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# 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)
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