From a95fb2c43f530843ab8db95718278e2539f77f62 Mon Sep 17 00:00:00 2001 From: Mark Wright Date: Wed, 4 Jul 2018 10:09:32 +1000 Subject: dev-lang/R: Bump to 3.5.1 Thanks to Neil for reporting, Daniel M. Weeks, John Dough and Marcel Schilling for commenting. Closes: https://bugs.gentoo.org/632364 Closes: https://bugs.gentoo.org/660294 Package-Manager: Portage-2.3.41, Repoman-2.3.9 --- dev-lang/R/Manifest | 2 +- dev-lang/R/R-3.5.1.ebuild | 204 ++++++++++++++++++++++++++++++++++++++++++ dev-lang/R/R-3.5.1_rc.ebuild | 207 ------------------------------------------- 3 files changed, 205 insertions(+), 208 deletions(-) create mode 100644 dev-lang/R/R-3.5.1.ebuild delete mode 100644 dev-lang/R/R-3.5.1_rc.ebuild (limited to 'dev-lang') diff --git a/dev-lang/R/Manifest b/dev-lang/R/Manifest index d69ac509af61..dd164dbdc77f 100644 --- a/dev-lang/R/Manifest +++ b/dev-lang/R/Manifest @@ -2,5 +2,5 @@ DIST R-20130129.bash_completion.bz2 4209 BLAKE2B 0afbe9548641cb68a521e4140c48019 DIST R-3.2.2.tar.gz 29772864 BLAKE2B f3f7ff9b9bd3cf685712e8997dd5a511a47e56ed261c1039b0540c29e4dd3131cc3052dad2c9a89af04b7bd595d9be7b9c8310206dd5b82244bb274f5a274603 SHA512 71ba470875262b9f00fb6970f209788df4dad30e0a28373b824b60d8bc6401afb7786e65387663c6490c7ddcd2bfd7f808a270a3e63238f3d7565d5f93607138 DIST R-3.3.2.tar.gz 29440670 BLAKE2B 37308fb0caf19c33196b496d5b6f2f1b5b6f75e3ed985f2f0c4b0633d6191181de7f4cbd1ec986d76089a101d8895493cfe3b8563cfbc36f0b72a1ea14c748c5 SHA512 06a98687c0b180cb0bfd57440ea26088212d9f48948d503136475bf54b42d72cfec5bea7e333c0cedd60733bd614dd0f8c2eced7e24478b6c89f48e8d0c43482 DIST R-3.4.1.tar.gz 30200109 BLAKE2B 03602e9a48759caee8ce047fa6273df7a54af089de4489e21953c0e3fc7bfdf720d924f1e0167d3dbf65f63ed42ac10dea8b45289b921cda1c0e6d25a0063ebb SHA512 19bd50c87dc001ef947c15c1760f27ac8986ff6b43c6d90d3093ae184e42963027ef06faf31ec57ac9e519af7a35a2f53f8ea23ef75d800ebbd02945cedc4651 +DIST R-3.5.1.tar.gz 29812849 BLAKE2B 9390934e5da5bd223eee717d4e4c5bd7d47291811318b2fdeac59216081cf9e63119f17bc8fee7235e2426852c50eb5948e6a2a3a632047f41b36460e2584967 SHA512 382cc6e200469dd168799948edcf3a0b869d7ef3b3176fdfc60752f3f37e6ba356323c47d8815a4d9ab6ad3a21cd045d26ef5e75107c8685328e0ffcfd172f7f DIST R-78d6830e28ea90a046da79a9b4f70c39594bb6d6.bash_completion 13596 BLAKE2B 53338e4a1c4f68beb69247216e553dbcac47f660fbf032bfebf7a660e32d2cff5b11ed35411c52de7e1fd6e00bbf5b5ea19369a325fa0a38bd93d63dc3288cbd SHA512 9ccd19bb1b0c18a2f13035ccd6809447429e197e298fb4d1df808ef345d723b42f75a1b91c349f6dbb46e4a82e59ef33e11300c495d79b63d670d0c0f2b16a06 -DIST R-patched_2018-06-29.tar.gz 29775566 BLAKE2B 905f2cacd01d151f4d35f1dcba5cdc850958f1dae2ecb334932ec652dad5f964ed861c54878dfee2b6c2880d4ea7894e1e71384975d90a2653f9289fa94e6f82 SHA512 2dafcd57e7821f5ccbce44915e312d24f13de35e6c9ece13185c941de1f4c71e52151a44dc0ad801fac90e0955a26d5c6b47d89656c07cddf4959b34a935d0f9 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 ${P}" + R CMD javareconf + fi +} diff --git a/dev-lang/R/R-3.5.1_rc.ebuild b/dev-lang/R/R-3.5.1_rc.ebuild deleted file mode 100644 index c77d3ebacb4b..000000000000 --- a/dev-lang/R/R-3.5.1_rc.ebuild +++ /dev/null @@ -1,207 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit bash-completion-r1 autotools eutils flag-o-matic fortran-2 multilib versionator toolchain-funcs - -# latest git commit for R bash completion: https://github.com/deepayan/rcompletion -BCPV=78d6830e28ea90a046da79a9b4f70c39594bb6d6 - -DESCRIPTION="Language and environment for statistical computing and graphics" -HOMEPAGE="http://www.r-project.org/" -# This release candidate is not on the CRAN mirrors -SRC_URI=" - https://stat.ethz.ch/R/daily/R-patched_2018-06-29.tar.gz - https://raw.githubusercontent.com/deepayan/rcompletion/${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 -) - -S="${WORKDIR}/R-rc" - -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 -} -- cgit v1.2.3-65-gdbad