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sci-mathematics/R: Bump to 3.5.3, thanks Neil for reporting
Add missing dependency net-libs/libtirpc, thanks to Victor Kustov for reporting. Change dependency from x11-libs/cairo[X] to x11-libs/cairo[X=], thanks to Cedric Sodhi for reporting, Felix W for helping. Closes: https://bugs.gentoo.org/674858 Closes: https://bugs.gentoo.org/661878 Closes: https://bugs.gentoo.org/638778 Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Mark Wright <[email protected]>
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,205 @@ | ||
| # Copyright 1999-2019 Gentoo Authors | ||
| # Distributed under the terms of the GNU General Public License v2 | ||
|
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||
| EAPI=7 | ||
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| inherit bash-completion-r1 autotools eutils flag-o-matic fortran-2 multilib toolchain-funcs | ||
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| # latest git commit for R bash completion: https://github.com/deepayan/rcompletion | ||
| BCPV=78d6830e28ea90a046da79a9b4f70c39594bb6d6 | ||
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|
||
| 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" | ||
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|
||
| LICENSE="|| ( GPL-2 GPL-3 ) LGPL-2.1" | ||
| SLOT="0" | ||
| KEYWORDS="~amd64 ~ia64 ~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-libs/libtirpc | ||
| 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 )" | ||
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||
| RESTRICT="minimal? ( test )" | ||
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| 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 | ||
| } | ||
|
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||
| 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) && ($(gcc-version) == 4.7) ]]; then | ||
| append-flags -fno-ipa-cp-clone | ||
| fi | ||
| } | ||
|
|
||
| src_prepare() { | ||
| default | ||
|
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||
| # fix packages.html for doc (gentoo bug #205103) | ||
| sed -e "s:../../../library:../../../../$(get_libdir)/R/library:g" \ | ||
| -i src/library/tools/R/Rd.R || die | ||
|
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||
| # 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" | ||
|
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||
| # fix HTML links to manual (gentoo bug #273957) | ||
| sed -e 's:\.\./manual/:manual/:g' \ | ||
| -i $(grep -Flr ../manual/ doc) || die "sed for HTML links failed" | ||
|
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||
| use lapack && \ | ||
| export LAPACK_LIBS="$($(tc-getPKG_CONFIG) --libs lapack)" | ||
|
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||
| if use X; then | ||
| export R_BROWSER="$(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 | ||
| } | ||
|
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||
| src_install() { | ||
| default | ||
| emake -j1 -C src/nmath/standalone DESTDIR="${D}" install | ||
|
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||
| if use doc; then | ||
| emake DESTDIR="${D}" install-info install-pdf | ||
| dosym ../manual /usr/share/doc/${PF}/html/manual | ||
| fi | ||
|
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||
| cat > 99R <<-EOF | ||
| LDPATH=${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} | ||
| } | ||
|
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||
| pkg_postinst() { | ||
| if use java; then | ||
| einfo "Re-initializing java paths for ${P}" | ||
| R CMD javareconf | ||
| fi | ||
| } |