spack/repos/builtin/packages/r-multcomp/package.py Normal file
View file

@ -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)

42
var/spack/repos/builtin/packages/r-mvtnorm/package.py Normal file
View file

@ -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)

56
var/spack/repos/builtin/packages/r-ncdf4/package.py Normal file
View file

@ -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)

43
var/spack/repos/builtin/packages/r-nlme/package.py Normal file
View file

@ -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)

47
var/spack/repos/builtin/packages/r-nloptr/package.py Normal file
View file

@ -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)

42
var/spack/repos/builtin/packages/r-nnet/package.py Normal file
View file

@ -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)

50
var/spack/repos/builtin/packages/r-np/package.py Normal file
View file

@ -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)

49
var/spack/repos/builtin/packages/r-pbkrtest/package.py Normal file
View file

@ -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)

41
var/spack/repos/builtin/packages/r-plotrix/package.py Normal file
View file

@ -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)

41
var/spack/repos/builtin/packages/r-praise/package.py Normal file
View file

@ -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)

42
var/spack/repos/builtin/packages/r-proto/package.py Normal file
View file

@ -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)

46
var/spack/repos/builtin/packages/r-quantmod/package.py Normal file
View file

@ -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)

50
var/spack/repos/builtin/packages/r-quantreg/package.py Normal file
View file

@ -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)

42
var/spack/repos/builtin/packages/r-randomforest/package.py Normal file
View file

@ -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)

47
var/spack/repos/builtin/packages/r-rgooglemaps/package.py Normal file
View file

@ -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)

41
var/spack/repos/builtin/packages/r-rjson/package.py Normal file
View file

@ -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)

55
var/spack/repos/builtin/packages/r-rjsonio/package.py Normal file
View file

@ -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)

48
var/spack/repos/builtin/packages/r-roxygen2/package.py Normal file
View file

@ -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)

44
var/spack/repos/builtin/packages/r-sandwich/package.py Normal file
View file

@ -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)

43
var/spack/repos/builtin/packages/r-sparsem/package.py Normal file
View file

@ -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)

47
var/spack/repos/builtin/packages/r-survey/package.py Normal file
View file

@ -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)

45
var/spack/repos/builtin/packages/r-survival/package.py Normal file
View file

@ -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)

44
var/spack/repos/builtin/packages/r-tarifx/package.py Normal file
View file

@ -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)

48
var/spack/repos/builtin/packages/r-testthat/package.py Normal file
View file

@ -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)

44
var/spack/repos/builtin/packages/r-thdata/package.py Normal file
View file

@ -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)

44
var/spack/repos/builtin/packages/r-ttr/package.py Normal file
View file

@ -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)

50
var/spack/repos/builtin/packages/r-vcd/package.py Normal file
View file

@ -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)

45
var/spack/repos/builtin/packages/r-xml/package.py Normal file
View file

@ -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)

46
var/spack/repos/builtin/packages/tree/package.py Normal file
View file

@ -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')

15
var/spack/repos/builtin/packages/trilinos/package.py
View file

@ -138,16 +138,23 @@ def install(self, spec, prefix):
'-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',