From 67e5603b2844a6657dd0438fa26626b013e5567f Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Mon, 24 Jun 2024 00:11:52 +0100 Subject: gentoo auto-resync : 24:06:2024 - 00:11:52 --- dev-lang/R/Manifest | 4 +- dev-lang/R/R-4.4.1.ebuild | 248 ++++++++++++++++++++++++++++++++++++++++++++++ dev-lang/R/metadata.xml | 3 + 3 files changed, 254 insertions(+), 1 deletion(-) create mode 100644 dev-lang/R/R-4.4.1.ebuild (limited to 'dev-lang/R') diff --git a/dev-lang/R/Manifest b/dev-lang/R/Manifest index 6475ffb4295c..ab3d1dffae42 100644 --- a/dev-lang/R/Manifest +++ b/dev-lang/R/Manifest @@ -3,7 +3,9 @@ AUX R-4.3.0-no-gzip-doc.patch 354 BLAKE2B 81f20b830ac99494a921b635a0d280dd90045c AUX R-4.3.0-parallel.patch 415 BLAKE2B e996c72c167b529765c82c8880bc3ea704d3c6e34b7fe09dff4fa93a8e42f8551dc723f44e0ab0638de84ce0f7fa60d4476e297d06eb3d6070d8daf5f79b9dba SHA512 6d36a2eb5df1ec8fa4230bfbc693cf53c95b41bb9269cfa473cfaa6dc8a42681e81a006f03278b86e8636e904bba188f2475d27d06599fdab86de8743401f5be DIST R-4.3.1.tar.gz 34899964 BLAKE2B 7aaacad01ce59e2faa46c4b830c10d2df8e4a3a1d4f11cf2aa622ceb53876f1e702dff94a820ca954ec29f53d58fa7e135ef15e8257602c50f2642b0a0c0a86a SHA512 f571c378dbdd675e267ef4419bb1141198924dadc08297c93c8dff58504994604918b3e045bb7139ba473972a063a68ed1c7426f37d4e8208b79358561d34d77 DIST R-4.3.2.tar.gz 35039225 BLAKE2B 2de3af9013c8648c118a1efe673b618aef84a694c6865657faef5b0ca5f780ef5273bb00b607f587219ee30a11f01ccc3b730b9124847242b9d9550de471f58c SHA512 125114357f20d4a3248aee86727768d1dc15e07e44353f8a68fe2ef1fedae508e85d944301d00c0edd61e8b012b0b3cdcde53ac60be903713f96542d83ad5b1d +DIST R-4.4.1.tar.gz 37353459 BLAKE2B 2c44fcab719cc2a2cef4566fd4e6c22386f02827a41045ffa074ca2a6883089275354644bce47c9978ef5c96e7b9b21576e946500746c27dc00946ef3cde4fce SHA512 cc30172227b7d89a9d6e9d65c8622b2042bcbbf3f1b5e36c7460f60958a1a0589980a1867ec9989df2589c1618233f3382d4732700b147361ace3be6680b5643 DIST R-78d6830e28ea90a046da79a9b4f70c39594bb6d6.bash_completion 13596 BLAKE2B 53338e4a1c4f68beb69247216e553dbcac47f660fbf032bfebf7a660e32d2cff5b11ed35411c52de7e1fd6e00bbf5b5ea19369a325fa0a38bd93d63dc3288cbd SHA512 9ccd19bb1b0c18a2f13035ccd6809447429e197e298fb4d1df808ef345d723b42f75a1b91c349f6dbb46e4a82e59ef33e11300c495d79b63d670d0c0f2b16a06 EBUILD R-4.3.1-r1.ebuild 7145 BLAKE2B 2635a3c8c165ad33c68dab1dc5ba648cd59295aec24a7a8f38f17dc173e29455d7a0c3f2e73a7d3a31b8e605bb3fd779569fe9db65166aba39c6b91e16157783 SHA512 d381bfcf37845fb33bef751e54d7bb607d8d08372f39ecc95d1d6b1969c6064756b7cd832641682cdf204cdb28a6da13aa87c212a22875c8d9bae1b479237cd0 EBUILD R-4.3.2-r1.ebuild 7148 BLAKE2B 00c7280e2b7e256b047dcec28d40712cf2af8513ce13548c43bace14334f83d56c10a97bdd9f36cc04a40ba59b119ea67806f866042fb30db47ddd29dc78a407 SHA512 285c9026732a06ba2a2f768f57c07120c859804a69dc8b023c3d5984061ed059a65c956295eb6d0323973f509e8bc38789f4f99a6f6286ad1727d47fdba6b023 -MISC metadata.xml 1212 BLAKE2B 6a3335018dc1a2a0b67c18bb6164e4a359ad0133bfdb3e7818173bec29d826e177934790d478d63bbcfc58fdbd3a25b9753c986604a52376ebc1fc6997206185 SHA512 68f4c1df03f6b9a00ce82dd7360dd3765a41dca257f0379820a0b631b64c0723536bba92a0247f12fd2efc82986c70b2afeefa4311239a68fd7949ea0af5358f +EBUILD R-4.4.1.ebuild 7258 BLAKE2B 3e922637eedd58ef9ba9b2121b04a2f54fa9f2002f630e85fa95c0b0ecdfcf4215fce1b16adbf840700fb2ed1849835a19a9a5cb26b69227ff0941301852ffc0 SHA512 9f53670f7ea2218eed5053b4ba5663de0c2bb32df1b071520c6821f77065c3ad3560f9b11dd3e837a30df0118bb02370dfe52d80ff2369fcaf51712fdce3b54f +MISC metadata.xml 1359 BLAKE2B 9cfca4def686f457622427e067bffba74608366f21125a167aa6efba5013db0c6c3e6d83d5b7012f436a7db44f4578061ce8c8673c8be95b417f52d66787f664 SHA512 1884aad4c68ddf884838c02f5e078966fcd932a7f2b1eac8298d895b4fb632bbc4abf7a849fdd870e0db7136c6642a4c3b1ccd5360e9f3253919b3a0b25a8555 diff --git a/dev-lang/R/R-4.4.1.ebuild b/dev-lang/R/R-4.4.1.ebuild new file mode 100644 index 000000000000..6282a9ecd337 --- /dev/null +++ b/dev-lang/R/R-4.4.1.ebuild @@ -0,0 +1,248 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit bash-completion-r1 autotools flag-o-matic fortran-2 toolchain-funcs + +# latest git commit for R bash completion: +# https://github.com/deepayan/rcompletion +BCPV=78d6830e28ea90a046da79a9b4f70c39594bb6d6 + +DESCRIPTION="Language and environment for statistical computing and graphics" +HOMEPAGE="https://www.r-project.org/" +SRC_URI=" + https://cran.r-project.org/src/base/R-4/${P}.tar.gz + https://raw.githubusercontent.com/deepayan/rcompletion/${BCPV}/bash_completion/R -> ${PN}-${BCPV}.bash_completion" + +LICENSE="|| ( GPL-2 GPL-3 ) LGPL-2.1" +SLOT="0" +KEYWORDS="~amd64 ~arm64 ~hppa ~ia64 ~loong ~sparc ~x86 ~amd64-linux ~x86-linux ~arm64-macos ~x64-macos" +IUSE="cairo doc icu java jpeg +libdeflate lto minimal nls openmp perl png prefix profile readline test tiff tk X" + +REQUIRED_USE=" + png? ( || ( cairo X ) ) + jpeg? ( || ( cairo X ) ) + tiff? ( || ( cairo X ) )" +RESTRICT=" + minimal? ( test ) + !test? ( test )" + +# At least one package installation in the test suite requires TeX, +# and will fail without it (bug #718056). +DEPEND=" + app-arch/bzip2 + app-arch/xz-utils + app-text/ghostscript-gpl + dev-libs/libpcre2:= + >=dev-libs/tre-0.8.0_p20210321[approx] + net-misc/curl + sys-libs/zlib[minizip] + sys-apps/coreutils + sys-libs/timezone-data + virtual/blas + virtual/lapack + cairo? ( + x11-libs/cairo:=[X=] + x11-libs/pango:= + ) + icu? ( dev-libs/icu:= ) + jpeg? ( media-libs/libjpeg-turbo:= ) + kernel_linux? ( net-libs/libtirpc:= ) + libdeflate? ( app-arch/libdeflate ) + perl? ( dev-lang/perl ) + png? ( media-libs/libpng:= ) + readline? ( sys-libs/readline:= ) + tiff? ( media-libs/tiff:= ) + tk? ( dev-lang/tk:= ) + X? ( + x11-libs/libX11 + x11-libs/libXmu + x11-libs/libXt + )" +RDEPEND="${DEPEND} + java? ( >=virtual/jre-1.8:* )" +BDEPEND=" + sys-apps/which + virtual/pkgconfig + doc? ( + virtual/latex-base + dev-texlive/texlive-fontsrecommended + ) + test? ( virtual/latex-base )" + +PATCHES=( + "${FILESDIR}"/R-4.3.0-parallel.patch + "${FILESDIR}"/R-4.3.0-no-LDFLAGS-in-libR-pkg-config.patch + "${FILESDIR}"/R-4.3.0-no-gzip-doc.patch +) + +# false positive, the linking step fails (as it should) +QA_CONFIG_IMPL_DECL_SKIP=( iconvlist ) + +pkg_pretend() { + [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp +} + +pkg_setup() { + if [[ ${MERGE_TYPE} != binary ]] && use openmp; then + tc-check-openmp + FORTRAN_NEED_OPENMP=1 + fi + + fortran-2_pkg_setup + + # avoid using existing R installation + unset R_HOME +} + +src_prepare() { + default + + # fix packages.html for doc (gentoo bug #205103) + sed -e "s:../../../library:../../../../$(get_libdir)/R/library:g" \ + -i src/library/tools/R/Rd.R || die + + # fix Rscript path when installed (gentoo bug #221061) + sed -e "s:-DR_HOME='\"\$(rhome)\"':-DR_HOME='\"${EPREFIX}/usr/$(get_libdir)/${PN}\"':" \ + -i src/unix/Makefile.in || die "sed unix Makefile failed" + + # fix HTML links to manual (gentoo bug #273957) + sed -e 's:\.\./manual/:manual/:g' \ + -i $(grep -Flr ../manual/ doc) || die "sed for HTML links failed" + + use perl && + export PERL5LIB="${S}/share/perl:${PERL5LIB:+:}${PERL5LIB}" + + # don't search /usr/local + sed -i -e '/FLAGS=.*\/local\//c\: # removed by ebuild' configure.ac || die + + # Fix for Darwin (macOS) + if use prefix; then + if [[ ${CHOST} == *-darwin* ]] ; then + sed -e 's:-install_name libR.dylib:-install_name ${libdir}/R/lib/libR.dylib:' \ + -e 's:-install_name libRlapack.dylib:-install_name ${libdir}/R/lib/libRlapack.dylib:' \ + -e 's:-install_name libRblas.dylib:-install_name ${libdir}/R/lib/libRblas.dylib:' \ + -e "/SHLIB_EXT/s/\.so/.dylib/" \ + -i configure.ac || die + # sort of "undo" 2.14.1-rmath-shared.patch + sed -e "s:-Wl,-soname=libRmath.so:-install_name ${EPREFIX}/usr/$(get_libdir)/libRmath.dylib:" \ + -i src/nmath/standalone/Makefile.in || die + else + append-ldflags -Wl,-rpath="${EPREFIX}/usr/$(get_libdir)/R/lib" + fi + fi + + AT_M4DIR=m4 eautoreconf +} + +src_configure() { + filter-ldflags -Wl,-Bdirect -Bdirect + + econf \ + --enable-byte-compiled-packages \ + --enable-R-shlib \ + --disable-R-framework \ + --disable-R-static-lib \ + --with-blas="$($(tc-getPKG_CONFIG) --libs blas)" \ + --with-lapack="$($(tc-getPKG_CONFIG) --libs lapack)" \ + rdocdir="${EPREFIX}/usr/share/doc/${PF}" \ + --with-system-tre \ + --without-aqua \ + --without-newAccelerate \ + $(use_enable java) \ + $(use_enable lto lto R) \ + $(use_enable nls) \ + $(use_enable openmp) \ + $(use_enable profile R-profiling) \ + $(use_enable profile memory-profiling) \ + $(use_with cairo) \ + $(use_with icu ICU) \ + $(use_with jpeg jpeglib) \ + $(use_with libdeflate libdeflate-compression) \ + $(use_with !minimal recommended-packages) \ + $(use_with png libpng) \ + $(use_with readline) \ + $(use_with tiff libtiff) \ + $(use_with tk tcltk) \ + $(use_with tk tk-config "${ESYSROOT}"/usr/$(get_libdir)/tkConfig.sh) \ + $(use_with tk tcl-config "${ESYSROOT}"/usr/$(get_libdir)/tclConfig.sh) \ + $(use_with X x) +} + +src_compile() { + export VARTEXFONTS="${T}"/fonts + emake AR="$(tc-getAR)" + emake -C src/nmath/standalone shared AR="$(tc-getAR)" + use doc && emake info pdf +} + +src_install() { + default + emake -C src/nmath/standalone DESTDIR="${D}" install + + if use doc; then + emake DESTDIR="${D}" install-info install-pdf + dosym ../manual /usr/share/doc/${PF}/html/manual + fi + + newenvd - 99R <<-_EOF_ + LDPATH="${EPREFIX}/usr/$(get_libdir)/${PN}/lib" + R_HOME="${EPREFIX}/usr/$(get_libdir)/${PN}" + _EOF_ + + newbashcomp "${DISTDIR}"/${PN}-${BCPV}.bash_completion ${PN} + # The buildsystem has a different understanding of install_names than + # we require. Since it builds modules like shared objects (wrong), many + # objects (all modules) get an incorrect install_name. Fixing the build + # system here is not really trivial. + if [[ ${CHOST} == *-darwin* ]] ; then + local mod + pushd "${ED}"/usr/$(get_libdir)/R >/dev/null || die + for mod in $(find . -name "*.dylib") ; do + mod=${mod#./} + install_name_tool -id "${EPREFIX}/usr/$(get_libdir)/R/${mod}" "${mod}" + done + popd >/dev/null || die + fi + + # Users are encouraged to access some of the the R documentation + # interactively, through functions like "contributors()" that + # tries to open the "AUTHORS" file. Other files can be accessed + # by name with RShowDoc(), and the documentation for e.g. license() + # and RShowDoc() suggests a few of these names. Here we try to + # collect as many names as possible that a user might actually + # try to view through R, because if we don't decompress them, + # then R doesn't know what to do with 'em. Bug #556706. + local INTERACTIVE_DOCS=( + AUTHORS + COPYING + FAQ + NEWS + THANKS + ) + + # Other data sources that are shipped as "documentation," but which + # need to be accessible via their original unmolested filenames. + local INTERACTIVE_DATA=( + BioC_mirrors.csv + CRAN_mirrors.csv + KEYWORDS.db + NEWS.rds + ) + + local f NOCOMPRESS_DOCS=( "${INTERACTIVE_DOCS[@]}" "${INTERACTIVE_DATA[@]}" ) + for f in "${NOCOMPRESS_DOCS[@]}"; do + docompress -x /usr/share/doc/${PF}/${f} + done + + # Finally, an extra copy of this started showing up at some point... + rm "${ED}"/usr/$(get_libdir)/R/COPYING || die +} + +pkg_postinst() { + if use java; then + einfo "Re-initializing java paths for ${P}" + R CMD javareconf + fi +} diff --git a/dev-lang/R/metadata.xml b/dev-lang/R/metadata.xml index c5ab836c4412..442394218fff 100644 --- a/dev-lang/R/metadata.xml +++ b/dev-lang/R/metadata.xml @@ -24,4 +24,7 @@ wch/r-source + + Use app-arch/libdeflate rather than sys-libs/zlib for lazy-loaded R objects. + -- cgit v1.2.3