commit: 39ea7b8baaf4a59680f07475e64fbce2b6a36e05 Author: Mikle Kolyada <zlogene <AT> gentoo <DOT> org> AuthorDate: Sat Apr 10 13:32:39 2021 +0000 Commit: Mikle Kolyada <zlogene <AT> gentoo <DOT> org> CommitDate: Sat Apr 10 13:33:07 2021 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=39ea7b8b
dev-lang/R: Version bump (v4.0.5) Package-Manager: Portage-3.0.17, Repoman-3.0.2 Signed-off-by: Mikle Kolyada <zlogene <AT> gentoo.org> dev-lang/R/Manifest | 1 + dev-lang/R/R-4.0.5.ebuild | 243 ++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 244 insertions(+) diff --git a/dev-lang/R/Manifest b/dev-lang/R/Manifest index fa930a03bf5..5a48a7b4c96 100644 --- a/dev-lang/R/Manifest +++ b/dev-lang/R/Manifest @@ -2,4 +2,5 @@ DIST R-3.4.1.tar.gz 30200109 BLAKE2B 03602e9a48759caee8ce047fa6273df7a54af089de4 DIST R-3.6.3.tar.gz 33308185 BLAKE2B f82751e21d3b502132f8f27d4fc47a921fb085a50c3da3b45e08fbbdd1ab3d42e89b4fa6653a570c21176d79f492277b1d0b86c3c9f4da1386d8b6e4771d4d2c SHA512 9b1dc78922e431bd1af81e6e560b10ad04d121718f680fed32db735d561fd40ea6028759976722db11559f1a78fe684119b766f0567128cb2ee5003aa87a0931 DIST R-4.0.2.tar.gz 33191186 BLAKE2B 2d5b99c17a9df48a36871f18701efacfaa1e6bb89c0e5c6516fc20966547f34f9079dc52ab18ac7816e0fed25d6230076246e83dc648501553fa2d0cad67b8e4 SHA512 b7330613ee9795f54cde3dd9f7509be83d9156fb8577c17179727ee01450db27704249f68bd48e0331e2df09c2d9833d8bb019c4f9ce9ba669df74650ff2e842 DIST R-4.0.4.tar.gz 33687611 BLAKE2B 40cdfd98fe6c9193deb729d151631c2b0f935accf5ea6251704b633d2688278af1a5a67317152be023fb4a10315c64e473f58276bb0c3fadb1141c35391ad22e SHA512 811c4407a083eb776f92c3cbacb1dc7eada8890a8c27678c6c82bef9db52b1afaefeb408fbe11e46922740adee498f32e7ddf7451b3ab89cf60773737e47f8be +DIST R-4.0.5.tar.gz 32466444 BLAKE2B 5dbbd289f4fd6347b4109eecaf65b50b5793a83edddd2cb391c20473607f136d91a8e9f4ab9e453f6927d2ca9145762920424e3a1dcea89309afde56efd5d32c SHA512 6ff5b0f9cb6b17f66cde1f5585d1b33659dbae8919d34c2e593f68a0bff4d0425aa9704d99284d103702a9cd42f613311f3a87af6b939b1af65dcec80bf2ca8c DIST R-78d6830e28ea90a046da79a9b4f70c39594bb6d6.bash_completion 13596 BLAKE2B 53338e4a1c4f68beb69247216e553dbcac47f660fbf032bfebf7a660e32d2cff5b11ed35411c52de7e1fd6e00bbf5b5ea19369a325fa0a38bd93d63dc3288cbd SHA512 9ccd19bb1b0c18a2f13035ccd6809447429e197e298fb4d1df808ef345d723b42f75a1b91c349f6dbb46e4a82e59ef33e11300c495d79b63d670d0c0f2b16a06 diff --git a/dev-lang/R/R-4.0.5.ebuild b/dev-lang/R/R-4.0.5.ebuild new file mode 100644 index 00000000000..560e83d01f7 --- /dev/null +++ b/dev-lang/R/R-4.0.5.ebuild @@ -0,0 +1,243 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +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="http://www.r-project.org/"; +SRC_URI=" + mirror://cran/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 ~sparc ~x86 ~amd64-linux ~x86-linux" +IUSE="cairo doc icu java jpeg lapack minimal nls openmp perl png prefix profile readline static-libs test tiff tk X" + +# One test required profiling in v4.0.2, check the upstream bug: +# +# https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17836 +# +REQUIRED_USE="png? ( || ( cairo X ) ) + jpeg? ( || ( cairo X ) ) + tiff? ( || ( cairo X ) ) + test? ( profile ) +" + +# At least one package installation in the test suite requires TeX, +# and will fail without it (bug #718056). +BDEPEND="virtual/pkgconfig + doc? ( + virtual/latex-base + dev-texlive/texlive-fontsrecommended + ) + test? ( virtual/latex-base )" +DEPEND=" + app-arch/bzip2:0= + app-arch/xz-utils:0= + app-text/ghostscript-gpl + dev-libs/libpcre2:= + net-libs/libtirpc + net-misc/curl + virtual/blas:0 + || ( sys-apps/coreutils app-misc/realpath ) + cairo? ( x11-libs/cairo:0=[X=] x11-libs/pango:0= ) + icu? ( dev-libs/icu:= ) + jpeg? ( virtual/jpeg:0 ) + lapack? ( virtual/lapack:0 ) + perl? ( dev-lang/perl ) + png? ( media-libs/libpng:0= ) + readline? ( sys-libs/readline:0= ) + tiff? ( media-libs/tiff:0= ) + tk? ( dev-lang/tk:0= ) + X? ( x11-libs/libXmu:0= x11-misc/xdg-utils )" + +RDEPEND="${DEPEND} + sys-libs/zlib:0[minizip] + java? ( >=virtual/jre-1.5 )" + +RESTRICT="minimal? ( test ) + !test? ( test )" + +PATCHES=( + "${FILESDIR}"/${PN}-3.4.1-parallel.patch + "${FILESDIR}"/${PN}-3.4.1-rmath-shared.patch + "${FILESDIR}"/${PN}-3.6.2-no-LDFLAGS-in-libR-pkg-config.patch + "${FILESDIR}"/${PN}-3.6.2-no-gzip-doc.patch +) + +pkg_pretend() { + [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp +} + +pkg_setup() { + if [[ ${MERGE_TYPE} != binary ]] && use openmp; then + FORTRAN_NEED_OPENMP=1 + fi + fortran-2_pkg_setup + filter-ldflags -Wl,-Bdirect -Bdirect + # avoid using existing R installation + unset R_HOME + # Temporary fix for bug #419761 + if [[ ($(tc-getCC) == *gcc) && ($(gcc-version) == 4.7) ]]; then + append-flags -fno-ipa-cp-clone + fi +} + +src_prepare() { + default + + # fix packages.html for doc (gentoo bug #205103) + sed -e "s:../../../library:../../../../$(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='\"${EROOT}/usr/$(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 $(grep -Flr ../manual/ doc) || die "sed for HTML links failed" + + use lapack && \ + export LAPACK_LIBS="$($(tc-getPKG_CONFIG) --libs lapack)" + + if use X; then + export R_BROWSER="$(type -p xdg-open)" + export R_PDFVIEWER="$(type -p xdg-open)" + fi + use perl && \ + export PERL5LIB="${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 (OS X) + 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 ${EROOT}/usr/$(get_libdir)/libRmath.dylib:" \ + -i src/nmath/standalone/Makefile.in || die + else + append-ldflags -Wl,-rpath="${EROOT}/usr/$(get_libdir)/R/lib" + fi + fi + AT_M4DIR=m4 + eautoreconf +} + +src_configure() { + # --with-system-tre \ + # tre is patched from upstream + econf \ + --enable-byte-compiled-packages \ + --enable-R-shlib \ + --disable-R-framework \ + --with-blas="$($(tc-getPKG_CONFIG) --libs blas)" \ + rdocdir="${EPREFIX}/usr/share/doc/${PF}" \ + $(use_enable java) \ + $(use_enable nls) \ + $(use_enable openmp) \ + $(use_enable profile R-profiling) \ + $(use_enable profile memory-profiling) \ + $(use_enable static-libs static) \ + $(use_enable static-libs R-static-lib) \ + $(use_with cairo) \ + $(use_with icu ICU) \ + $(use_with jpeg jpeglib) \ + $(use_with lapack) \ + $(use_with !minimal recommended-packages) \ + $(use_with png libpng) \ + $(use_with readline) \ + $(use_with tiff libtiff) \ + $(use_with tk tcltk) \ + $(use_with tk tk-config "${EPREFIX}"/usr/$(get_libdir)/tkConfig.sh) \ + $(use_with tk tcl-config "${EPREFIX}"/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 $(use static-libs && echo static) AR="$(tc-getAR)" + use doc && emake info pdf +} + +src_install() { + default + emake -j1 -C src/nmath/standalone DESTDIR="${D}" install + + if use doc; then + emake DESTDIR="${D}" install-info install-pdf + dosym ../manual /usr/share/doc/${PF}/html/manual + fi + + cat > 99R <<-EOF + LDPATH=${EROOT}/usr/$(get_libdir)/${PN}/lib + R_HOME=${EROOT}/usr/$(get_libdir)/${PN} + EOF + doenvd 99R + newbashcomp "${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 + for mod in $(find . -name "*.dylib") ; do + mod=${mod#./} + install_name_tool -id "${EPREFIX}/usr/$(get_libdir)/R/${mod}" \ + "${mod}" + done + popd > /dev/null + 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. + 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. + INTERACTIVE_DATA=( + BioC_mirrors.csv + CRAN_mirrors.csv + KEYWORDS.db + NEWS.rds + ) + + NOCOMPRESS_DOCS=( "${INTERACTIVE_DOCS[@]}" "${INTERACTIVE_DATA[@]}" ) + + for f in "${NOCOMPRESS_DOCS[@]}"; do + docompress -x "/usr/share/doc/${PF}/${f}" + done +} + +pkg_postinst() { + if use java; then + einfo "Re-initializing java paths for ${P}" + R CMD javareconf + fi +}
