9ddc98e46a
* Methods setting the environment now do it separately for build and run Before this commit the `*_environment` methods were setting modifications to both the build-time and run-time environment simultaneously. This might cause issues as the two environments inherently rely on different preconditions: 1. The build-time environment is set before building a package, thus the package prefix doesn't exist and can't be inspected 2. The run-time environment instead is set assuming the target package has been already installed Here we split each of these functions into two: one setting the build-time environment, one the run-time. We also adopt a fallback strategy that inspects for old methods and executes them as before, but prints a deprecation warning to tty. This permits to port packages to use the new methods in a distributed way, rather than having to modify all the packages at once. * Added a test that fails if any package uses the old API Marked the test xfail for now as we have a lot of packages in that state. * Added a test to check that a package modified by a PR is up to date This test can be used any time we deprecate a method call to ensure that during the first modification of the package we update also the deprecated calls. * Updated documentation
220 lines
9.2 KiB
Python
220 lines
9.2 KiB
Python
# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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import os
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import re
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from spack import *
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class R(AutotoolsPackage):
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"""R is 'GNU S', a freely available language and environment for
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statistical computing and graphics which provides a wide variety of
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statistical and graphical techniques: linear and nonlinear modelling,
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statistical tests, time series analysis, classification, clustering, etc.
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Please consult the R project homepage for further information."""
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homepage = "https://www.r-project.org"
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url = "https://cloud.r-project.org/src/base/R-3/R-3.4.3.tar.gz"
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extendable = True
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version('3.6.1', sha256='5baa9ebd3e71acecdcc3da31d9042fb174d55a42829f8315f2457080978b1389')
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version('3.6.0', sha256='36fcac3e452666158e62459c6fc810adc247c7109ed71c5b6c3ad5fc2bf57509')
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version('3.5.3', sha256='2bfa37b7bd709f003d6b8a172ddfb6d03ddd2d672d6096439523039f7a8e678c')
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version('3.5.2', sha256='e53d8c3cf20f2b8d7a9c1631b6f6a22874506fb392034758b3bb341c586c5b62')
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version('3.5.1', sha256='0463bff5eea0f3d93fa071f79c18d0993878fd4f2e18ae6cf22c1639d11457ed')
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version('3.5.0', sha256='fd1725535e21797d3d9fea8963d99be0ba4c3aecadcf081b43e261458b416870')
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version('3.4.4', sha256='b3e97d2fab7256d1c655c4075934725ba1cd7cb9237240a11bb22ccdad960337')
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version('3.4.3', sha256='7a3cb831de5b4151e1f890113ed207527b7d4b16df9ec6b35e0964170007f426')
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version('3.4.2', sha256='971e30c2436cf645f58552905105d75788bd9733bddbcb7c4fbff4c1a6d80c64')
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version('3.4.1', sha256='02b1135d15ea969a3582caeb95594a05e830a6debcdb5b85ed2d5836a6a3fc78')
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version('3.4.0', sha256='288e9ed42457c47720780433b3d5c3c20983048b789291cc6a7baa11f9428b91')
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version('3.3.3', sha256='5ab768053a275084618fb669b4fbaadcc39158998a87e8465323829590bcfc6c')
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version('3.3.2', sha256='d294ad21e9f574fb4828ebb3a94b8cb34f4f304a41687a994be00dd41a4e514c')
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version('3.3.1', sha256='3dc59ae5831f5380f83c169bac2103ad052efe0ecec4ffa74bde4d85a0fda9e2')
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version('3.3.0', sha256='9256b154b1a5993d844bee7b1955cd49c99ad72cef03cce3cd1bdca1310311e4')
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version('3.2.5', sha256='60745672dce5ddc201806fa59f6d4e0ba6554d8ed78d0f9f0d79a629978f80b5')
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version('3.2.3', sha256='b93b7d878138279234160f007cb9b7f81b8a72c012a15566e9ec5395cfd9b6c1')
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version('3.2.2', sha256='9c9152e74134b68b0f3a1c7083764adc1cb56fd8336bec003fd0ca550cd2461d')
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version('3.2.1', sha256='d59dbc3f04f4604a5cf0fb210b8ea703ef2438b3ee65fd5ab536ec5234f4c982')
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version('3.2.0', sha256='f5ae953f18ba6f3d55b46556bbbf73441350f9fd22625402b723a2b81ff64f35')
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version('3.1.3', sha256='07e98323935baa38079204bfb9414a029704bb9c0ca5ab317020ae521a377312')
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version('3.1.2', sha256='bcd150afcae0e02f6efb5f35a6ab72432be82e849ec52ce0bb89d8c342a8fa7a')
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variant('external-lapack', default=False,
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description='Links to externally installed BLAS/LAPACK')
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variant('X', default=False,
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description='Enable X11 support (call configure --with-x)')
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variant('memory_profiling', default=False,
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description='Enable memory profiling')
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variant('rmath', default=False,
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description='Build standalone Rmath library')
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# Virtual dependencies
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depends_on('blas', when='+external-lapack')
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depends_on('lapack', when='+external-lapack')
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# Concrete dependencies.
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depends_on('readline')
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depends_on('ncurses')
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depends_on('icu4c')
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depends_on('glib')
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depends_on('zlib@1.2.5:')
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depends_on('bzip2')
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depends_on('libtiff')
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depends_on('jpeg')
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depends_on('cairo+pdf')
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depends_on('cairo+X', when='+X')
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depends_on('cairo~X', when='~X')
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depends_on('pango')
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depends_on('pango+X', when='+X')
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depends_on('pango~X', when='~X')
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depends_on('freetype')
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depends_on('tcl')
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depends_on('tk', when='+X')
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depends_on('libx11', when='+X')
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depends_on('libxt', when='+X')
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depends_on('libxmu', when='+X')
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depends_on('curl')
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depends_on('pcre')
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depends_on('java')
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patch('zlib.patch', when='@:3.3.2')
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filter_compiler_wrappers(
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'Makeconf', relative_root=os.path.join('rlib', 'R', 'etc')
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)
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@property
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def etcdir(self):
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return join_path(prefix, 'rlib', 'R', 'etc')
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@run_after('build')
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def build_rmath(self):
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if '+rmath' in self.spec:
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with working_dir('src/nmath/standalone'):
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make()
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@run_after('install')
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def install_rmath(self):
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if '+rmath' in self.spec:
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with working_dir('src/nmath/standalone'):
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make('install')
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def configure_args(self):
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spec = self.spec
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prefix = self.prefix
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tcl_config_path = join_path(spec['tcl'].prefix.lib, 'tclConfig.sh')
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config_args = [
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'--libdir={0}'.format(join_path(prefix, 'rlib')),
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'--enable-R-shlib',
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'--enable-BLAS-shlib',
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'--enable-R-framework=no',
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'--with-tcl-config={0}'.format(tcl_config_path),
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'LDFLAGS=-L{0} -Wl,-rpath,{0}'.format(join_path(prefix, 'rlib',
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'R', 'lib')),
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]
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if '^tk' in spec:
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tk_config_path = join_path(spec['tk'].prefix.lib, 'tkConfig.sh')
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config_args.append('--with-tk-config={0}'.format(tk_config_path))
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if '+external-lapack' in spec:
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if '^mkl' in spec and 'gfortran' in self.compiler.fc:
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mkl_re = re.compile(r'(mkl_)intel(_i?lp64\b)')
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config_args.extend([
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mkl_re.sub(r'\g<1>gf\g<2>',
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'--with-blas={0}'.format(
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spec['blas'].libs.ld_flags)),
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'--with-lapack'
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])
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else:
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config_args.extend([
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'--with-blas={0}'.format(spec['blas'].libs.ld_flags),
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'--with-lapack'
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])
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if '+X' in spec:
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config_args.append('--with-x')
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else:
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config_args.append('--without-x')
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if '+memory_profiling' in spec:
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config_args.append('--enable-memory-profiling')
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# Set FPICFLAGS for compilers except 'gcc'.
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if self.compiler.name != 'gcc':
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config_args.append('FPICFLAGS={0}'.format(self.compiler.pic_flag))
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return config_args
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@run_after('install')
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def copy_makeconf(self):
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# Make a copy of Makeconf because it will be needed to properly build R
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# dependencies in Spack.
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src_makeconf = join_path(self.etcdir, 'Makeconf')
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dst_makeconf = join_path(self.etcdir, 'Makeconf.spack')
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install(src_makeconf, dst_makeconf)
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# ========================================================================
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# Set up environment to make install easy for R extensions.
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# ========================================================================
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@property
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def r_lib_dir(self):
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return join_path('rlib', 'R', 'library')
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def setup_dependent_build_environment(self, env, dependent_spec):
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# Set R_LIBS to include the library dir for the
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# extension and any other R extensions it depends on.
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r_libs_path = []
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for d in dependent_spec.traverse(
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deptype=('build', 'run'), deptype_query='run'):
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if d.package.extends(self.spec):
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r_libs_path.append(join_path(d.prefix, self.r_lib_dir))
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r_libs_path = ':'.join(r_libs_path)
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env.set('R_LIBS', r_libs_path)
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env.set('R_MAKEVARS_SITE',
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join_path(self.etcdir, 'Makeconf.spack'))
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# Use the number of make_jobs set in spack. The make program will
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# determine how many jobs can actually be started.
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env.set('MAKEFLAGS', '-j{0}'.format(make_jobs))
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def setup_dependent_run_environment(self, env, dependent_spec):
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# For run time environment set only the path for dependent_spec and
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# prepend it to R_LIBS
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if dependent_spec.package.extends(self.spec):
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env.prepend_path('R_LIBS', join_path(
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dependent_spec.prefix, self.r_lib_dir))
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def setup_run_environment(self, env):
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env.prepend_path('LIBRARY_PATH',
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join_path(self.prefix, 'rlib', 'R', 'lib'))
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env.prepend_path('LD_LIBRARY_PATH',
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join_path(self.prefix, 'rlib', 'R', 'lib'))
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env.prepend_path('CPATH',
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join_path(self.prefix, 'rlib', 'R', 'include'))
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def setup_dependent_package(self, module, dependent_spec):
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"""Called before R modules' install() methods. In most cases,
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extensions will only need to have one line:
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R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
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self.stage.source_path)"""
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# R extension builds can have a global R executable function
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module.R = Executable(join_path(self.spec.prefix.bin, 'R'))
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# Add variable for library directry
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module.r_lib_dir = join_path(dependent_spec.prefix, self.r_lib_dir)
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# Make the site packages directory for extensions, if it does not exist
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# already.
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if dependent_spec.package.is_extension:
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mkdirp(module.r_lib_dir)
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