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Merge pull request #1000 from glennpj/new_R

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Add version 3.3.0 of R and extensions
This commit is contained in:
Todd Gamblin 2016-06-20 10:33:43 -07:00 committed by GitHub
commit 0fbd2fe224
6 changed files with 79 additions and 45 deletions
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63
var/spack/repos/builtin/packages/R/package.py
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@ -22,30 +22,25 @@
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
import functools
import glob
import inspect
import os
import re
from contextlib import closing
import spack
from llnl.util.lang import match_predicate
from spack import *
from spack.util.environment import *
class R(Package):
"""
R is 'GNU S', a freely available language and environment for statistical computing and graphics which provides a
wide variety of statistical and graphical techniques: linear and nonlinear modelling, statistical tests, time series
analysis, classification, clustering, etc. Please consult the R project homepage for further information.
"""
"""R is 'GNU S', a freely available language and environment for
statistical computing and graphics which provides a wide variety of
statistical and graphical techniques: linear and nonlinear modelling,
statistical tests, time series analysis, classification, clustering, etc.
Please consult the R project homepage for further information."""
homepage = "https://www.r-project.org"
url = "http://cran.cnr.berkeley.edu/src/base/R-3/R-3.1.2.tar.gz"
extendable = True
version('3.3.0', '5a7506c8813432d1621c9725e86baf7a')
version('3.2.3', '1ba3dac113efab69e706902810cc2970')
version('3.2.2', '57cef5c2e210a5454da1979562a10e5b')
version('3.2.1', 'c2aac8b40f84e08e7f8c9068de9239a3')
@ -53,7 +48,8 @@ class R(Package):
version('3.1.3', '53a85b884925aa6b5811dfc361d73fc4')
version('3.1.2', '3af29ec06704cbd08d4ba8d69250ae74')
variant('external-lapack', default=False, description='Links to externally installed BLAS/LAPACK')
variant('external-lapack', default=False,
description='Links to externally installed BLAS/LAPACK')
# Virtual dependencies
depends_on('blas', when='+external-lapack')
@ -65,6 +61,7 @@ class R(Package):
depends_on('icu')
depends_on('glib')
depends_on('zlib')
depends_on('bzip2')
depends_on('libtiff')
depends_on('jpeg')
depends_on('cairo')
@ -72,18 +69,21 @@ class R(Package):
depends_on('freetype')
depends_on('tcl')
depends_on('tk')
depends_on('curl')
depends_on('pcre')
depends_on('jdk')
def install(self, spec, prefix):
rlibdir = join_path(prefix, 'rlib')
options = ['--prefix=%s' % prefix,
'--libdir=%s' % rlibdir,
'--enable-R-shlib',
'--enable-BLAS-shlib',
'--enable-R-framework=no']
configure_args = ['--prefix=%s' % prefix,
'--libdir=%s' % rlibdir,
'--enable-R-shlib',
'--enable-BLAS-shlib',
'--enable-R-framework=no']
if '+external-lapack' in spec:
options.extend(['--with-blas', '--with-lapack'])
configure_args.extend(['--with-blas', '--with-lapack'])
configure(*options)
configure(*configure_args)
make()
make('install')
@ -106,25 +106,24 @@ def setup_dependent_environment(self, spack_env, run_env, extension_spec):
r_libs_path = ':'.join(r_libs_path)
spack_env.set('R_LIBS', r_libs_path)
# For run time environment set only the path for extension_spec and prepend it to R_LIBS
# 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(extension_spec.prefix, self.r_lib_dir))
run_env.prepend_path('R_LIBS', os.path.join(
extension_spec.prefix, self.r_lib_dir))
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.archive_file)
"""
"""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 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)
# Make the site packages directory for extensions, if it does not exist already.
# Make the site packages directory for extensions, if it does not exist
# already.
if ext_spec.package.is_extension:
mkdirp(module.r_lib_dir)

11
var/spack/repos/builtin/packages/pcre/package.py
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@ -29,6 +29,7 @@ class Pcre(Package):
"""The PCRE package contains Perl Compatible Regular Expression
libraries. These are useful for implementing regular expression
pattern matching using the same syntax and semantics as Perl 5."""
homepage = "http://www.pcre.org"""
url = "ftp://ftp.csx.cam.ac.uk/pub/software/programming/pcre/pcre-8.36.tar.bz2"
@ -37,7 +38,15 @@ class Pcre(Package):
patch("intel.patch")
variant('utf', default=True,
description='Enable support for UTF-8/16/32, '
'incompatible with EBCDIC.')
def install(self, spec, prefix):
configure("--prefix=%s" % prefix)
configure_args = ['--prefix=%s' % prefix]
if '+utf' in spec:
configure_args.append('--enable-utf')
configure(*configure_args)
make()
make("install")

28
var/spack/repos/builtin/packages/r-BiocGenerics/package.py
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@ -24,15 +24,33 @@
##############################################################################
from spack import *
class RBiocgenerics(Package):
"""S4 generic functions needed by many Bioconductor packages."""
homepage = 'https://www.bioconductor.org/packages/release/bioc/html/BiocGenerics.html'
url = "https://www.bioconductor.org/packages/release/bioc/src/contrib/BiocGenerics_0.16.1.tar.gz"
version('0.16.1', 'c2148ffd86fc6f1f819c7f68eb2c744f', expand=False)
homepage = 'https://bioconductor.org/packages/BiocGenerics/'
version('bioc-3.3',
git='https://github.com/Bioconductor-mirror/BiocGenerics.git',
branch='release-3.3')
version('bioc-3.2',
git='https://github.com/Bioconductor-mirror/BiocGenerics.git',
branch='release-3.2')
extends('R')
def validate(self, spec):
"""
Checks that the version of R is appropriate for the Bioconductor
version.
"""
if spec.satisfies('@bioc-3.3'):
if not spec.satisfies('^R@3.3.0:3.3.9'):
raise InstallError('Must use R-3.3 for Bioconductor-3.3')
elif spec.satisfies('@bioc-3.2'):
if not spec.satisfies('^R@3.2.0:3.2.9'):
raise InstallError('Must use R-3.2 for Bioconductor-3.2')
def install(self, spec, prefix):
R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file)
self.validate(spec)
R('CMD', 'INSTALL', '--library=%s' %
self.module.r_lib_dir, '%s' % self.stage.source_path)

8
var/spack/repos/builtin/packages/r-abind/package.py
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@ -24,6 +24,7 @@
##############################################################################
from spack import *
class RAbind(Package):
"""Combine multidimensional arrays into a single array. This is a
generalization of 'cbind' and 'rbind'. Works with vectors, matrices, and
@ -32,11 +33,12 @@ class RAbind(Package):
homepage = "https://cran.r-project.org/"
url = "https://cran.r-project.org/src/contrib/abind_1.4-3.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/abind"
version('1.4-3', '10fcf80c677b991bf263d38be35a1fc5', expand=False)
version('1.4-3', '10fcf80c677b991bf263d38be35a1fc5')
extends('R')
def install(self, spec, prefix):
R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file)
R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
self.stage.source_path)

7
var/spack/repos/builtin/packages/r-filehash/package.py
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@ -24,6 +24,7 @@
##############################################################################
from spack import *
class RFilehash(Package):
"""Implements a simple key-value style database where character string keys
are associated with data values that are stored on the disk. A simple
@ -37,10 +38,12 @@ class RFilehash(Package):
homepage = 'https://cran.r-project.org/'
url = "https://cran.r-project.org/src/contrib/filehash_2.3.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/filehash"
version('2.3', '01fffafe09b148ccadc9814c103bdc2f', expand=False)
version('2.3', '01fffafe09b148ccadc9814c103bdc2f')
extends('R')
def install(self, spec, prefix):
R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file)
R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
self.stage.source_path)

7
var/spack/repos/builtin/packages/r-magic/package.py
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@ -24,6 +24,7 @@
##############################################################################
from spack import *
class RMagic(Package):
"""A collection of efficient, vectorized algorithms for the creation and
investigation of magic squares and hypercubes, including a variety of
@ -32,12 +33,14 @@ class RMagic(Package):
homepage = "https://cran.r-project.org/"
url = "https://cran.r-project.org/src/contrib/magic_1.5-6.tar.gz"
list_url = "https://cran.r-project.org/src/contrib/Archive/magic"
version('1.5-6', 'a68e5ced253b2196af842e1fc84fd029', expand=False)
version('1.5-6', 'a68e5ced253b2196af842e1fc84fd029')
extends('R')
depends_on('r-abind')
def install(self, spec, prefix):
R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file)
R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
self.stage.source_path)