gentoo auto-resync : 25:03:2023 - 00:48:54

3 files changed, 249 insertions, 0 deletions

diff --git a/dev-lang/Manifest.gz b/dev-lang/Manifest.gz
index 5f1b1a05a8ac..38c2ef978cb0 100644
--- a/dev-lang/Manifest.gz
+++ b/dev-lang/Manifest.gz
diff --git a/dev-lang/R/Manifest b/dev-lang/R/Manifest
index 49d24d4283cc..b5505aa42132 100644
--- a/dev-lang/R/Manifest
+++ b/dev-lang/R/Manifest
@@ -8,7 +8,9 @@ AUX R-4.2.2-isspace-without-readline.patch 733 BLAKE2B 4306378c4ac5a72d19f3f1cbb
 AUX R-4.2.2-parallel-rmath-h-install.patch 1193 BLAKE2B 20435abe07a9afd81f6c313fff093a3a18c5da025d0f398cee93e95589e10f42562367790285d7b0dc77f9f8af8680ed199c44fa23e9bd693f0de5a01a918895 SHA512 e1445995eaadda3a5ad15e7bd2720fff727fe1ce731381678e07e1d18013533d21beab09881f3400bc7e51323cceef9c17ed05b72b6d5f2342b5b28ffc5a5315
 DIST R-4.2.1.tar.gz 37601544 BLAKE2B b898262a05c92e125c36a661a89be34b1698177832002f7aa21ccfcf0b30a06481e2154eea9e77a94b1ad8ca35c7bc4aead2be99b862dca7450acee1bec6a99f SHA512 c1baf46d22304c425dde79301183f80f99f2752300137b0b6f902c3e55e2419d5e9185c97de6e3c840a38f6345a6c334aa24161656d4a7f6fa01570390f1122f
 DIST R-4.2.2.tar.gz 33987014 BLAKE2B 083d07b055308451e32133d378abc4aea7dd6da341554dca96ed5863fe2bc937aa3faa94bbd8d3620d3e6e020f806975cbc375ca28c599bd645267b97b2a49d4 SHA512 abbf1c7d016f8e1a9a0c4ad5dee2509a164449da34729f3e98d99ad8678ab398005fb8ed20288d4a6ed1e46ad4c70ad246f31a1a07aab99ba8fc6a5f02e1a309
+DIST R-4.2.3.tar.gz 34010655 BLAKE2B 688403c693de348bdc404c0ebc2df08d3415db216f6017beca8c0408dc70830239ba26ff89f020a249c8af6471363ed742f52c816da84aac8161ec4a522df405 SHA512 060bb4e1d1f1a5a0383a3b4372ac9247c0a20285020da17cebeb40ddc54da12d5f369ea243ea04d2c6970986fe22b3f9c37fbdfb3405cd8aa4f2353091ea9c5c
 DIST R-78d6830e28ea90a046da79a9b4f70c39594bb6d6.bash_completion 13596 BLAKE2B 53338e4a1c4f68beb69247216e553dbcac47f660fbf032bfebf7a660e32d2cff5b11ed35411c52de7e1fd6e00bbf5b5ea19369a325fa0a38bd93d63dc3288cbd SHA512 9ccd19bb1b0c18a2f13035ccd6809447429e197e298fb4d1df808ef345d723b42f75a1b91c349f6dbb46e4a82e59ef33e11300c495d79b63d670d0c0f2b16a06
 EBUILD R-4.2.1.ebuild 7216 BLAKE2B 2aaa42ab58b3408d544d6902ae4629a473aacf04802474296aad08a4c489cfa3312ca7a4464b3679f6670015356d0a54a1a0d9e55dcaf53638a0c9a3ae89e158 SHA512 7100728db02324e66ca3d2b7c597abdeddedabfde503dd62770dfc1912b9eff0f6dc3ace463fbab5c9141d5fb8ba303ee0dab200cdcdd82df8d9940cad8923be
 EBUILD R-4.2.2.ebuild 7207 BLAKE2B 9f39262165aef3b16147413a0247811d0ade7928cdc782eaa836da3687d11bd6c3ac10d83f31fa84ad456e969f2c7620b54ca7e542cf3a108ac573d2b8dc367f SHA512 bab1ea536c51b2a3e738dbd49d26dc38b978581ced9882e67c88fc1dbbfb6ed8e11b283fbd87c7459ab068db8c8a6982064df7f16985072236e9da9840306901
+EBUILD R-4.2.3.ebuild 7165 BLAKE2B fd3c515df2ec552f7cdfa9479b0be8782e62c9e6ee39a71d8b364267c7442b5d4efcf3466a2ac83eca38fed4d4c4465544ceeeb75fc4bf292118efd39d9f8045 SHA512 d027a793f2e9a89c4d2ff6e67c0346a7257535ad580ff1a15349607fd228f64808d35d629d8547b45ec3f47db48f8d20f5f226c5aa8fce2e3c7e9c7daf5ab527
 MISC metadata.xml 1344 BLAKE2B c47085197e990eecc6d316980dddcd2f6b2a5f5cfeae4a92b2de2ee5733de56f1aaa182f0c4e8b1b62207518123b60150685edb2ee5b734098121f09e6d963f6 SHA512 d959b84becffe57ac8d49aef9d2d7a294a7428972a8e4e438e26f99c09b4515db3723a09f7a75a6c5649c5cff38898fa13d2f894181060a8eaff1ee4a12dd07d
diff --git a/dev-lang/R/R-4.2.3.ebuild b/dev-lang/R/R-4.2.3.ebuild
new file mode 100644
index 000000000000..f07363fe354d
--- /dev/null
+++ b/dev-lang/R/R-4.2.3.ebuild
@@ -0,0 +1,247 @@
+# Copyright 1999-2023 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 ~loong ~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).
+DEPEND="
+	app-arch/bzip2
+	app-arch/xz-utils
+	app-text/ghostscript-gpl
+	dev-libs/libpcre2:=
+	>=dev-libs/tre-0.8.0_p20210321[approx]
+	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? ( media-libs/libjpeg-turbo:= )
+	kernel_linux? ( net-libs/libtirpc )
+	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
+	)"
+RDEPEND="${DEPEND}
+	java? ( >=virtual/jre-1.8:* )"
+BDEPEND="
+	virtual/pkgconfig
+	doc? (
+		virtual/latex-base
+		dev-texlive/texlive-fontsrecommended
+	)
+	test? ( virtual/latex-base )"
+
+PATCHES=(
+	"${FILESDIR}"/R-3.4.1-parallel.patch
+	"${FILESDIR}"/R-3.6.2-no-LDFLAGS-in-libR-pkg-config.patch
+	"${FILESDIR}"/R-3.6.2-no-gzip-doc.patch
+	"${FILESDIR}"/R-4.2.2-browser-pdf-prefs.patch
+	"${FILESDIR}"/R-4.2.2-isspace-without-readline.patch
+	"${FILESDIR}/"R-4.2.2-parallel-rmath-h-install.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 $(grep -Flr ../manual/ doc) || die "sed for HTML links failed"
+
+	use lapack &&
+		export LAPACK_LIBS="$($(tc-getPKG_CONFIG) --libs lapack)"
+
+	use perl &&
+		export PERL5LIB="${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
+
+	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}" \
+		--with-system-tre \
+		$(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 -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}/${f}
+	done
+
+	# Finally, an extra copy of this started showing up at some point...
+	rm "${ED}"/usr/$(get_libdir)/R/COPYING || die
+}
+
+pkg_postinst() {
+	if use java; then
+		einfo "Re-initializing java paths for ${P}"
+		R CMD javareconf
+	fi
+}