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# Copyright 2013-2019 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
import re
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('3.6.1', sha256='5baa9ebd3e71acecdcc3da31d9042fb174d55a42829f8315f2457080978b1389')
version('3.6.0', sha256='36fcac3e452666158e62459c6fc810adc247c7109ed71c5b6c3ad5fc2bf57509')
version('3.5.3', sha256='2bfa37b7bd709f003d6b8a172ddfb6d03ddd2d672d6096439523039f7a8e678c')
version('3.5.2', sha256='e53d8c3cf20f2b8d7a9c1631b6f6a22874506fb392034758b3bb341c586c5b62')
version('3.5.1', sha256='0463bff5eea0f3d93fa071f79c18d0993878fd4f2e18ae6cf22c1639d11457ed')
version('3.5.0', sha256='fd1725535e21797d3d9fea8963d99be0ba4c3aecadcf081b43e261458b416870')
version('3.4.4', sha256='b3e97d2fab7256d1c655c4075934725ba1cd7cb9237240a11bb22ccdad960337')
version('3.4.3', sha256='7a3cb831de5b4151e1f890113ed207527b7d4b16df9ec6b35e0964170007f426')
version('3.4.2', sha256='971e30c2436cf645f58552905105d75788bd9733bddbcb7c4fbff4c1a6d80c64')
version('3.4.1', sha256='02b1135d15ea969a3582caeb95594a05e830a6debcdb5b85ed2d5836a6a3fc78')
version('3.4.0', sha256='288e9ed42457c47720780433b3d5c3c20983048b789291cc6a7baa11f9428b91')
version('3.3.3', sha256='5ab768053a275084618fb669b4fbaadcc39158998a87e8465323829590bcfc6c')
version('3.3.2', sha256='d294ad21e9f574fb4828ebb3a94b8cb34f4f304a41687a994be00dd41a4e514c')
version('3.3.1', sha256='3dc59ae5831f5380f83c169bac2103ad052efe0ecec4ffa74bde4d85a0fda9e2')
version('3.3.0', sha256='9256b154b1a5993d844bee7b1955cd49c99ad72cef03cce3cd1bdca1310311e4')
version('3.2.5', sha256='60745672dce5ddc201806fa59f6d4e0ba6554d8ed78d0f9f0d79a629978f80b5')
version('3.2.3', sha256='b93b7d878138279234160f007cb9b7f81b8a72c012a15566e9ec5395cfd9b6c1')
version('3.2.2', sha256='9c9152e74134b68b0f3a1c7083764adc1cb56fd8336bec003fd0ca550cd2461d')
version('3.2.1', sha256='d59dbc3f04f4604a5cf0fb210b8ea703ef2438b3ee65fd5ab536ec5234f4c982')
version('3.2.0', sha256='f5ae953f18ba6f3d55b46556bbbf73441350f9fd22625402b723a2b81ff64f35')
version('3.1.3', sha256='07e98323935baa38079204bfb9414a029704bb9c0ca5ab317020ae521a377312')
version('3.1.2', sha256='bcd150afcae0e02f6efb5f35a6ab72432be82e849ec52ce0bb89d8c342a8fa7a')
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')
variant('rmath', default=False,
description='Build standalone Rmath library')
# 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+pdf')
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', when='+X')
depends_on('libx11', when='+X')
depends_on('libxt', when='+X')
depends_on('libxmu', 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')
@run_after('build')
def build_rmath(self):
if '+rmath' in self.spec:
with working_dir('src/nmath/standalone'):
make()
@run_after('install')
def install_rmath(self):
if '+rmath' in self.spec:
with working_dir('src/nmath/standalone'):
make('install')
def configure_args(self):
spec = self.spec
prefix = self.prefix
tcl_config_path = join_path(spec['tcl'].prefix.lib, 'tclConfig.sh')
if not os.path.exists(tcl_config_path):
tcl_config_path = join_path(spec['tcl'].prefix,
'lib64', 'tclConfig.sh')
config_args = [
'--libdir={0}'.format(join_path(prefix, 'rlib')),
'--enable-R-shlib',
'--enable-BLAS-shlib',
'--enable-R-framework=no',
'--without-recommended-packages',
'--with-tcl-config={0}'.format(tcl_config_path),
'LDFLAGS=-L{0} -Wl,-rpath,{0}'.format(join_path(prefix, 'rlib',
'R', 'lib')),
]
if '^tk' in spec:
tk_config_path = join_path(spec['tk'].prefix.lib, 'tkConfig.sh')
if not os.path.exists(tk_config_path):
tk_config_path = join_path(spec['tk'].prefix,
'lib64', 'tkConfig.sh')
config_args.append('--with-tk-config={0}'.format(tk_config_path))
if '+external-lapack' in spec:
if '^mkl' in spec and 'gfortran' in self.compiler.fc:
mkl_re = re.compile(r'(mkl_)intel(_i?lp64\b)')
config_args.extend([
mkl_re.sub(r'\g<1>gf\g<2>',
'--with-blas={0}'.format(
spec['blas'].libs.ld_flags)),
'--with-lapack'
])
else:
config_args.extend([
'--with-blas={0}'.format(spec['blas'].libs.ld_flags),
'--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')
# Set FPICFLAGS for compilers except 'gcc'.
if self.compiler.name != 'gcc':
config_args.append('FPICFLAGS={0}'.format(self.compiler.pic_flag))
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_build_environment(self, 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)
env.set('R_LIBS', r_libs_path)
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.
env.set('MAKEFLAGS', '-j{0}'.format(make_jobs))
def setup_dependent_run_environment(self, env, dependent_spec):
# For run time environment set only the path for dependent_spec and
# prepend it to R_LIBS
if dependent_spec.package.extends(self.spec):
env.prepend_path('R_LIBS', join_path(
dependent_spec.prefix, self.r_lib_dir))
def setup_run_environment(self, env):
env.prepend_path('LIBRARY_PATH',
join_path(self.prefix, 'rlib', 'R', 'lib'))
env.prepend_path('LD_LIBRARY_PATH',
join_path(self.prefix, 'rlib', 'R', 'lib'))
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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