gentoo auto-resync : 11:03:2025 - 01:49:36HEADmaster

3 files changed, 16 insertions, 259 deletions

diff --git a/dev-lang/R/Manifest b/dev-lang/R/Manifest
index 171d3a4796d8..9f671c5a87d9 100644
--- a/dev-lang/R/Manifest
+++ b/dev-lang/R/Manifest
@@ -1,13 +1,11 @@
 AUX R-4.3.0-no-LDFLAGS-in-libR-pkg-config.patch 380 BLAKE2B db9fcf9d0c73aa5352110bc27f5881db4f793c963e8f9d46b8681101eb7e062f5f1bf50fd06c53aa392994cd455f6d8cffc680f81a06487694c860297e5e06b6 SHA512 380c6489520c60016cef730822ff973a63460b40726b6c84a9c4ba69d75f93bc8eeb6c45dbb64bcb3277fe2ffd8b1d1fcc40ae668d77269acb4fbc5babdb686e
 AUX R-4.3.0-no-gzip-doc.patch 354 BLAKE2B 81f20b830ac99494a921b635a0d280dd90045c7dd3d1ed02f1fbf46a717ec3b13e7c730c9d4c87dd8d55d5f366db1a60671718511852d134f8dc91fddfbb8505 SHA512 f3f7bd438eac7637b969206c5134f0638ca79c862a6d432545b126422903248e5badde5ff893b4f44e14104734419372c2414380034d17748001f0dfadb5c7b0
 AUX R-4.3.0-parallel.patch 415 BLAKE2B e996c72c167b529765c82c8880bc3ea704d3c6e34b7fe09dff4fa93a8e42f8551dc723f44e0ab0638de84ce0f7fa60d4476e297d06eb3d6070d8daf5f79b9dba SHA512 6d36a2eb5df1ec8fa4230bfbc693cf53c95b41bb9269cfa473cfaa6dc8a42681e81a006f03278b86e8636e904bba188f2475d27d06599fdab86de8743401f5be
-DIST R-4.3.1.tar.gz 34899964 BLAKE2B 7aaacad01ce59e2faa46c4b830c10d2df8e4a3a1d4f11cf2aa622ceb53876f1e702dff94a820ca954ec29f53d58fa7e135ef15e8257602c50f2642b0a0c0a86a SHA512 f571c378dbdd675e267ef4419bb1141198924dadc08297c93c8dff58504994604918b3e045bb7139ba473972a063a68ed1c7426f37d4e8208b79358561d34d77
-DIST R-4.3.2.tar.gz 35039225 BLAKE2B 2de3af9013c8648c118a1efe673b618aef84a694c6865657faef5b0ca5f780ef5273bb00b607f587219ee30a11f01ccc3b730b9124847242b9d9550de471f58c SHA512 125114357f20d4a3248aee86727768d1dc15e07e44353f8a68fe2ef1fedae508e85d944301d00c0edd61e8b012b0b3cdcde53ac60be903713f96542d83ad5b1d
 DIST R-4.4.1.tar.gz 37353459 BLAKE2B 2c44fcab719cc2a2cef4566fd4e6c22386f02827a41045ffa074ca2a6883089275354644bce47c9978ef5c96e7b9b21576e946500746c27dc00946ef3cde4fce SHA512 cc30172227b7d89a9d6e9d65c8622b2042bcbbf3f1b5e36c7460f60958a1a0589980a1867ec9989df2589c1618233f3382d4732700b147361ace3be6680b5643
 DIST R-4.4.2.tar.gz 37582785 BLAKE2B bda7e3d49c63095830d12d77bb91946c2e7b657895f3388b892ca29091dc6c23b42a6b7822910d6889f69715c3ad58f8031ab7a811f34efe0b352232e5135175 SHA512 b29d82242f70487f52849a5726610c03dffa4e54f1a32a9f3f76784fcf61f91d5c40cddee1029eeb9c9837ff26f382f348e8518dd68c84e9fc2192b981013d9a
+DIST R-4.4.3.tar.gz 40234425 BLAKE2B 2a7efdf1841c7bae66a0e8aef07b9e79dec9d2f1b4c32f12640eaf84f99b05ca2846eaf10a5d03e0a7fb6d0a4f00ab16cd84a618ebef7bec29c31bc04458f0db SHA512 2a1d1e5ee2e18c928e2b3e58df372083b4bbd0822863a8441404999209035436e236c8ffe3970827fbf3d765157365800ebb0bb46f361c6abe473ddec30be06f
 DIST R-78d6830e28ea90a046da79a9b4f70c39594bb6d6.bash_completion 13596 BLAKE2B 53338e4a1c4f68beb69247216e553dbcac47f660fbf032bfebf7a660e32d2cff5b11ed35411c52de7e1fd6e00bbf5b5ea19369a325fa0a38bd93d63dc3288cbd SHA512 9ccd19bb1b0c18a2f13035ccd6809447429e197e298fb4d1df808ef345d723b42f75a1b91c349f6dbb46e4a82e59ef33e11300c495d79b63d670d0c0f2b16a06
-EBUILD R-4.3.1-r1.ebuild 7139 BLAKE2B 6ad669bf41cbef1e56cd10728fa2390043cd7ddde0c095f917f0779b625fbe92c4176a17e60cd0fcd23e0106a28bdf739a311c01768a4ba12a70fc238153af6d SHA512 96c50da1fbebfcf22a3cf9a558cba9df0e655f1456986a806dfd6d2362560a1cde8d922dca02cdcdd67279fe1e4191d74892b6dc1a9194399632642d3ec9adf1
-EBUILD R-4.3.2-r1.ebuild 7142 BLAKE2B 076b384f913f4f3c3dc311b1fb18c21e1bb34bf22c0b9ee3cd178f45737b37efcfa962e0f08caa844f2c84fe742a5a0bb0a1918d50ae8887b37bdac81f249718 SHA512 7aa832f3be64244db12e6ad2a875491b07c9b476f7cf549ca3c77a4597113cbef9b3daac76b29f1c4d15ee15170664bdf29e6a814fe9f3e4cbe6cfe41f820859
 EBUILD R-4.4.1.ebuild 7249 BLAKE2B bac9534523954fcb65e21dbda6e5e76d4824a55ff169de79bcdbfbe8c23f186a90e7773a92b08260c48083a736f5ebbc7621a76abb1bcd2ef17f3c23fa08bb84 SHA512 0bbb5f9113ff876f79ce0bb88d821bae3812442b087bc00b6fff5c90b6422d198e44ed6e437467a2558af8645f6ac12e347afefd3f9385c29032e876ca412db0
 EBUILD R-4.4.2.ebuild 7321 BLAKE2B ab811639add4d10d3344ee972eca5eedeb7c17920cdf150018c20c8d137ced6957db9187062c8059bde3597110c4889c823a00591232f000ea3f3571dfb1b2ba SHA512 39a75a9893f5771c85fe064fa112924a1859b2d43736983be6159f81c2bf5874d4c12a8789a15405f8eaa808ce2cf8f05b79929e039ca10b3e5fadeda8287fc2
+EBUILD R-4.4.3.ebuild 7321 BLAKE2B 80af26b37391baca4d718c36b62fda41f6fb36451e176cee0ed870157c9c4835c647c46f4d7e309dd52d935e045653989acfefbb1e05ceb710137586eb306b39 SHA512 c3d20847f5702da99f7aaccd1b524bd8fcb682d6ee91c0b4c6a0bbd071adc5fadafda0fe2564945cfed5a97693490069543b82eb40dab7db6e04854bf4b820fe
 MISC metadata.xml 1359 BLAKE2B 9cfca4def686f457622427e067bffba74608366f21125a167aa6efba5013db0c6c3e6d83d5b7012f436a7db44f4578061ce8c8673c8be95b417f52d66787f664 SHA512 1884aad4c68ddf884838c02f5e078966fcd932a7f2b1eac8298d895b4fb632bbc4abf7a849fdd870e0db7136c6642a4c3b1ccd5360e9f3253919b3a0b25a8555
diff --git a/dev-lang/R/R-4.3.1-r1.ebuild b/dev-lang/R/R-4.3.1-r1.ebuild
deleted file mode 100644
index 4a5751c35f33..000000000000
--- a/dev-lang/R/R-4.3.1-r1.ebuild
+++ /dev/null
@@ -1,246 +0,0 @@
-# Copyright 1999-2024 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="
-	https://cran.r-project.org/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 ~loong sparc ~x86 ~amd64-linux ~x86-linux ~arm64-macos ~x64-macos"
-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
-	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="${DEPEND}
-	java? ( >=virtual/jre-1.8:* )"
-BDEPEND="
-	sys-apps/which
-	virtual/pkgconfig
-	doc? (
-		virtual/latex-base
-		dev-texlive/texlive-fontsrecommended
-	)
-	test? ( virtual/latex-base )"
-
-PATCHES=(
-	"${FILESDIR}"/R-4.3.0-parallel.patch
-	"${FILESDIR}"/R-4.3.0-no-LDFLAGS-in-libR-pkg-config.patch
-	"${FILESDIR}"/R-4.3.0-no-gzip-doc.patch
-)
-
-# false positive, the linking step fails (as it should)
-QA_CONFIG_IMPL_DECL_SKIP=( iconvlist )
-
-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 \
-		--without-aqua \
-		$(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
-}
diff --git a/dev-lang/R/R-4.3.2-r1.ebuild b/dev-lang/R/R-4.4.3.ebuild
index 24fefe89c155..8be7dc789db0 100644
--- a/dev-lang/R/R-4.3.2-r1.ebuild
+++ b/dev-lang/R/R-4.4.3.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2024 Gentoo Authors
+# Copyright 1999-2025 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
@@ -18,7 +18,7 @@ SRC_URI="
 LICENSE="|| ( GPL-2 GPL-3 ) LGPL-2.1"
 SLOT="0"
 KEYWORDS="~amd64 ~arm64 ~hppa ~loong ~sparc ~x86 ~amd64-linux ~x86-linux ~arm64-macos ~x64-macos"
-IUSE="cairo doc icu java jpeg lapack lto minimal nls openmp perl png prefix profile readline test tiff tk X"
+IUSE="cairo doc icu java jpeg +libdeflate lto minimal nls openmp perl png prefix profile readline test tiff tk X"
 
 REQUIRED_USE="
 	png? ( || ( cairo X ) )
@@ -37,23 +37,26 @@ DEPEND="
 	dev-libs/libpcre2:=
 	>=dev-libs/tre-0.8.0_p20210321[approx]
 	net-misc/curl
-	virtual/blas
 	sys-libs/zlib[minizip]
 	sys-apps/coreutils
+	sys-libs/timezone-data
+	virtual/blas
+	virtual/lapack
 	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 )
+	kernel_linux? ( net-libs/libtirpc:= )
+	libdeflate? ( app-arch/libdeflate )
 	perl? ( dev-lang/perl )
 	png? ( media-libs/libpng:= )
 	readline? ( sys-libs/readline:= )
 	tiff? ( media-libs/tiff:= )
 	tk? ( dev-lang/tk:= )
 	X? (
+		x11-libs/libX11
 		x11-libs/libXmu
 		x11-libs/libXt
 	)"
@@ -108,9 +111,6 @@ src_prepare() {
 	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}"
 
@@ -137,6 +137,9 @@ src_prepare() {
 }
 
 src_configure() {
+	# bug #944066 (try reomving after 4.4.2)
+	append-cflags -std=gnu17
+
 	filter-ldflags -Wl,-Bdirect -Bdirect
 
 	econf \
@@ -145,9 +148,11 @@ src_configure() {
 		--disable-R-framework \
 		--disable-R-static-lib \
 		--with-blas="$($(tc-getPKG_CONFIG) --libs blas)" \
+		--with-lapack="$($(tc-getPKG_CONFIG) --libs lapack)" \
 		rdocdir="${EPREFIX}/usr/share/doc/${PF}" \
 		--with-system-tre \
 		--without-aqua \
+		--without-newAccelerate \
 		$(use_enable java) \
 		$(use_enable lto lto R) \
 		$(use_enable nls) \
@@ -157,7 +162,7 @@ src_configure() {
 		$(use_with cairo) \
 		$(use_with icu ICU) \
 		$(use_with jpeg jpeglib) \
-		$(use_with lapack) \
+		$(use_with libdeflate libdeflate-compression) \
 		$(use_with !minimal recommended-packages) \
 		$(use_with png libpng) \
 		$(use_with readline) \