# 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', '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') 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') 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), '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') 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_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)