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authorV3n3RiX <venerix@redcorelinux.org>2021-07-17 19:04:28 +0100
committerV3n3RiX <venerix@redcorelinux.org>2021-07-17 19:04:28 +0100
commit514d1bbe260df2521fe60f1a3ec87cfcfde1a829 (patch)
tree555c194dbeb0fb2ac4ad3cde7c0f6a80fd330ce2 /dev-lang/R
parent4df3bf9762850b34cd1ead5c80374d1a0fc3362e (diff)
gentoo resync : 17.07.2021
Diffstat (limited to 'dev-lang/R')
-rw-r--r--dev-lang/R/Manifest4
-rw-r--r--dev-lang/R/R-4.1.0-r1.ebuild235
-rw-r--r--dev-lang/R/metadata.xml5
3 files changed, 243 insertions, 1 deletions
diff --git a/dev-lang/R/Manifest b/dev-lang/R/Manifest
index 25e3455107cb..a0f7f4011fec 100644
--- a/dev-lang/R/Manifest
+++ b/dev-lang/R/Manifest
@@ -4,7 +4,9 @@ AUX R-3.6.2-no-LDFLAGS-in-libR-pkg-config.patch 469 BLAKE2B ee716b068316bbac0c07
AUX R-3.6.2-no-gzip-doc.patch 443 BLAKE2B 1154e9f67f08e1d8b286152bd093789a0b94b3a2422bdb54d1d1d03729bd892811e68121309c41ef4323ed31efcea82f3e265b37445e9870bbd88c5413311345 SHA512 99678dbf809761a2991cd5cbe6ff5ba8d1c3e9388f69d94b30726caae4eee29ae50ee74aa24e3851d41559f804381ec18a2cd818b97b5417bf7ae660c93ad2a6
DIST R-4.0.4.tar.gz 33687611 BLAKE2B 40cdfd98fe6c9193deb729d151631c2b0f935accf5ea6251704b633d2688278af1a5a67317152be023fb4a10315c64e473f58276bb0c3fadb1141c35391ad22e SHA512 811c4407a083eb776f92c3cbacb1dc7eada8890a8c27678c6c82bef9db52b1afaefeb408fbe11e46922740adee498f32e7ddf7451b3ab89cf60773737e47f8be
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-78d6830e28ea90a046da79a9b4f70c39594bb6d6.bash_completion 13596 BLAKE2B 53338e4a1c4f68beb69247216e553dbcac47f660fbf032bfebf7a660e32d2cff5b11ed35411c52de7e1fd6e00bbf5b5ea19369a325fa0a38bd93d63dc3288cbd SHA512 9ccd19bb1b0c18a2f13035ccd6809447429e197e298fb4d1df808ef345d723b42f75a1b91c349f6dbb46e4a82e59ef33e11300c495d79b63d670d0c0f2b16a06
EBUILD R-4.0.4.ebuild 7311 BLAKE2B 63fc04096321ca5d5e3c947816ad02bf1b1fee47ea9e4500006ebc356dbf4aa70aca631497988ac33fb5a1e8ab2999a23f6b1d4519206a73993cefb79d2f9884 SHA512 6bcae68392035fcb25cf55e5e0dda41ad746ab5dcd1868477da801d8d7af82b0e3d0b52fa2d82009b43ea892bd9cf2c5b57c62aca4a7ee36a431e6f55b4cdf44
EBUILD R-4.0.5-r1.ebuild 7315 BLAKE2B 0eca2b7badbd113c8acfcc8b76dd5fa505b93f8e7db26c54738b1d7454866567ad7c4e999ed7cb31f512501fbc4de5e2bb81f630a7aea3af200799ae7a99a3d0 SHA512 f1c78cbda7bce8ab0b32f7f01c4050e83c0b9da268b66bb86638fe6e5ccfa67b6409c8debdb6106a29b8fdfc43268ec602f7b865e134b72fb4bb2371ace26762
-MISC metadata.xml 1140 BLAKE2B 774221eb531b4e80f0650b627b9ce53d9a2daf6342b1f19579d2d046e1c83aa497cc764870406b7ea3cf6cbae899cb6d460af92991d62bc6aea8da026a441822 SHA512 297c7e17998f92fb836b0599ce5221aee1ba1e7b1504edb348a602b695faf381d51f32f6118f5ef4bb353f02e92ffc5b3520b8d317d3e30a68a3cce0254fa6b1
+EBUILD R-4.1.0-r1.ebuild 7080 BLAKE2B 312412a327e25891d3b4236f648d4958b0d7ffcada36add367baeced3f325af645cb21c5126190643bfd92eba34d169c14a68e2cdfdc3b9c98de7e7254171e3b SHA512 978cf3808415dbcea5fcbf81a3e9877e236317bb89a821b2f812f0673631fee2e4be63a66c9b26ced3f85ef429ddca4482624e7e8d87b9c9172e87707d7325c8
+MISC metadata.xml 1260 BLAKE2B eb0399a7ff9cb5c8a2f26944065ea176fb379bfd509fe2f6115dc0deb625d0c92a6cf62736572024f9c1342865cbd8a6ed43f8c427939a08ded55dd73f5514df SHA512 71c20b8afc3a72627e89bf032db5c19369738bfe35fc6d3a2550f21bf70be1eec1a697ec13690f48a1f2604cd3973140311af6b745719fd724dea595b964e6ae
diff --git a/dev-lang/R/R-4.1.0-r1.ebuild b/dev-lang/R/R-4.1.0-r1.ebuild
new file mode 100644
index 000000000000..ebf4b5c27c2e
--- /dev/null
+++ b/dev-lang/R/R-4.1.0-r1.ebuild
@@ -0,0 +1,235 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+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 static-libs test tiff tk X"
+
+REQUIRED_USE="png? ( || ( cairo X ) )
+ jpeg? ( || ( cairo X ) )
+ tiff? ( || ( cairo X ) )
+"
+
+# 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/bzip2:0=
+ app-arch/xz-utils:0=
+ app-text/ghostscript-gpl
+ dev-libs/libpcre2:=
+ net-libs/libtirpc
+ net-misc/curl
+ virtual/blas:0
+ || ( sys-apps/coreutils 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-libs/libXt x11-misc/xdg-utils )"
+
+RDEPEND="${DEPEND}
+ sys-libs/zlib:0[minizip]
+ java? ( >=virtual/jre-1.8:* )"
+
+RESTRICT="minimal? ( test )
+ !test? ( test )"
+
+PATCHES=(
+ "${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 [[ ${MERGE_TYPE} != binary ]] && use openmp; then
+ FORTRAN_NEED_OPENMP=1
+ fi
+ fortran-2_pkg_setup
+ filter-ldflags -Wl,-Bdirect -Bdirect
+ # avoid using existing R installation
+ unset R_HOME
+}
+
+src_prepare() {
+ default
+
+ # fix packages.html for doc (gentoo bug #205103)
+ sed -e "s:../../../library:../../../../$(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='\"${EROOT}/usr/$(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)" \
+ rdocdir="${EPREFIX}/usr/share/doc/${PF}" \
+ $(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_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
+
+ # 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.
+ 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.
+ INTERACTIVE_DATA=(
+ BioC_mirrors.csv
+ CRAN_mirrors.csv
+ KEYWORDS.db
+ NEWS.rds
+ )
+
+ NOCOMPRESS_DOCS=( "${INTERACTIVE_DOCS[@]}" "${INTERACTIVE_DATA[@]}" )
+
+ for f in "${NOCOMPRESS_DOCS[@]}"; do
+ docompress -x "/usr/share/doc/${PF}/${f}"
+ done
+}
+
+pkg_postinst() {
+ if use java; then
+ einfo "Re-initializing java paths for ${P}"
+ R CMD javareconf
+ fi
+}
diff --git a/dev-lang/R/metadata.xml b/dev-lang/R/metadata.xml
index 8972d9ed88ca..e9bebc0e016a 100644
--- a/dev-lang/R/metadata.xml
+++ b/dev-lang/R/metadata.xml
@@ -5,6 +5,11 @@
<email>sci-mathematics@gentoo.org</email>
<name>Gentoo Mathematics Project</name>
</maintainer>
+ <use>
+ <flag name="lto">
+ Use link-time optimization for R and its recommended packages.
+ </flag>
+ </use>
<longdescription lang="en">
R is GNU S, a system for statistical computation and graphics. It
consists of a language plus a run-time environment with graphics, a