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# 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="http://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 minimal nls openmp perl png prefix profile readline static-libs test tiff tk X"
# One test required profiling in v4.0.2, check the upstream bug:
#
# https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17836
#
REQUIRED_USE="png? ( || ( cairo X ) )
jpeg? ( || ( cairo X ) )
tiff? ( || ( cairo X ) )
test? ( profile )
"
# 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-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 [[ ${MERGE_TYPE} != binary ]] && use openmp; then
FORTRAN_NEED_OPENMP=1
fi
fortran-2_pkg_setup
filter-ldflags -Wl,-Bdirect -Bdirect
# avoid using existing R installation
unset R_HOME
# Temporary fix for bug #419761
if [[ ($(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)" \
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
# 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
}
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