diff --git a/dev-lang/R/Manifest b/dev-lang/R/Manifest index e8801a77e..1f38b245c 100644 --- a/dev-lang/R/Manifest +++ b/dev-lang/R/Manifest @@ -1,2 +1,3 @@ DIST R-4.4.3.tar.gz 40234425 BLAKE2B 2a7efdf1841c7bae66a0e8aef07b9e79dec9d2f1b4c32f12640eaf84f99b05ca2846eaf10a5d03e0a7fb6d0a4f00ab16cd84a618ebef7bec29c31bc04458f0db SHA512 2a1d1e5ee2e18c928e2b3e58df372083b4bbd0822863a8441404999209035436e236c8ffe3970827fbf3d765157365800ebb0bb46f361c6abe473ddec30be06f +DIST R-4.5.0.tar.gz 40466335 BLAKE2B 29ebfab54139320a7da30dfc976e5e210c3536c7be13014210e0ea51529a688962ec0f5298fe82989174ecd1fcec3146aad9c29de3882e8e5bbe0dbeb187c880 SHA512 e32de0115f32c3e44f3a003deae6b35fa0ae1ed951f8a74d815e8a417de0e84547c2ec5386cf965208cc1c81e5d43a3706a15af929d295056201f2ffe6b9d84b DIST rcompletion-78d6830e28ea90a046da79a9b4f70c39594bb6d6.tar.gz 5043 BLAKE2B edf0182d8e47971e6e916d8b42d25ca48f111d4486c8c73ff38282a097fcbc506d18bf62da1fa0098a5d5d8baad670c12faec80840991cdc9543c99d382a571e SHA512 5ee5c177cea9e992cd00d9468c723dd82119d11163796ecfe980fe6715a53194cef13124460e25a665d63467e3281784be37cc4b4f82f67a1fc7988d1e80ed7a diff --git a/dev-lang/R/R-4.5.0.ebuild b/dev-lang/R/R-4.5.0.ebuild new file mode 100644 index 000000000..1802621ed --- /dev/null +++ b/dev-lang/R/R-4.5.0.ebuild @@ -0,0 +1,235 @@ +# 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="https://www.r-project.org/" +SRC_URI=" + https://cran.r-project.org/src/base/R-4/R-4.5.0.tar.gz -> R-4.5.0.tar.gz + https://github.com/deepayan/rcompletion/archive/78d6830e28ea90a046da79a9b4f70c39594bb6d6.tar.gz -> rcompletion-78d6830e28ea90a046da79a9b4f70c39594bb6d6.tar.gz" + +LICENSE="|| ( GPL-2 GPL-3 ) LGPL-2.1" +SLOT="0" +KEYWORDS="*" +IUSE="cairo doc icu java jpeg +lapack lto minimal nls openmp perl png prefix profile readline static-libs test tiff tk X" + +REQUIRED_USE="png? ( || ( cairo X ) ) + jpeg? ( || ( cairo X ) ) + tiff? ( || ( cairo X ) ) +" + +# 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-libs/libXt x11-misc/xdg-utils )" + +RDEPEND="${DEPEND} + sys-libs/zlib:0[minizip] + java? ( >=virtual/jre-1.8:* )" + +RESTRICT="minimal? ( test ) + !test? ( test )" + +PATCHES=( + "${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 [[ ${MERGE_TYPE} != binary ]] && use openmp; then + FORTRAN_NEED_OPENMP=1 + fi + fortran-2_pkg_setup + filter-ldflags -Wl,-Bdirect -Bdirect + # avoid using existing R installation + unset R_HOME +} + +src_prepare() { + default + + # fix packages.html for doc (gentoo bug #205103) + sed -e "s:../../../library:../../../../$(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 lto lto R) \ + $(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)/${PN} + EOF + doenvd 99R + + newbashcomp "${WORKDIR}/rcompletion-${BCPV}/bash_completion/R" ${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 +} \ No newline at end of file