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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.
"""
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('3.2.3', '1ba3dac113efab69e706902810cc2970')
version('3.2.2', '57cef5c2e210a5454da1979562a10e5b')
version('3.2.1', 'c2aac8b40f84e08e7f8c9068de9239a3')
version('3.2.0', '66fa17ad457d7e618191aa0f52fc402e')
version('3.1.3', '53a85b884925aa6b5811dfc361d73fc4')
version('3.1.2', '3af29ec06704cbd08d4ba8d69250ae74')
variant('external-lapack', default=False, description='Links to externally installed BLAS/LAPACK')
# Virtual dependencies
depends_on('blas', when='+external-lapack')
depends_on('lapack', when='+external-lapack')
# Concrete dependencies
depends_on('readline')
depends_on('ncurses')
depends_on('icu')
depends_on('glib')
depends_on('zlib')
depends_on('libtiff')
depends_on('jpeg')
depends_on('cairo')
depends_on('pango')
depends_on('freetype')
depends_on('tcl')
depends_on('tk')
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']
if '+external-lapack' in spec:
options.extend(['--with-blas', '--with-lapack'])
configure(*options)
make()
make('install')
# ========================================================================
# Set up environment to make install easy for R extensions.
# ========================================================================
@property
def r_lib_dir(self):
return os.path.join('rlib', 'R', 'library')
def setup_dependent_environment(self, spack_env, run_env, extension_spec):
# Set R_LIBS to include the library dir for the
# extension and any other R extensions it depends on.
r_libs_path = []
for d in extension_spec.traverse():
if d.package.extends(self.spec):
r_libs_path.append(os.path.join(d.prefix, self.r_lib_dir))
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
if extension_spec.package.extends(self.spec):
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)
"""
# 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.
if ext_spec.package.is_extension:
mkdirp(module.r_lib_dir)
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