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# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import os
from spack import *
class R(AutotoolsPackage):
"""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 = "https://cloud.r-project.org/src/base/R-3/R-3.4.3.tar.gz"
extendable = True
version('3.5.1', sha256='0463bff5eea0f3d93fa071f79c18d0993878fd4f2e18ae6cf22c1639d11457ed')
version('3.5.0', 'c0455dbfa76ca807e4dfa93d49dcc817')
version('3.4.4', '9d6f73be072531e95884c7965ff80cd8')
version('3.4.3', 'bc55db54f992fda9049201ca62d2a584')
version('3.4.2', '1cd6d37850188e7f190f1eb94a24ca1f')
version('3.4.1', '3a79c01dc0527c62e80ffb1c489297ea')
version('3.4.0', '75083c23d507b9c16d5c6afbd7a827e7')
version('3.3.3', '0ac211ec15e813a24f8f4a5a634029a4')
version('3.3.2', '2437014ef40641cdc9673e89c040b7a8')
version('3.3.1', 'f50a659738b73036e2f5635adbd229c5')
version('3.3.0', '5a7506c8813432d1621c9725e86baf7a')
version('3.2.5', '7b23ee70cfb383be3bd4360e3c71d8c3')
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')
variant('X', default=False,
description='Enable X11 support (call configure --with-x)')
variant('memory_profiling', default=False,
description='Enable memory profiling')
# Virtual dependencies
depends_on('blas', when='+external-lapack')
depends_on('lapack', when='+external-lapack')
# Concrete dependencies.
depends_on('readline')
depends_on('ncurses')
depends_on('icu4c')
depends_on('glib')
depends_on('zlib@1.2.5:')
depends_on('bzip2')
depends_on('libtiff')
depends_on('jpeg')
depends_on('cairo')
depends_on('cairo+X', when='+X')
depends_on('cairo~X', when='~X')
depends_on('pango')
depends_on('pango+X', when='+X')
depends_on('pango~X', when='~X')
depends_on('freetype')
depends_on('tcl')
depends_on('tk')
depends_on('libx11', when='+X')
depends_on('libxt', when='+X')
depends_on('curl')
depends_on('pcre')
depends_on('java')
patch('zlib.patch', when='@:3.3.2')
filter_compiler_wrappers(
'Makeconf', relative_root=os.path.join('rlib', 'R', 'etc')
)
@property
def etcdir(self):
return join_path(prefix, 'rlib', 'R', 'etc')
def configure_args(self):
spec = self.spec
prefix = self.prefix
tcl_config_path = join_path(spec['tcl'].prefix.lib, 'tclConfig.sh')
tk_config_path = join_path(spec['tk'].prefix.lib, 'tkConfig.sh')
config_args = [
'--libdir={0}'.format(join_path(prefix, 'rlib')),
'--enable-R-shlib',
'--enable-BLAS-shlib',
'--enable-R-framework=no',
'--with-tcl-config={0}'.format(tcl_config_path),
'--with-tk-config={0}'.format(tk_config_path),
]
if '+external-lapack' in spec:
config_args.extend([
'--with-blas={0}'.format(spec['blas'].libs),
'--with-lapack'
])
if '+X' in spec:
config_args.append('--with-x')
else:
config_args.append('--without-x')
if '+memory_profiling' in spec:
config_args.append('--enable-memory-profiling')
return config_args
@run_after('install')
def copy_makeconf(self):
# 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')
install(src_makeconf, dst_makeconf)
# ========================================================================
# Set up environment to make install easy for R extensions.
# ========================================================================
@property
def r_lib_dir(self):
return join_path('rlib', 'R', 'library')
def setup_dependent_environment(self, spack_env, run_env, dependent_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 dependent_spec.traverse(
deptype=('build', 'run'), deptype_query='run'):
if d.package.extends(self.spec):
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 dependent_spec and
# prepend it to R_LIBS
if dependent_spec.package.extends(self.spec):
run_env.prepend_path('R_LIBS', join_path(
dependent_spec.prefix, self.r_lib_dir))
def setup_environment(self, spack_env, run_env):
run_env.prepend_path('LIBRARY_PATH',
join_path(self.prefix, 'rlib', 'R', 'lib'))
run_env.prepend_path('LD_LIBRARY_PATH',
join_path(self.prefix, 'rlib', 'R', 'lib'))
run_env.prepend_path('CPATH',
join_path(self.prefix, 'rlib', 'R', 'include'))
def setup_dependent_package(self, module, dependent_spec):
"""Called before R modules' install() methods. In most cases,
extensions will only need to have one line:
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 = join_path(dependent_spec.prefix, self.r_lib_dir)
# Make the site packages directory for extensions, if it does not exist
# already.
if dependent_spec.package.is_extension:
mkdirp(module.r_lib_dir)
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