gentoo resync : 02.02.2022

2 files changed, 250 insertions, 0 deletions

diff --git a/dev-lang/R/Manifest b/dev-lang/R/Manifest
index 0f1e44f1dff9..c40a1dc016d0 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-4.0.5.tar.gz 32466444 BLAKE2B 5dbbd289f4fd6347b4109eecaf65b50b5793a83edddd2cb391c20473607f136d91a8e9f4ab9e453f6927d2ca9145762920424e3a1dcea89309afde56efd5d32c SHA512 6ff5b0f9cb6b17f66cde1f5585d1b33659dbae8919d34c2e593f68a0bff4d0425aa9704d99284d103702a9cd42f613311f3a87af6b939b1af65dcec80bf2ca8c
 DIST R-4.1.0.tar.gz 33714683 BLAKE2B 22ba966b5a29f153f3ce6cbc467e815c397e7c6aade0db62c7d2ae044056d9227da4dcb8fbf33e661548f4f434c328415e297c6b07b3932ef3f47358c2543f42 SHA512 41519bf06a1ebc2bb582e9a7c35d0e82e213312dec8147861a7f9b28ee750cd40dfbf02737602d05698641fcea6182b0da8131e83edacc358e98eca0a393b729
+DIST R-4.1.2.tar.gz 34009074 BLAKE2B 7ca14b28fc40548180dde979d57f93f41fb3966697d58f686cf63e24e4cbf2de8166240952e708fc94f97846cd57bbd559b4edb688500e1db2a6704de16f508c SHA512 657c7950a88f632f1bbb08dbd0b3fb485732a25d8bbcb8a7939a40b23c7a235fdb9b46c296acaa9f72eabebe96e270ecbdcd7970fc9d3a299e6687bea45f2d3f
 DIST R-78d6830e28ea90a046da79a9b4f70c39594bb6d6.bash_completion 13596 BLAKE2B 53338e4a1c4f68beb69247216e553dbcac47f660fbf032bfebf7a660e32d2cff5b11ed35411c52de7e1fd6e00bbf5b5ea19369a325fa0a38bd93d63dc3288cbd SHA512 9ccd19bb1b0c18a2f13035ccd6809447429e197e298fb4d1df808ef345d723b42f75a1b91c349f6dbb46e4a82e59ef33e11300c495d79b63d670d0c0f2b16a06
 EBUILD R-4.0.5-r1.ebuild 7313 BLAKE2B fd84cc2304d72deaf1f723bffed2906cbd810b913d4c636a37c12f4dab6ffa866ee769636bb700e2447a8a771dbed5cad9df3f289d510d9593f08f9c167f0a3f SHA512 50a086dade0562b6494623eb56f7fb2b98982a8d1b3d9f5ec27c35399ccf2de13c3c5a0ac51dc7d46abaac74d9838869aeeb274a7ac5120bfdc87c3a05354747
 EBUILD R-4.1.0-r2.ebuild 7080 BLAKE2B 312412a327e25891d3b4236f648d4958b0d7ffcada36add367baeced3f325af645cb21c5126190643bfd92eba34d169c14a68e2cdfdc3b9c98de7e7254171e3b SHA512 978cf3808415dbcea5fcbf81a3e9877e236317bb89a821b2f812f0673631fee2e4be63a66c9b26ced3f85ef429ddca4482624e7e8d87b9c9172e87707d7325c8
+EBUILD R-4.1.2.ebuild 7038 BLAKE2B 3e7ac8d5428f980703482a3ce4078aebbc9b983b7a80cb14f724f105473446ad5f235de6460ab2cf7b1c8d6699ddba755b63cad7edc21580aa070714c40e2af3 SHA512 fa144fa713a765892b8c9365aefe34b157f55f7e81aba0930188f9309363c1b6cca373d1e7335909310c4edb9781f2f572a4c552533d1187364ed41fb50d49a1
 MISC metadata.xml 1261 BLAKE2B 468178b60e894bd8dff85ecbf74d10dce61bdb21fc8b61f43d7778dbc345234fc6b5e28c7608534d558c95fa6583b5acd2e55cef7096c4cff88e84776e93e03a SHA512 0d42cb1e3b951e3b1cbf09e6e48d47cf7635c8b16708b5b1edb6c5d1b422cad2f16ce5c6f7c603efb365eb9d5b794d2d2653b408147aa9e921cd57feb3840013
diff --git a/dev-lang/R/R-4.1.2.ebuild b/dev-lang/R/R-4.1.2.ebuild
new file mode 100644
index 000000000000..a29cab314d2a
--- /dev/null
+++ b/dev-lang/R/R-4.1.2.ebuild
@@ -0,0 +1,248 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+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 test tiff tk X"
+
+REQUIRED_USE="
+	png? ( || ( cairo X ) )
+	jpeg? ( || ( cairo X ) )
+	tiff? ( || ( cairo X ) )"
+RESTRICT="
+	minimal? ( test )
+	!test? ( test )"
+
+# 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
+	app-arch/xz-utils
+	app-text/ghostscript-gpl
+	dev-libs/libpcre2:=
+	net-libs/libtirpc
+	net-misc/curl
+	virtual/blas
+	sys-libs/zlib[minizip]
+	|| (
+		sys-apps/coreutils
+		app-misc/realpath
+	)
+	cairo? (
+		x11-libs/cairo:=[X=]
+		x11-libs/pango:=
+	)
+	icu? ( dev-libs/icu:= )
+	jpeg? ( virtual/jpeg )
+	lapack? ( virtual/lapack )
+	perl? ( dev-lang/perl )
+	png? ( media-libs/libpng:= )
+	readline? ( sys-libs/readline:= )
+	tiff? ( media-libs/tiff:= )
+	tk? ( dev-lang/tk:= )
+	X? (
+		x11-libs/libXmu
+		x11-libs/libXt
+		x11-misc/xdg-utils
+	)"
+RDEPEND="${DEPEND}
+	java? ( >=virtual/jre-1.8:* )"
+
+PATCHES=(
+	"${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 [[ ${MERGE_TYPE} != binary ]] && use openmp; then
+		tc-check-openmp
+		FORTRAN_NEED_OPENMP=1
+	fi
+
+	fortran-2_pkg_setup
+
+	# avoid using existing R installation
+	unset R_HOME
+}
+
+src_prepare() {
+	default
+
+	# fix packages.html for doc (gentoo bug #205103)
+	sed -e "s:../../../library:../../../../$(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='\"${EPREFIX}/usr/$(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 (macOS)
+	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 ${EPREFIX}/usr/$(get_libdir)/libRmath.dylib:" \
+				-i src/nmath/standalone/Makefile.in || die
+		else
+			append-ldflags -Wl,-rpath="${EPREFIX}/usr/$(get_libdir)/R/lib"
+		fi
+	fi
+
+	AT_M4DIR=m4 eautoreconf
+}
+
+src_configure() {
+	filter-ldflags -Wl,-Bdirect -Bdirect
+
+	#	--with-system-tre \
+	# tre is patched from upstream
+	econf \
+		--enable-byte-compiled-packages \
+		--enable-R-shlib \
+		--disable-R-framework \
+		--disable-R-static-lib \
+		--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_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) \
+		$(use_with tk tk-config "${ESYSROOT}"/usr/$(get_libdir)/tkConfig.sh) \
+		$(use_with tk tcl-config "${ESYSROOT}"/usr/$(get_libdir)/tclConfig.sh) \
+		$(use_with X x)
+}
+
+src_compile() {
+	export VARTEXFONTS="${T}"/fonts
+	emake AR="$(tc-getAR)"
+	emake -C src/nmath/standalone shared AR="$(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/${PF}/html/manual
+	fi
+
+	newenvd - 99R <<-_EOF_
+		LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}/lib
+		R_HOME=${EPREFIX}/usr/$(get_libdir)/${PN}
+	_EOF_
+
+	newbashcomp "${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 || die
+		for mod in $(find . -name "*.dylib") ; do
+			mod=${mod#./}
+			install_name_tool -id "${EPREFIX}/usr/$(get_libdir)/R/${mod}" \
+				"${mod}"
+		done
+		popd >/dev/null || die
+	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.
+	local 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.
+	local INTERACTIVE_DATA=(
+		BioC_mirrors.csv
+		CRAN_mirrors.csv
+		KEYWORDS.db
+		NEWS.rds
+	)
+
+	local f 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
+}