commit: ddf00116a89246a9d213a8d35a7b8bb7bc311938 Author: Michael Orlitzky <mjo <AT> gentoo <DOT> org> AuthorDate: Sat May 7 22:29:07 2022 +0000 Commit: Michael Orlitzky <mjo <AT> gentoo <DOT> org> CommitDate: Sat May 7 22:29:25 2022 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=ddf00116
dev-lang/R: new upstream version R-4.2.0. Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Michael Orlitzky <mjo <AT> gentoo.org> dev-lang/R/Manifest | 1 + dev-lang/R/R-4.2.0.ebuild | 256 ++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 257 insertions(+) diff --git a/dev-lang/R/Manifest b/dev-lang/R/Manifest index ff6f613c6b32..d051562da6ab 100644 --- a/dev-lang/R/Manifest +++ b/dev-lang/R/Manifest @@ -1,4 +1,5 @@ DIST R-4.0.5.tar.gz 32466444 BLAKE2B 5dbbd289f4fd6347b4109eecaf65b50b5793a83edddd2cb391c20473607f136d91a8e9f4ab9e453f6927d2ca9145762920424e3a1dcea89309afde56efd5d32c SHA512 6ff5b0f9cb6b17f66cde1f5585d1b33659dbae8919d34c2e593f68a0bff4d0425aa9704d99284d103702a9cd42f613311f3a87af6b939b1af65dcec80bf2ca8c DIST R-4.1.0.tar.gz 33714683 BLAKE2B 22ba966b5a29f153f3ce6cbc467e815c397e7c6aade0db62c7d2ae044056d9227da4dcb8fbf33e661548f4f434c328415e297c6b07b3932ef3f47358c2543f42 SHA512 41519bf06a1ebc2bb582e9a7c35d0e82e213312dec8147861a7f9b28ee750cd40dfbf02737602d05698641fcea6182b0da8131e83edacc358e98eca0a393b729 DIST R-4.1.2.tar.gz 34009074 BLAKE2B 7ca14b28fc40548180dde979d57f93f41fb3966697d58f686cf63e24e4cbf2de8166240952e708fc94f97846cd57bbd559b4edb688500e1db2a6704de16f508c SHA512 657c7950a88f632f1bbb08dbd0b3fb485732a25d8bbcb8a7939a40b23c7a235fdb9b46c296acaa9f72eabebe96e270ecbdcd7970fc9d3a299e6687bea45f2d3f +DIST R-4.2.0.tar.gz 37585694 BLAKE2B 5ba4d3b9397e92b72af729d88ff562655e0dd7c547bd371638aa76d4f1701f4f8a7911d500cf4f10d87b62457f8f8ce7a946d893477ceb7268b06bd59bc10f3d SHA512 99e71dad00b63e44bfcb8dc9539ff1951809112882d9ee7e06a4e99bce2e6ceac24e8348fd598c21e6d5ab0e0629a85170cde208bfa8145af91c398ac4ef7bcd DIST R-78d6830e28ea90a046da79a9b4f70c39594bb6d6.bash_completion 13596 BLAKE2B 53338e4a1c4f68beb69247216e553dbcac47f660fbf032bfebf7a660e32d2cff5b11ed35411c52de7e1fd6e00bbf5b5ea19369a325fa0a38bd93d63dc3288cbd SHA512 9ccd19bb1b0c18a2f13035ccd6809447429e197e298fb4d1df808ef345d723b42f75a1b91c349f6dbb46e4a82e59ef33e11300c495d79b63d670d0c0f2b16a06 diff --git a/dev-lang/R/R-4.2.0.ebuild b/dev-lang/R/R-4.2.0.ebuild new file mode 100644 index 000000000000..28e62a99b24d --- /dev/null +++ b/dev-lang/R/R-4.2.0.ebuild @@ -0,0 +1,256 @@ +# Copyright 1999-2022 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=" + 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 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). +BDEPEND=" + virtual/pkgconfig + doc? ( + virtual/latex-base + dev-texlive/texlive-fontsrecommended + ) + test? ( virtual/latex-base )" +DEPEND=" + app-arch/bzip2 + app-arch/xz-utils + app-text/ghostscript-gpl + dev-libs/libpcre2:= + >=dev-libs/tre-0.8.0_p20210321[approx] + net-libs/libtirpc + net-misc/curl + virtual/blas + sys-libs/zlib[minizip] + || ( + sys-apps/coreutils + app-misc/realpath + ) + cairo? ( + x11-libs/cairo:=[X=] + x11-libs/pango:= + ) + icu? ( dev-libs/icu:= ) + jpeg? ( virtual/jpeg ) + lapack? ( virtual/lapack ) + perl? ( dev-lang/perl ) + png? ( media-libs/libpng:= ) + readline? ( sys-libs/readline:= ) + tiff? ( media-libs/tiff:= ) + tk? ( dev-lang/tk:= ) + X? ( + x11-libs/libXmu + x11-libs/libXt + x11-misc/xdg-utils + )" +RDEPEND="${DEPEND} + java? ( >=virtual/jre-1.8:* )" + +PATCHES=( + "${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 [[ ${MERGE_TYPE} != binary ]] && use openmp; then + tc-check-openmp + FORTRAN_NEED_OPENMP=1 + fi + + fortran-2_pkg_setup + + # avoid using existing R installation + unset R_HOME +} + +src_prepare() { + default + + # fix packages.html for doc (gentoo bug #205103) + sed -e "s:../../../library:../../../../$(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 $(grep -Flr ../manual/ doc) || die "sed for HTML links failed" + + # Disable this test until it passes again, + # https://bugs.r-project.org/show_bug.cgi?id=18338 + sed -e 's/ reg-packages.R / /' \ + -i tests/Makefile.common || die + + use lapack && \ + export LAPACK_LIBS="$($(tc-getPKG_CONFIG) --libs lapack)" + + if use X; then + export R_BROWSER="$(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 (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)" \ + rdocdir="${EPREFIX}/usr/share/doc/${PF}" \ + --with-system-tre \ + $(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 lapack) \ + $(use_with !minimal recommended-packages) \ + $(use_with png libpng) \ + $(use_with readline) \ + $(use_with tiff libtiff) \ + $(use_with tk tcltk) \ + $(use_with tk tk-config "${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 -j1 -C src/nmath/standalone DESTDIR="${D}" install + + if use doc; then + emake DESTDIR="${D}" install-info install-pdf + dosym ../manual /usr/share/doc/${PF}/html/manual + fi + + newenvd - 99R <<-_EOF_ + LDPATH=${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 +}
