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Diffstat (limited to 'var/spack/repos/builtin/packages/r/package.py')
| -rw-r--r-- | var/spack/repos/builtin/packages/r/package.py | 184 |
1 files changed, 184 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/r/package.py b/var/spack/repos/builtin/packages/r/package.py new file mode 100644 index 0000000000..a60fa8122c --- /dev/null +++ b/var/spack/repos/builtin/packages/r/package.py @@ -0,0 +1,184 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * +from spack.util.environment import * +import shutil + + +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('3.3.1', 'f50a659738b73036e2f5635adbd229c5') + version('3.3.0', '5a7506c8813432d1621c9725e86baf7a') + 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)') + + # 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') + depends_on('zlib@:1.2.8', when='@:3.3.1') + 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('freetype') + depends_on('tcl') + depends_on('tk') + depends_on('tk+X', when='+X') + depends_on('tk~X', when='~X') + depends_on('libx11', when='+X') + depends_on('libxt', when='+X') + depends_on('curl') + depends_on('pcre') + depends_on('jdk') + + @property + def etcdir(self): + return join_path(prefix, 'rlib', 'R', 'etc') + + def install(self, spec, prefix): + rlibdir = join_path(prefix, 'rlib') + configure_args = ['--prefix=%s' % prefix, + '--libdir=%s' % rlibdir, + '--enable-R-shlib', + '--enable-BLAS-shlib', + '--enable-R-framework=no'] + if '+external-lapack' in spec: + configure_args.extend(['--with-blas', '--with-lapack']) + + configure(*configure_args) + make() + make('install') + + # 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') + shutil.copy(src_makeconf, dst_makeconf) + + self.filter_compilers(spec, prefix) + + def filter_compilers(self, spec, prefix): + """Run after install to tell the configuration files and Makefiles + to use the compilers that Spack built the package with. + + If this isn't done, they'll have CC and CXX set to Spack's generic + cc and c++. We want them to be bound to whatever compiler + they were built with.""" + + kwargs = {'ignore_absent': True, 'backup': False, 'string': True} + + filter_file(env['CC'], self.compiler.cc, + join_path(self.etcdir, 'Makeconf'), **kwargs) + filter_file(env['CXX'], self.compiler.cxx, + join_path(self.etcdir, 'Makeconf'), **kwargs) + filter_file(env['F77'], self.compiler.f77, + join_path(self.etcdir, 'Makeconf'), **kwargs) + filter_file(env['FC'], self.compiler.fc, + join_path(self.etcdir, 'Makeconf'), **kwargs) + + # ======================================================================== + # 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, 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(deptype=nolink, 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 extension_spec and + # prepend it to R_LIBS + if extension_spec.package.extends(self.spec): + run_env.prepend_path('R_LIBS', join_path( + extension_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, ext_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(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) |