diff options
Diffstat (limited to 'var/spack/repos/builtin/packages/r/package.py')
| -rw-r--r-- | var/spack/repos/builtin/packages/r/package.py | 293 |
1 files changed, 140 insertions, 153 deletions
diff --git a/var/spack/repos/builtin/packages/r/package.py b/var/spack/repos/builtin/packages/r/package.py index 6418d11ebf..78bec3848a 100644 --- a/var/spack/repos/builtin/packages/r/package.py +++ b/var/spack/repos/builtin/packages/r/package.py @@ -21,174 +21,167 @@ class R(AutotoolsPackage): extendable = True - maintainers = ['glennpj'] - - version('4.2.0', sha256='38eab7719b7ad095388f06aa090c5a2b202791945de60d3e2bb0eab1f5097488') - version('4.1.3', sha256='15ff5b333c61094060b2a52e9c1d8ec55cc42dd029e39ca22abdaa909526fed6') - version('4.1.2', sha256='2036225e9f7207d4ce097e54972aecdaa8b40d7d9911cd26491fac5a0fab38af') - version('4.1.1', sha256='515e03265752257d0b7036f380f82e42b46ed8473f54f25c7b67ed25bbbdd364') - version('4.1.0', sha256='e8e68959d7282ca147360fc9644ada9bd161bab781bab14d33b8999a95182781') - version('4.0.5', sha256='0a3ee079aa772e131fe5435311ab627fcbccb5a50cabc54292e6f62046f1ffef') - version('4.0.4', sha256='523f27d69744a08c8f0bd5e1e6c3d89a4db29ed983388ba70963a3cd3a4a802e') - version('4.0.3', sha256='09983a8a78d5fb6bc45d27b1c55f9ba5265f78fa54a55c13ae691f87c5bb9e0d') - version('4.0.2', sha256='d3bceab364da0876625e4097808b42512395fdf41292f4915ab1fd257c1bbe75') - version('4.0.1', sha256='95fe24a4d8d8f8f888460c8f5fe4311cec656e7a1722d233218bc03861bc6f32') - version('4.0.0', sha256='06beb0291b569978484eb0dcb5d2339665ec745737bdfb4e873e7a5a75492940') - version('3.6.3', sha256='89302990d8e8add536e12125ec591d6951022cf8475861b3690bc8bf1cefaa8f') - version('3.6.2', sha256='bd65a45cddfb88f37370fbcee4ac8dd3f1aebeebe47c2f968fd9770ba2bbc954') - 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 (TCLTK, PNG, JPEG, TIFF, CAIRO)') - variant('memory_profiling', default=False, - description='Enable memory profiling') - variant('rmath', default=False, - description='Build standalone Rmath library') - - depends_on('blas', when='+external-lapack') - depends_on('lapack', when='+external-lapack') - depends_on('bzip2') - depends_on('curl+libidn2') - depends_on('icu4c') - depends_on('java') - depends_on('ncurses') - depends_on('pcre', when='@:3.6.3') - depends_on('pcre2', when='@4:') - depends_on('readline') - depends_on('xz') - depends_on('which', type=('build', 'run')) - depends_on('zlib@1.2.5:') - depends_on('cairo+X+gobject+pdf', when='+X') - depends_on('pango+X', when='+X') - depends_on('harfbuzz+graphite2', when='+X') - depends_on('jpeg', when='+X') - depends_on('libpng', when='+X') - depends_on('libtiff', when='+X') - depends_on('libx11', when='+X') - depends_on('libxmu', when='+X') - depends_on('libxt', when='+X') - depends_on('tk', when='+X') - - patch('zlib.patch', when='@:3.3.2') + maintainers = ["glennpj"] + + version("4.2.0", sha256="38eab7719b7ad095388f06aa090c5a2b202791945de60d3e2bb0eab1f5097488") + version("4.1.3", sha256="15ff5b333c61094060b2a52e9c1d8ec55cc42dd029e39ca22abdaa909526fed6") + version("4.1.2", sha256="2036225e9f7207d4ce097e54972aecdaa8b40d7d9911cd26491fac5a0fab38af") + version("4.1.1", sha256="515e03265752257d0b7036f380f82e42b46ed8473f54f25c7b67ed25bbbdd364") + version("4.1.0", sha256="e8e68959d7282ca147360fc9644ada9bd161bab781bab14d33b8999a95182781") + version("4.0.5", sha256="0a3ee079aa772e131fe5435311ab627fcbccb5a50cabc54292e6f62046f1ffef") + version("4.0.4", sha256="523f27d69744a08c8f0bd5e1e6c3d89a4db29ed983388ba70963a3cd3a4a802e") + version("4.0.3", sha256="09983a8a78d5fb6bc45d27b1c55f9ba5265f78fa54a55c13ae691f87c5bb9e0d") + version("4.0.2", sha256="d3bceab364da0876625e4097808b42512395fdf41292f4915ab1fd257c1bbe75") + version("4.0.1", sha256="95fe24a4d8d8f8f888460c8f5fe4311cec656e7a1722d233218bc03861bc6f32") + version("4.0.0", sha256="06beb0291b569978484eb0dcb5d2339665ec745737bdfb4e873e7a5a75492940") + version("3.6.3", sha256="89302990d8e8add536e12125ec591d6951022cf8475861b3690bc8bf1cefaa8f") + version("3.6.2", sha256="bd65a45cddfb88f37370fbcee4ac8dd3f1aebeebe47c2f968fd9770ba2bbc954") + 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 (TCLTK, PNG, JPEG, TIFF, CAIRO)") + variant("memory_profiling", default=False, description="Enable memory profiling") + variant("rmath", default=False, description="Build standalone Rmath library") + + depends_on("blas", when="+external-lapack") + depends_on("lapack", when="+external-lapack") + depends_on("bzip2") + depends_on("curl+libidn2") + depends_on("icu4c") + depends_on("java") + depends_on("ncurses") + depends_on("pcre", when="@:3.6.3") + depends_on("pcre2", when="@4:") + depends_on("readline") + depends_on("xz") + depends_on("which", type=("build", "run")) + depends_on("zlib@1.2.5:") + depends_on("cairo+X+gobject+pdf", when="+X") + depends_on("pango+X", when="+X") + depends_on("harfbuzz+graphite2", when="+X") + depends_on("jpeg", when="+X") + depends_on("libpng", when="+X") + depends_on("libtiff", when="+X") + depends_on("libx11", when="+X") + depends_on("libxmu", when="+X") + depends_on("libxt", when="+X") + depends_on("tk", when="+X") + + patch("zlib.patch", when="@:3.3.2") # R cannot be built with '-O2' optimization # with Fujitsu Compiler @4.1.0 now. # Until the Fujitsu compiler resolves this problem, # temporary fix to lower the optimization level. - patch('change_optflags_tmp.patch', when='%fj@4.1.0') + patch("change_optflags_tmp.patch", when="%fj@4.1.0") # R custom URL version def url_for_version(self, version): """Handle R's customed URL versions""" - url = 'https://cloud.r-project.org/src/base' - return url + '/R-%s/R-%s.tar.gz' % (version.up_to(1), version) + url = "https://cloud.r-project.org/src/base" + return url + "/R-%s/R-%s.tar.gz" % (version.up_to(1), version) - filter_compiler_wrappers( - 'Makeconf', relative_root=os.path.join('rlib', 'R', 'etc') - ) + filter_compiler_wrappers("Makeconf", relative_root=os.path.join("rlib", "R", "etc")) @property def etcdir(self): - return join_path(prefix, 'rlib', 'R', 'etc') + return join_path(prefix, "rlib", "R", "etc") - @run_after('install') + @run_after("install") def install_rmath(self): - if '+rmath' in self.spec: - with working_dir('src/nmath/standalone'): + if "+rmath" in self.spec: + with working_dir("src/nmath/standalone"): make() - make('install', parallel=False) + make("install", parallel=False) def configure_args(self): - spec = self.spec + spec = self.spec prefix = self.prefix config_args = [ - '--libdir={0}'.format(join_path(prefix, 'rlib')), - '--enable-R-shlib', - '--enable-BLAS-shlib', - '--enable-R-framework=no', - '--without-recommended-packages', - 'LDFLAGS=-L{0} -Wl,-rpath,{0}'.format(join_path(prefix, 'rlib', - 'R', 'lib')), + "--libdir={0}".format(join_path(prefix, "rlib")), + "--enable-R-shlib", + "--enable-BLAS-shlib", + "--enable-R-framework=no", + "--without-recommended-packages", + "LDFLAGS=-L{0} -Wl,-rpath,{0}".format(join_path(prefix, "rlib", "R", "lib")), ] - 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' - ]) + 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-cairo') - config_args.append('--with-jpeglib') - config_args.append('--with-libpng') - config_args.append('--with-libtiff') - config_args.append('--with-tcltk') - config_args.append('--with-x') - - tcl_config_path = join_path( - spec['tcl'].libs.directories[0], 'tclConfig.sh') - config_args.append('--with-tcl-config={0}'.format(tcl_config_path)) - - tk_config_path = join_path( - spec['tk'].libs.directories[0], 'tkConfig.sh') - config_args.append('--with-tk-config={0}'.format(tk_config_path)) + config_args.extend( + ["--with-blas={0}".format(spec["blas"].libs.ld_flags), "--with-lapack"] + ) + + if "+X" in spec: + config_args.append("--with-cairo") + config_args.append("--with-jpeglib") + config_args.append("--with-libpng") + config_args.append("--with-libtiff") + config_args.append("--with-tcltk") + config_args.append("--with-x") + + tcl_config_path = join_path(spec["tcl"].libs.directories[0], "tclConfig.sh") + config_args.append("--with-tcl-config={0}".format(tcl_config_path)) + + tk_config_path = join_path(spec["tk"].libs.directories[0], "tkConfig.sh") + config_args.append("--with-tk-config={0}".format(tk_config_path)) else: - config_args.append('--without-cairo') - config_args.append('--without-jpeglib') - config_args.append('--without-libpng') - config_args.append('--without-libtiff') - config_args.append('--without-tcltk') - config_args.append('--without-x') + config_args.append("--without-cairo") + config_args.append("--without-jpeglib") + config_args.append("--without-libpng") + config_args.append("--without-libtiff") + config_args.append("--without-tcltk") + config_args.append("--without-x") - if '+memory_profiling' in spec: - config_args.append('--enable-memory-profiling') + 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.cc_pic_flag)) + if self.compiler.name != "gcc": + config_args.append("FPICFLAGS={0}".format(self.compiler.cc_pic_flag)) return config_args - @run_after('install') + @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') + src_makeconf = join_path(self.etcdir, "Makeconf") + dst_makeconf = join_path(self.etcdir, "Makeconf.spack") install(src_makeconf, dst_makeconf) # ======================================================================== @@ -197,47 +190,41 @@ class R(AutotoolsPackage): @property def r_lib_dir(self): - return join_path('rlib', 'R', 'library') + 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'): + 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) + r_libs_path = ":".join(r_libs_path) + env.set("R_LIBS", r_libs_path) # R_LIBS_USER gets set to a directory in HOME/R if it is not set, such as # during package installation with the --vanilla flag. Set it to null # to ensure that it does not point to a directory that may contain R # packages. - env.set('R_LIBS_USER', '') - env.set('R_MAKEVARS_SITE', - join_path(self.etcdir, 'Makeconf.spack')) + env.set("R_LIBS_USER", "") + 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)) + 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)) + env.prepend_path("R_LIBS", join_path(dependent_spec.prefix, self.r_lib_dir)) def setup_run_environment(self, env): - env.prepend_path('LD_LIBRARY_PATH', - join_path(self.prefix, 'rlib', 'R', 'lib')) - env.prepend_path('PKG_CONFIG_PATH', - join_path(self.prefix, 'rlib', 'pkgconfig')) + env.prepend_path("LD_LIBRARY_PATH", join_path(self.prefix, "rlib", "R", "lib")) + env.prepend_path("PKG_CONFIG_PATH", join_path(self.prefix, "rlib", "pkgconfig")) - if '+rmath' in self.spec: - env.prepend_path('LD_LIBRARY_PATH', - join_path(self.prefix, 'rlib')) + if "+rmath" in self.spec: + env.prepend_path("LD_LIBRARY_PATH", join_path(self.prefix, "rlib")) def setup_dependent_package(self, module, dependent_spec): """Called before R modules' install() methods. In most cases, @@ -246,7 +233,7 @@ class R(AutotoolsPackage): self.stage.source_path)""" # R extension builds can have a global R executable function - module.R = Executable(join_path(self.spec.prefix.bin, 'R')) + 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) |