From 8376ef56580626e9c0f796d5b85b53a0a1c7d5f5 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Sat, 14 Jul 2018 21:03:06 +0100 Subject: gentoo resync : 14.07.2018 --- dev-lang/R/Manifest | 17 ++ dev-lang/R/R-3.2.2.ebuild | 205 +++++++++++++++++++++ dev-lang/R/R-3.3.2.ebuild | 201 ++++++++++++++++++++ dev-lang/R/R-3.4.1.ebuild | 204 ++++++++++++++++++++ dev-lang/R/R-3.5.1.ebuild | 204 ++++++++++++++++++++ dev-lang/R/files/R-2.11.1-parallel.patch | 17 ++ dev-lang/R/files/R-2.13.1-zlib_header_fix.patch | 20 ++ dev-lang/R/files/R-3.0.0-rmath-shared.patch | 28 +++ .../R/files/R-3.3.2-zlib-1.2.10-backport.patch | 20 ++ dev-lang/R/files/R-3.4.1-parallel.patch | 11 ++ dev-lang/R/files/R-3.4.1-rmath-shared.patch | 21 +++ dev-lang/R/metadata.xml | 24 +++ 12 files changed, 972 insertions(+) create mode 100644 dev-lang/R/Manifest create mode 100644 dev-lang/R/R-3.2.2.ebuild create mode 100644 dev-lang/R/R-3.3.2.ebuild create mode 100644 dev-lang/R/R-3.4.1.ebuild create mode 100644 dev-lang/R/R-3.5.1.ebuild create mode 100644 dev-lang/R/files/R-2.11.1-parallel.patch create mode 100644 dev-lang/R/files/R-2.13.1-zlib_header_fix.patch create mode 100644 dev-lang/R/files/R-3.0.0-rmath-shared.patch create mode 100644 dev-lang/R/files/R-3.3.2-zlib-1.2.10-backport.patch create mode 100644 dev-lang/R/files/R-3.4.1-parallel.patch create mode 100644 dev-lang/R/files/R-3.4.1-rmath-shared.patch create mode 100644 dev-lang/R/metadata.xml (limited to 'dev-lang/R') diff --git a/dev-lang/R/Manifest b/dev-lang/R/Manifest new file mode 100644 index 000000000000..1944609313e8 --- /dev/null +++ b/dev-lang/R/Manifest @@ -0,0 +1,17 @@ +AUX R-2.11.1-parallel.patch 685 BLAKE2B 877a6cc17cc415e9cc6e76a2c1e4807c6549c9ad65a9bc014fa7de186c32509af945ae96d0ba976243efa38c32eb0dea1f67e9c97c5d7f99af54c3ab36011989 SHA512 30491365eee00389f6f09c2093b5b5a568f4567c110cc0cb3332a53d6a7fcd87fe8f46f9f8521cf21bf1f0cfa24f4282a6e22396902f454c43f26542ac22c2a9 +AUX R-2.13.1-zlib_header_fix.patch 591 BLAKE2B 89087e6a37cffbe1c2f879d5ed8bae39d6d05813a121ec13f1d4e27cf65daf615b46d1246765f2deb7704487ed3382a5c1435710ec2f23d257defd427caeddb2 SHA512 1ada5a3ccb0ff902f7df35d6a42f4e99fee6a1f7b36ece000b9e2fed2b731abf5c3687d22239cd324ff6677bf8edff3415aca57c31beef33c73b98073206136a +AUX R-3.0.0-rmath-shared.patch 1137 BLAKE2B dbae2fd70ec163edf4707aec5ad28737b4b9af20c98a0807a7d947496cd3536834c24a435f9ec641205237c71dc3378ac307ebc013f0e21939f9a4aaff4a53be SHA512 92b950703f1bb6dc82b5cee5e4165fddbdf6a2aa2670980460268dae0918f884c8c0ced069b5d106853c7be814025153e8b3fe9689f1db7eeb387cf73b18a4d4 +AUX R-3.3.2-zlib-1.2.10-backport.patch 511 BLAKE2B c5210ed01461c0f2f22e7668a1952593ca4732debd7061df94f6f43536fdbe8accb3338eceffc00b8c321dc5979b045adb7b49390450a330e202175500f3b585 SHA512 29fa5be3de023f0699bab8fec5095f83936d4e40be1cbc43595a7e5ff0023d586c1bfcfe5ed8edde805fa699443e2c6be61779000e6c91be22d7b19309cbb09a +AUX R-3.4.1-parallel.patch 487 BLAKE2B 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774221eb531b4e80f0650b627b9ce53d9a2daf6342b1f19579d2d046e1c83aa497cc764870406b7ea3cf6cbae899cb6d460af92991d62bc6aea8da026a441822 SHA512 297c7e17998f92fb836b0599ce5221aee1ba1e7b1504edb348a602b695faf381d51f32f6118f5ef4bb353f02e92ffc5b3520b8d317d3e30a68a3cce0254fa6b1 diff --git a/dev-lang/R/R-3.2.2.ebuild b/dev-lang/R/R-3.2.2.ebuild new file mode 100644 index 000000000000..ae27f02d702e --- /dev/null +++ b/dev-lang/R/R-3.2.2.ebuild @@ -0,0 +1,205 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit bash-completion-r1 autotools eutils flag-o-matic fortran-2 multilib versionator toolchain-funcs + +BCP=${PN}-20130129.bash_completion +DESCRIPTION="Language and environment for statistical computing and graphics" +HOMEPAGE="http://www.r-project.org/" +SRC_URI=" + mirror://cran/src/base/R-3/${P}.tar.gz + https://dev.gentoo.org/~bicatali/distfiles/${BCP}.bz2" + +LICENSE="|| ( GPL-2 GPL-3 ) LGPL-2.1" +SLOT="0" +KEYWORDS="amd64 hppa ia64 ppc ppc64 sparc x86 ~x86-fbsd ~amd64-linux ~x86-linux ~x64-macos" +IUSE="cairo doc icu java jpeg lapack minimal nls openmp perl png prefix profile readline static-libs tiff tk X" +REQUIRED_USE="png? ( || ( cairo X ) ) jpeg? ( || ( cairo X ) ) tiff? ( || ( cairo X ) )" + +CDEPEND=" + app-arch/bzip2:0= + app-arch/xz-utils:0= + app-text/ghostscript-gpl + >=dev-libs/libpcre-8.35:3= + virtual/blas:0 + || ( >=sys-apps/coreutils-8.15 sys-freebsd/freebsd-bin app-misc/realpath ) + cairo? ( x11-libs/cairo:0=[X] x11-libs/pango:0= ) + icu? ( dev-libs/icu:= ) + jpeg? ( virtual/jpeg:0 ) + lapack? ( virtual/lapack:0 ) + perl? ( dev-lang/perl ) + png? ( media-libs/libpng:0= ) + readline? ( sys-libs/readline:0= ) + tiff? ( media-libs/tiff:0= ) + tk? ( dev-lang/tk:0= ) + X? ( x11-libs/libXmu:0= x11-misc/xdg-utils )" + +DEPEND="${CDEPEND} + virtual/pkgconfig + doc? ( + virtual/latex-base + dev-texlive/texlive-fontsrecommended + )" + +RDEPEND="${CDEPEND} + >=sys-libs/zlib-1.2.5.1-r2:0[minizip] + java? ( >=virtual/jre-1.5 )" + +RESTRICT="minimal? ( test )" + +R_DIR="${EROOT%/}/usr/$(get_libdir)/${PN}" + +pkg_setup() { + if use openmp; then + if [[ $(tc-getCC) == *gcc ]] && ! tc-has-openmp; then + ewarn "OpenMP is not available in your current selected gcc" + die "need openmp capable gcc" + fi + FORTRAN_NEED_OPENMP=1 + fi + fortran-2_pkg_setup + filter-ldflags -Wl,-Bdirect -Bdirect + # avoid using existing R installation + unset R_HOME + # Temporary fix for bug #419761 + if [[ ($(tc-getCC) == *gcc) && ($(gcc-version) == 4.7) ]]; then + append-flags -fno-ipa-cp-clone + fi +} + +src_prepare() { + epatch \ + "${FILESDIR}"/${PN}-2.11.1-parallel.patch \ + "${FILESDIR}"/${PN}-2.13.1-zlib_header_fix.patch \ + "${FILESDIR}"/${PN}-3.0.0-rmath-shared.patch + + # fix packages.html for doc (gentoo bug #205103) + sed -i \ + -e "s:../../../library:../../../../$(get_libdir)/R/library:g" \ + src/library/tools/R/Rd.R || die + + # fix Rscript path when installed (gentoo bug #221061) + sed -i \ + -e "s:-DR_HOME='\"\$(rhome)\"':-DR_HOME='\"${R_DIR}\"':" \ + src/unix/Makefile.in || die "sed unix Makefile failed" + + # fix HTML links to manual (gentoo bug #273957) + sed -i \ + -e 's:\.\./manual/:manual/:g' \ + $(grep -Flr ../manual/ doc) || die "sed for HTML links failed" + + use lapack && \ + export LAPACK_LIBS="$($(tc-getPKG_CONFIG) --libs lapack)" + + if use X; then + export R_BROWSER="$(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 -i \ + -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/" \ + configure.ac || die + # sort of "undo" 2.14.1-rmath-shared.patch + sed -i \ + -e "s:-Wl,-soname=libRmath.so:-install_name ${EROOT%/}/usr/$(get_libdir)/libRmath.dylib:" \ + src/nmath/standalone/Makefile.in || die + else + append-ldflags -Wl,-rpath="${EROOT%/}/usr/$(get_libdir)/R/lib" + fi + fi + AT_M4DIR=m4 eaclocal + eautoconf +} + +src_configure() { + # --with-system-tre \ + # tre is patched from upstream + econf \ + --enable-byte-compiled-packages \ + --enable-R-shlib \ + --disable-R-framework \ + --with-system-zlib \ + --with-system-bzlib \ + --with-system-pcre \ + --with-system-xz \ + --with-blas="$($(tc-getPKG_CONFIG) --libs blas)" \ + --docdir="${EPREFIX}/usr/share/doc/${PF}" \ + rdocdir="${EPREFIX}/usr/share/doc/${PF}" \ + $(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/lib/tkConfig.sh) \ + $(use_with tk tcl-config "${EPREFIX}"/usr/lib/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/${PF}/html/manual + fi + + cat > 99R <<-EOF + LDPATH=${R_DIR}/lib + R_HOME=${R_DIR} + EOF + doenvd 99R + newbashcomp "${WORKDIR}"/${BCP} ${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/lib/R > /dev/null + for mod in $(find . -name "*.dylib") ; do + mod=${mod#./} + install_name_tool -id "${EPREFIX}/usr/lib/R/${mod}" \ + "${mod}" + done + popd > /dev/null + fi + docompress -x /usr/share/doc/${PF}/NEWS.rds +} + +pkg_postinst() { + if use java; then + einfo "Re-initializing java paths for ${P}" + R CMD javareconf + fi +} diff --git a/dev-lang/R/R-3.3.2.ebuild b/dev-lang/R/R-3.3.2.ebuild new file mode 100644 index 000000000000..fb9bde8c312a --- /dev/null +++ b/dev-lang/R/R-3.3.2.ebuild @@ -0,0 +1,201 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit bash-completion-r1 autotools eutils flag-o-matic fortran-2 multilib versionator toolchain-funcs + +BCP=${PN}-20130129.bash_completion +DESCRIPTION="Language and environment for statistical computing and graphics" +HOMEPAGE="http://www.r-project.org/" +SRC_URI=" + mirror://cran/src/base/R-3/${P}.tar.gz + https://dev.gentoo.org/~bicatali/distfiles/${BCP}.bz2" + +LICENSE="|| ( GPL-2 GPL-3 ) LGPL-2.1" +SLOT="0" +KEYWORDS="~amd64 ~hppa ~ia64 ~ppc ~ppc64 ~sparc ~x86 ~x86-fbsd ~amd64-linux ~x86-linux ~x64-macos" +IUSE="cairo doc icu java jpeg lapack minimal nls openmp perl png prefix profile readline static-libs tiff tk X" +REQUIRED_USE="png? ( || ( cairo X ) ) jpeg? ( || ( cairo X ) ) tiff? ( || ( cairo X ) )" + +CDEPEND=" + app-arch/bzip2:0= + app-arch/xz-utils:0= + app-text/ghostscript-gpl + >=dev-libs/libpcre-8.35:3= + virtual/blas:0 + || ( >=sys-apps/coreutils-8.15 sys-freebsd/freebsd-bin 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 )" + +DEPEND="${CDEPEND} + virtual/pkgconfig + doc? ( + virtual/latex-base + dev-texlive/texlive-fontsrecommended + )" + +RDEPEND="${CDEPEND} + >=sys-libs/zlib-1.2.5.1-r2:0[minizip] + java? ( >=virtual/jre-1.5 )" + +RESTRICT="minimal? ( test )" + +pkg_setup() { + if use openmp; then + if [[ $(tc-getCC) == *gcc ]] && ! tc-has-openmp; then + ewarn "OpenMP is not available in your current selected gcc" + die "need openmp capable gcc" + fi + FORTRAN_NEED_OPENMP=1 + fi + fortran-2_pkg_setup + filter-ldflags -Wl,-Bdirect -Bdirect + # avoid using existing R installation + unset R_HOME + # Temporary fix for bug #419761 + if [[ ($(tc-getCC) == *gcc) && ($(gcc-version) == 4.7) ]]; then + append-flags -fno-ipa-cp-clone + fi +} + +src_prepare() { + epatch \ + "${FILESDIR}"/${PN}-2.11.1-parallel.patch \ + "${FILESDIR}"/${PN}-2.13.1-zlib_header_fix.patch \ + "${FILESDIR}"/${PN}-3.0.0-rmath-shared.patch \ + "${FILESDIR}"/${P}-zlib-1.2.10-backport.patch + + # fix packages.html for doc (gentoo bug #205103) + sed -i \ + -e "s:../../../library:../../../../$(get_libdir)/R/library:g" \ + src/library/tools/R/Rd.R || die + + # fix Rscript path when installed (gentoo bug #221061) + sed -i \ + -e "s:-DR_HOME='\"\$(rhome)\"':-DR_HOME='\"${EROOT%/}/usr/$(get_libdir)/${PN}\"':" \ + src/unix/Makefile.in || die "sed unix Makefile failed" + + # fix HTML links to manual (gentoo bug #273957) + sed -i \ + -e 's:\.\./manual/:manual/:g' \ + $(grep -Flr ../manual/ doc) || die "sed for HTML links failed" + + use lapack && \ + export LAPACK_LIBS="$($(tc-getPKG_CONFIG) --libs lapack)" + + if use X; then + export R_BROWSER="$(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 -i \ + -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/" \ + configure.ac || die + # sort of "undo" 2.14.1-rmath-shared.patch + sed -i \ + -e "s:-Wl,-soname=libRmath.so:-install_name ${EROOT%/}/usr/$(get_libdir)/libRmath.dylib:" \ + src/nmath/standalone/Makefile.in || die + else + append-ldflags -Wl,-rpath="${EROOT%/}/usr/$(get_libdir)/R/lib" + fi + fi + AT_M4DIR=m4 eaclocal + eautoconf +} + +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)" \ + --docdir="${EPREFIX}/usr/share/doc/${PF}" \ + 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/lib/tkConfig.sh) \ + $(use_with tk tcl-config "${EPREFIX}"/usr/lib/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}"/${BCP} ${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/lib/R > /dev/null + for mod in $(find . -name "*.dylib") ; do + mod=${mod#./} + install_name_tool -id "${EPREFIX}/usr/lib/R/${mod}" \ + "${mod}" + done + popd > /dev/null + fi + docompress -x /usr/share/doc/${PF}/{BioC_mirrors.csv,CRAN_mirrors.csv,KEYWORDS.db,NEWS.rds} +} + +pkg_postinst() { + if use java; then + einfo "Re-initializing java paths for ${P}" + R CMD javareconf + fi +} diff --git a/dev-lang/R/R-3.4.1.ebuild b/dev-lang/R/R-3.4.1.ebuild new file mode 100644 index 000000000000..45c84fd36498 --- /dev/null +++ b/dev-lang/R/R-3.4.1.ebuild @@ -0,0 +1,204 @@ +# Copyright 1999-2018 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit bash-completion-r1 autotools eutils flag-o-matic fortran-2 multilib versionator toolchain-funcs + +# latest git commit for R bash completion: https://github.com/deepayan/rcompletion +BCPV=78d6830e28ea90a046da79a9b4f70c39594bb6d6 + +DESCRIPTION="Language and environment for statistical computing and graphics" +HOMEPAGE="http://www.r-project.org/" +SRC_URI=" + mirror://cran/src/base/R-3/${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 ~hppa ia64 ~ppc ~ppc64 ~sparc x86 ~x86-fbsd ~amd64-linux ~x86-linux ~x64-macos" +IUSE="cairo doc icu java jpeg lapack minimal nls openmp perl png prefix profile readline static-libs tiff tk X" +REQUIRED_USE="png? ( || ( cairo X ) ) jpeg? ( || ( cairo X ) ) tiff? ( || ( cairo X ) )" + +CDEPEND=" + app-arch/bzip2:0= + app-arch/xz-utils:0= + app-text/ghostscript-gpl + >=dev-libs/libpcre-8.35:3= + net-misc/curl + virtual/blas:0 + || ( >=sys-apps/coreutils-8.15 sys-freebsd/freebsd-bin 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 )" + +DEPEND="${CDEPEND} + virtual/pkgconfig + doc? ( + virtual/latex-base + dev-texlive/texlive-fontsrecommended + )" + +RDEPEND="${CDEPEND} + >=sys-libs/zlib-1.2.5.1-r2:0[minizip] + java? ( >=virtual/jre-1.5 )" + +RESTRICT="minimal? ( test )" + +PATCHES=( + "${FILESDIR}"/${PN}-3.4.1-parallel.patch + "${FILESDIR}"/${PN}-3.4.1-rmath-shared.patch +) + +pkg_pretend() { + [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp +} + +pkg_setup() { + if [[ ${MERGE_TYPE} != binary ]] && use openmp; then + if ! tc-check-openmp; then + ewarn "OpenMP is not available in your current selected compiler" + die "need openmp capable compiler" + fi + FORTRAN_NEED_OPENMP=1 + fi + fortran-2_pkg_setup + filter-ldflags -Wl,-Bdirect -Bdirect + # avoid using existing R installation + unset R_HOME + # Temporary fix for bug #419761 + if [[ ($(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 eaclocal + eautoconf +} + +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)" \ + --docdir="${EPREFIX}/usr/share/doc/${PF}" \ + 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 + docompress -x /usr/share/doc/${PF}/{BioC_mirrors.csv,CRAN_mirrors.csv,KEYWORDS.db,NEWS.rds} +} + +pkg_postinst() { + if use java; then + einfo "Re-initializing java paths for ${P}" + R CMD javareconf + fi +} diff --git a/dev-lang/R/R-3.5.1.ebuild b/dev-lang/R/R-3.5.1.ebuild new file mode 100644 index 000000000000..96c6fe5ac785 --- /dev/null +++ b/dev-lang/R/R-3.5.1.ebuild @@ -0,0 +1,204 @@ +# Copyright 1999-2018 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit bash-completion-r1 autotools eutils flag-o-matic fortran-2 multilib versionator toolchain-funcs + +# latest git commit for R bash completion: https://github.com/deepayan/rcompletion +BCPV=78d6830e28ea90a046da79a9b4f70c39594bb6d6 + +DESCRIPTION="Language and environment for statistical computing and graphics" +HOMEPAGE="http://www.r-project.org/" +SRC_URI=" + mirror://cran/src/base/R-3/${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 ~hppa ~ia64 ~ppc ~ppc64 ~sparc ~x86 ~x86-fbsd ~amd64-linux ~x86-linux ~x64-macos" +IUSE="cairo doc icu java jpeg lapack minimal nls openmp perl png prefix profile readline static-libs tiff tk X" +REQUIRED_USE="png? ( || ( cairo X ) ) jpeg? ( || ( cairo X ) ) tiff? ( || ( cairo X ) )" + +CDEPEND=" + app-arch/bzip2:0= + app-arch/xz-utils:0= + app-text/ghostscript-gpl + >=dev-libs/libpcre-8.35:3= + net-misc/curl + virtual/blas:0 + || ( >=sys-apps/coreutils-8.15 sys-freebsd/freebsd-bin 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 )" + +DEPEND="${CDEPEND} + virtual/pkgconfig + doc? ( + virtual/latex-base + dev-texlive/texlive-fontsrecommended + )" + +RDEPEND="${CDEPEND} + >=sys-libs/zlib-1.2.5.1-r2:0[minizip] + java? ( >=virtual/jre-1.5 )" + +RESTRICT="minimal? ( test )" + +PATCHES=( + "${FILESDIR}"/${PN}-3.4.1-parallel.patch + "${FILESDIR}"/${PN}-3.4.1-rmath-shared.patch +) + +pkg_pretend() { + [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp +} + +pkg_setup() { + if [[ ${MERGE_TYPE} != binary ]] && use openmp; then + if ! tc-check-openmp; then + ewarn "OpenMP is not available in your current selected compiler" + die "need openmp capable compiler" + fi + FORTRAN_NEED_OPENMP=1 + fi + fortran-2_pkg_setup + filter-ldflags -Wl,-Bdirect -Bdirect + # avoid using existing R installation + unset R_HOME + # Temporary fix for bug #419761 + if [[ ($(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)" \ + --docdir="${EPREFIX}/usr/share/doc/${PF}" \ + 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 + docompress -x /usr/share/doc/${PF}/{BioC_mirrors.csv,CRAN_mirrors.csv,KEYWORDS.db,NEWS.rds} +} + +pkg_postinst() { + if use java; then + einfo "Re-initializing java paths for ${P}" + R CMD javareconf + fi +} diff --git a/dev-lang/R/files/R-2.11.1-parallel.patch b/dev-lang/R/files/R-2.11.1-parallel.patch new file mode 100644 index 000000000000..c713d335badd --- /dev/null +++ b/dev-lang/R/files/R-2.11.1-parallel.patch @@ -0,0 +1,17 @@ +Fix ocasional failure with parallel install +Gentoo bug: https://bugs.gentoo.org/show_bug.cgi?id=322965 +R bug: https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=14505 + +Patch by Sebastien Fabbro + +--- src/include/Makefile.in.orig 2010-06-15 18:18:54.000000000 +0000 ++++ src/include/Makefile.in 2010-06-15 18:19:48.000000000 +0000 +@@ -81,7 +81,7 @@ + Rmath.h0: $(srcdir)/Rmath.h0.in $(top_builddir)/config.status + @cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ + +-install: installdirs install-intl-@USE_INCLUDED_LIBINTL@ ++install: $(OBJ_HEADERS) installdirs install-intl-@USE_INCLUDED_LIBINTL@ + @for d in $(SUBDIRS); do \ + (cd $${d} && $(MAKE) $@) || exit 1; \ + done diff --git a/dev-lang/R/files/R-2.13.1-zlib_header_fix.patch b/dev-lang/R/files/R-2.13.1-zlib_header_fix.patch new file mode 100644 index 000000000000..136acb26055f --- /dev/null +++ b/dev-lang/R/files/R-2.13.1-zlib_header_fix.patch @@ -0,0 +1,20 @@ +Update for zlib header changes for zlib > 1.2.5 + +Gentoo bug: https://bugs.gentoo.org/show_bug.cgi?id=383431 +R bug: https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=14951 + +Patch by Michael Schreckenbauer + +--- src/main/unzip.h.orig 2011-09-24 19:35:53.000000000 -0700 ++++ src/main/unzip.h 2011-09-24 19:37:06.000000000 -0700 +@@ -58,6 +58,10 @@ + #define ZLIB_FILEFUNC_SEEK_END (2) + #define ZLIB_FILEFUNC_SEEK_SET (0) + ++#ifndef OF ++#define OF(x) x ++#endif ++ + #define ZLIB_FILEFUNC_MODE_READ (1) + #define ZLIB_FILEFUNC_MODE_WRITE (2) + #define ZLIB_FILEFUNC_MODE_READWRITEFILTER (3) diff --git a/dev-lang/R/files/R-3.0.0-rmath-shared.patch b/dev-lang/R/files/R-3.0.0-rmath-shared.patch new file mode 100644 index 000000000000..f53fb7910511 --- /dev/null +++ b/dev-lang/R/files/R-3.0.0-rmath-shared.patch @@ -0,0 +1,28 @@ +Link with libm to fix unresolved symbols when linked with as-needed +and add a soname to the standalone math library +R bug: https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=14953 + +Patch by Sebastien Fabbro +Adapted to R-3.0.0 by Denis Dupeyron + +--- src/nmath/standalone/Makefile.in.orig 2013-04-04 14:39:15.777544946 -0600 ++++ src/nmath/standalone/Makefile.in 2013-04-04 14:40:51.256153179 -0600 +@@ -64,7 +64,8 @@ + Rexeclibdir_LTLIBRARIES = $(libRmath_la) + libRmath_la_SOURCES = $(SOURCES) + libRmath_la_OBJECTS = $(OBJECTS:.o=.lo) +-libRmath_la_LDFLAGS = ++libRmath_la_LDFLAGS = -Wl,-soname=libRmath.so ++libRmath_la_LIBADD = $(LIBM) + + CLEANFILES = Makedeps *.d *.o *.lo test $(SOURCES) + DISTCLEANFILES = Makefile $(Rexeclibdir_LIBRARIES) $(Rexeclibdir_LTLIBRARIES) +@@ -117,7 +118,7 @@ + + ## under peculiar circumstances, $(LIBM) here helps. + $(libRmath_la): $(libRmath_la_OBJECTS) +- $(DYLIB_LINK) -o $@ $(libRmath_la_LDFLAGS) $(libRmath_la_OBJECTS) $(LIBM) ++ $(DYLIB_LINK) $(libRmath_la_LDFLAGS) $(libRmath_la_OBJECTS) $(libRmath_la_LIBADD) -o $@ + + test: $(srcdir)/test.c + $(CC) -o $@ $(ALL_CPPFLAGS) $(ALL_CFLAGS) $(srcdir)/test.c \ diff --git a/dev-lang/R/files/R-3.3.2-zlib-1.2.10-backport.patch b/dev-lang/R/files/R-3.3.2-zlib-1.2.10-backport.patch new file mode 100644 index 000000000000..2cfb30da90fd --- /dev/null +++ b/dev-lang/R/files/R-3.3.2-zlib-1.2.10-backport.patch @@ -0,0 +1,20 @@ +Index: R.m4 +=================================================================== +--- m4/R.m4 (revision 71152) ++++ m4/R.m4 (revision 71889) +@@ -3105,10 +3105,11 @@ + #include + #include + int main() { +-#ifdef ZLIB_VERSION +-/* Work around Debian bug: it uses 1.2.3.4 even though there was no such +- version on the master site zlib.net */ +- exit(strncmp(ZLIB_VERSION, "1.2.5", 5) < 0); ++#ifdef ZLIB_VERNUM ++ if (ZLIB_VERNUM < 0x1250) { ++ exit(1); ++ } ++ exit(0); + #else + exit(1); + #endif diff --git a/dev-lang/R/files/R-3.4.1-parallel.patch b/dev-lang/R/files/R-3.4.1-parallel.patch new file mode 100644 index 000000000000..6fac15b9ffb7 --- /dev/null +++ b/dev-lang/R/files/R-3.4.1-parallel.patch @@ -0,0 +1,11 @@ +--- a/src/include/Makefile.in 2017-07-05 23:09:09.682703655 +0000 ++++ b/src/include/Makefile.in 2017-07-05 23:06:56.533612308 +0000 +@@ -81,7 +81,7 @@ + Rmath.h0: $(srcdir)/Rmath.h0.in $(top_builddir)/config.status + @cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ + +-install: installdirs install-intl-@USE_INCLUDED_LIBINTL@ ++install: $(OBJ_HEADERS) installdirs install-intl-@USE_INCLUDED_LIBINTL@ + @for d in $(SUBDIRS); do \ + (cd $${d} && $(MAKE) $@) || exit 1; \ + done diff --git a/dev-lang/R/files/R-3.4.1-rmath-shared.patch b/dev-lang/R/files/R-3.4.1-rmath-shared.patch new file mode 100644 index 000000000000..8bc6233de6df --- /dev/null +++ b/dev-lang/R/files/R-3.4.1-rmath-shared.patch @@ -0,0 +1,21 @@ +--- a/src/nmath/standalone/Makefile.in 2017-07-05 23:20:26.098087600 +0000 ++++ b/src/nmath/standalone/Makefile.in 2017-07-05 23:21:55.087480310 +0000 +@@ -64,7 +64,8 @@ + Rexeclibdir_LTLIBRARIES = $(libRmath_la) + libRmath_la_SOURCES = $(SOURCES) + libRmath_la_OBJECTS = $(OBJECTS:.o=.lo) +-libRmath_la_LDFLAGS = ++libRmath_la_LDFLAGS = -Wl,-soname=libRmath.so ++libRmath_la_LIBADD = $(LIBM) + + CLEANFILES = Makedeps *.d *.o *.lo test check.log $(SOURCES) + DISTCLEANFILES = Makefile $(Rexeclibdir_LIBRARIES) $(Rexeclibdir_LTLIBRARIES) +@@ -127,7 +128,7 @@ + + ## under peculiar circumstances, $(LIBM) here helps. + $(libRmath_la): $(libRmath_la_OBJECTS) +- $(DYLIB_LINK) -o $@ $(libRmath_la_LDFLAGS) $(libRmath_la_OBJECTS) $(LIBM) ++ $(DYLIB_LINK) $(libRmath_la_LDFLAGS) $(libRmath_la_OBJECTS) $(libRmath_la_LIBADD) -o $@ + + test: $(srcdir)/test.c + $(CC) -o $@ $(ALL_CPPFLAGS) $(ALL_CFLAGS) $(srcdir)/test.c \ diff --git a/dev-lang/R/metadata.xml b/dev-lang/R/metadata.xml new file mode 100644 index 000000000000..8972d9ed88ca --- /dev/null +++ b/dev-lang/R/metadata.xml @@ -0,0 +1,24 @@ + + + + + sci-mathematics@gentoo.org + Gentoo Mathematics Project + + + R is GNU S, a system for statistical computation and graphics. It + consists of a language plus a run-time environment with graphics, a + debugger, access to certain system functions, and the ability to run + programs stored in script files. + + The core of R is an interpreted computer language which allows + branching and looping as well as modular programming using functions. + The R distribution contains functionality for a large number of + statistical procedures such as: linear and generalized linear + models, nonlinear regression models, time series analysis, classical + parametric and nonparametric tests, clustering, smoothing and + graphical data representations. Additional modules ("add-on + packages") are available for a variety of specific purposes but are + not distributed with this package. + + -- cgit v1.2.3