3 files changed, 254 insertions, 1 deletions
diff --git a/dev-lang/R/Manifest b/dev-lang/R/Manifest
index 6475ffb4295c..ab3d1dffae42 100644
--- a/dev-lang/R/Manifest
+++ b/dev-lang/R/Manifest
@@ -3,7 +3,9 @@ AUX R-4.3.0-no-gzip-doc.patch 354 BLAKE2B 81f20b830ac99494a921b635a0d280dd90045c
 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-78d6830e28ea90a046da79a9b4f70c39594bb6d6.bash_completion 13596 BLAKE2B 53338e4a1c4f68beb69247216e553dbcac47f660fbf032bfebf7a660e32d2cff5b11ed35411c52de7e1fd6e00bbf5b5ea19369a325fa0a38bd93d63dc3288cbd SHA512 9ccd19bb1b0c18a2f13035ccd6809447429e197e298fb4d1df808ef345d723b42f75a1b91c349f6dbb46e4a82e59ef33e11300c495d79b63d670d0c0f2b16a06
 EBUILD R-4.3.1-r1.ebuild 7145 BLAKE2B 2635a3c8c165ad33c68dab1dc5ba648cd59295aec24a7a8f38f17dc173e29455d7a0c3f2e73a7d3a31b8e605bb3fd779569fe9db65166aba39c6b91e16157783 SHA512 d381bfcf37845fb33bef751e54d7bb607d8d08372f39ecc95d1d6b1969c6064756b7cd832641682cdf204cdb28a6da13aa87c212a22875c8d9bae1b479237cd0
 EBUILD R-4.3.2-r1.ebuild 7148 BLAKE2B 00c7280e2b7e256b047dcec28d40712cf2af8513ce13548c43bace14334f83d56c10a97bdd9f36cc04a40ba59b119ea67806f866042fb30db47ddd29dc78a407 SHA512 285c9026732a06ba2a2f768f57c07120c859804a69dc8b023c3d5984061ed059a65c956295eb6d0323973f509e8bc38789f4f99a6f6286ad1727d47fdba6b023
-MISC metadata.xml 1212 BLAKE2B 6a3335018dc1a2a0b67c18bb6164e4a359ad0133bfdb3e7818173bec29d826e177934790d478d63bbcfc58fdbd3a25b9753c986604a52376ebc1fc6997206185 SHA512 68f4c1df03f6b9a00ce82dd7360dd3765a41dca257f0379820a0b631b64c0723536bba92a0247f12fd2efc82986c70b2afeefa4311239a68fd7949ea0af5358f
+EBUILD R-4.4.1.ebuild 7258 BLAKE2B 3e922637eedd58ef9ba9b2121b04a2f54fa9f2002f630e85fa95c0b0ecdfcf4215fce1b16adbf840700fb2ed1849835a19a9a5cb26b69227ff0941301852ffc0 SHA512 9f53670f7ea2218eed5053b4ba5663de0c2bb32df1b071520c6821f77065c3ad3560f9b11dd3e837a30df0118bb02370dfe52d80ff2369fcaf51712fdce3b54f
+MISC metadata.xml 1359 BLAKE2B 9cfca4def686f457622427e067bffba74608366f21125a167aa6efba5013db0c6c3e6d83d5b7012f436a7db44f4578061ce8c8673c8be95b417f52d66787f664 SHA512 1884aad4c68ddf884838c02f5e078966fcd932a7f2b1eac8298d895b4fb632bbc4abf7a849fdd870e0db7136c6642a4c3b1ccd5360e9f3253919b3a0b25a8555
diff --git a/dev-lang/R/R-4.4.1.ebuild b/dev-lang/R/R-4.4.1.ebuild
new file mode 100644
index 000000000000..6282a9ecd337
--- /dev/null
+++ b/dev-lang/R/R-4.4.1.ebuild
@@ -0,0 +1,248 @@
+# 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 ~ia64 ~loong ~sparc ~x86 ~amd64-linux ~x86-linux ~arm64-macos ~x64-macos"
+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 ) )
+	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
+	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:= )
+	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
+	)"
+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 $(grep -Flr ../manual/ doc) || die "sed for HTML links failed"
+
+	use perl &&
+		export PERL5LIB="${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)" \
+		--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) \
+		$(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 libdeflate libdeflate-compression) \
+		$(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/metadata.xml b/dev-lang/R/metadata.xml
index c5ab836c4412..442394218fff 100644
--- a/dev-lang/R/metadata.xml
+++ b/dev-lang/R/metadata.xml
@@ -24,4 +24,7 @@
 	<upstream>
 		<remote-id type="github">wch/r-source</remote-id>
 	</upstream>
+	<use>
+		<flag name="libdeflate">Use <pkg>app-arch/libdeflate</pkg> rather than <pkg>sys-libs/zlib</pkg> for lazy-loaded R objects.</flag>
+	</use>
 </pkgmetadata>