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From: "Mark Wright" <gienah@gentoo.org>
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Subject: [gentoo-commits] repo/gentoo:master commit in: dev-lang/R/
X-VCS-Repository: repo/gentoo
X-VCS-Files: dev-lang/R/Manifest dev-lang/R/R-3.5.3.ebuild
X-VCS-Directories: dev-lang/R/
X-VCS-Committer: gienah
X-VCS-Committer-Name: Mark Wright
X-VCS-Revision: 408cbc8406b0ca0f91f46052b3a9e1f6bb4f71f9
X-VCS-Branch: master
Date: Sun, 7 Apr 2019 10:00:36 +0000 (UTC)
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commit: 408cbc8406b0ca0f91f46052b3a9e1f6bb4f71f9
Author: Mark Wright <gienah <AT> gentoo <DOT> org>
AuthorDate: Sun Apr 7 09:59:43 2019 +0000
Commit: Mark Wright <gienah <AT> gentoo <DOT> org>
CommitDate: Sun Apr 7 09:59:43 2019 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=408cbc84
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 <gienah <AT> gentoo.org>
dev-lang/R/Manifest | 1 +
dev-lang/R/R-3.5.3.ebuild | 205 ++++++++++++++++++++++++++++++++++++++++++++++
2 files changed, 206 insertions(+)
diff --git a/dev-lang/R/Manifest b/dev-lang/R/Manifest
index dd164dbdc77..ef092e2cf42 100644
--- a/dev-lang/R/Manifest
+++ b/dev-lang/R/Manifest
@@ -3,4 +3,5 @@ DIST R-3.2.2.tar.gz 29772864 BLAKE2B f3f7ff9b9bd3cf685712e8997dd5a511a47e56ed261
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-3.5.3.tar.gz 30205979 BLAKE2B 60dde4c1a7874df0b113630577d943d581d9e0844383a5cb7eda7f62470177d541704a888c33ded216f8b1f088cda493d7716693f5e2451effe3639ce2286dd1 SHA512 077cbd4bc9f19a3a2485afbd4d8e08e0754ddcb9a10164cbc8478f239d5ed0ffaf6796929f154cce1c8aea549c32d460049fc036dc326174d1dbb0a1ddb5f5ef
DIST R-78d6830e28ea90a046da79a9b4f70c39594bb6d6.bash_completion 13596 BLAKE2B 53338e4a1c4f68beb69247216e553dbcac47f660fbf032bfebf7a660e32d2cff5b11ed35411c52de7e1fd6e00bbf5b5ea19369a325fa0a38bd93d63dc3288cbd SHA512 9ccd19bb1b0c18a2f13035ccd6809447429e197e298fb4d1df808ef345d723b42f75a1b91c349f6dbb46e4a82e59ef33e11300c495d79b63d670d0c0f2b16a06
diff --git a/dev-lang/R/R-3.5.3.ebuild b/dev-lang/R/R-3.5.3.ebuild
new file mode 100644
index 00000000000..39eee89799d
--- /dev/null
+++ b/dev-lang/R/R-3.5.3.ebuild
@@ -0,0 +1,205 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit bash-completion-r1 autotools eutils flag-o-matic fortran-2 multilib 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 ~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 )"
+
+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
+}