# Copyright 2013-2024 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 from spack.package 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 license("GPL-2.0-or-later") version("4.3.2", sha256="b3f5760ac2eee8026a3f0eefcb25b47723d978038eee8e844762094c860c452a") version("4.3.1", sha256="8dd0bf24f1023c6f618c3b317383d291b4a494f40d73b983ac22ffea99e4ba99") version("4.3.0", sha256="45dcc48b6cf27d361020f77fde1a39209e997b81402b3663ca1c010056a6a609") version("4.2.3", sha256="55e4a9a6d43be314e2c03d0266a6fa5444afdce50b303bfc3b82b3979516e074") version("4.2.2", sha256="0ff62b42ec51afa5713caee7c4fde7a0c45940ba39bef8c5c9487fef0c953df5") version("4.2.1", sha256="4d52db486d27848e54613d4ee977ad952ec08ce17807e1b525b10cd4436c643f") 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("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") depends_on("lapack") depends_on("bzip2") depends_on("curl+libidn2") # R didn't anticipate the celebratory non-breaking major version bump of curl 8. depends_on("curl@:7", when="@:4.2") depends_on("icu4c") depends_on("java") depends_on("libtirpc") 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-api") depends_on("zlib@1.2.5:", when="^zlib") depends_on("texinfo", type="build") with when("+X"): depends_on("cairo+X+gobject+pdf") depends_on("pango+X") depends_on("harfbuzz+graphite2") depends_on("jpeg") depends_on("libpng") depends_on("libtiff") depends_on("libx11") depends_on("libxmu") depends_on("libxt") depends_on("tk") 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") build_directory = "spack-build" # 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) @property def etcdir(self): return join_path(prefix, "rlib", "R", "etc") @run_after("install") def install_rmath(self): if "+rmath" in self.spec: with working_dir(join_path(self.build_directory, "src", "nmath", "standalone")): make() make("install", parallel=False) def configure_args(self): spec = self.spec prefix = self.prefix extra_rpath = join_path(prefix, "rlib", "R", "lib") blas_flags: str = spec["blas"].libs.ld_flags lapack_flags: str = spec["lapack"].libs.ld_flags # R uses LAPACK in Fortran, which requires libmkl_gf_* when gfortran is used. # TODO: cleaning this up seem to require both compilers as dependencies and use variants. if spec["lapack"].name in INTEL_MATH_LIBRARIES and "gfortran" in self.compiler.fc: xlp64 = "ilp64" if spec["lapack"].satisfies("+ilp64") else "lp64" blas_flags = blas_flags.replace(f"mkl_intel_{xlp64}", f"mkl_gf_{xlp64}") lapack_flags = lapack_flags.replace(f"mkl_intel_{xlp64}", f"mkl_gf_{xlp64}") config_args = [ "--with-internal-tzcode", "--libdir={0}".format(join_path(prefix, "rlib")), "--enable-R-shlib", "--enable-R-framework=no", "--without-recommended-packages", f"LDFLAGS=-Wl,-rpath,{extra_rpath}", f"--with-blas={blas_flags}", f"--with-lapack={lapack_flags}", # cannot disable docs with a normal configure option "ac_cv_path_PDFLATEX=", "ac_cv_path_PDFTEX=", "ac_cv_path_TEX=", "ac_cv_path_TEXI2DVI=", ] 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") 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.spec.satisfies("@:3.6.1 %gcc@10:"): config_args.append("CFLAGS=-fcommon") config_args.append("FFLAGS=-fallow-argument-mismatch") 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) # To respect order of execution, we should filter after we made the copy above filter_compiler_wrappers("Makeconf", relative_root=os.path.join("rlib", "R", "etc")) # ======================================================================== # 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")): 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_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")) # 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("R_HOME", join_path(self.prefix, "rlib", "R")) 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 env.set("R_HOME", join_path(self.prefix, "rlib", "R")) 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("LD_LIBRARY_PATH", join_path(self.prefix, "rlib", "R", "lib")) env.prepend_path("PKG_CONFIG_PATH", join_path(self.prefix, "rlib", "pkgconfig")) env.set("R_HOME", join_path(self.prefix, "rlib", "R")) 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, 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)