gentoo resync : 28.04.2019

2 files changed, 207 insertions, 0 deletions

diff --git a/dev-lang/R/Manifest b/dev-lang/R/Manifest
index d5bf39a65475..0597db3fc89d 100644
--- a/dev-lang/R/Manifest
+++ b/dev-lang/R/Manifest
@@ -9,9 +9,11 @@ DIST R-3.2.2.tar.gz 29772864 BLAKE2B f3f7ff9b9bd3cf685712e8997dd5a511a47e56ed261
 DIST R-3.3.2.tar.gz 29440670 BLAKE2B 37308fb0caf19c33196b496d5b6f2f1b5b6f75e3ed985f2f0c4b0633d6191181de7f4cbd1ec986d76089a101d8895493cfe3b8563cfbc36f0b72a1ea14c748c5 SHA512 06a98687c0b180cb0bfd57440ea26088212d9f48948d503136475bf54b42d72cfec5bea7e333c0cedd60733bd614dd0f8c2eced7e24478b6c89f48e8d0c43482
 DIST R-3.4.1.tar.gz 30200109 BLAKE2B 03602e9a48759caee8ce047fa6273df7a54af089de4489e21953c0e3fc7bfdf720d924f1e0167d3dbf65f63ed42ac10dea8b45289b921cda1c0e6d25a0063ebb SHA512 19bd50c87dc001ef947c15c1760f27ac8986ff6b43c6d90d3093ae184e42963027ef06faf31ec57ac9e519af7a35a2f53f8ea23ef75d800ebbd02945cedc4651
 DIST R-3.5.1.tar.gz 29812849 BLAKE2B 9390934e5da5bd223eee717d4e4c5bd7d47291811318b2fdeac59216081cf9e63119f17bc8fee7235e2426852c50eb5948e6a2a3a632047f41b36460e2584967 SHA512 382cc6e200469dd168799948edcf3a0b869d7ef3b3176fdfc60752f3f37e6ba356323c47d8815a4d9ab6ad3a21cd045d26ef5e75107c8685328e0ffcfd172f7f
+DIST R-3.5.3.tar.gz 30205979 BLAKE2B 60dde4c1a7874df0b113630577d943d581d9e0844383a5cb7eda7f62470177d541704a888c33ded216f8b1f088cda493d7716693f5e2451effe3639ce2286dd1 SHA512 077cbd4bc9f19a3a2485afbd4d8e08e0754ddcb9a10164cbc8478f239d5ed0ffaf6796929f154cce1c8aea549c32d460049fc036dc326174d1dbb0a1ddb5f5ef
 DIST R-78d6830e28ea90a046da79a9b4f70c39594bb6d6.bash_completion 13596 BLAKE2B 53338e4a1c4f68beb69247216e553dbcac47f660fbf032bfebf7a660e32d2cff5b11ed35411c52de7e1fd6e00bbf5b5ea19369a325fa0a38bd93d63dc3288cbd SHA512 9ccd19bb1b0c18a2f13035ccd6809447429e197e298fb4d1df808ef345d723b42f75a1b91c349f6dbb46e4a82e59ef33e11300c495d79b63d670d0c0f2b16a06
 EBUILD R-3.2.2.ebuild 6029 BLAKE2B 53a91af83eed96a2c47c61ea3505efdb4f3960206bb6c5c39fbd758578b7b3cebc9d154d6a96c9ea9dfedbe851c0b97ff7066bac74ce598f3821730eb880e6e5 SHA512 45d3213900ba5a817867d1143e5f9d3aa2a418452ff7bd80b5ffdd2c8e056d281b85c0fcc222e3b7c11134ddf097503efee2d1ca5e152f17daa1d41026f69a21
 EBUILD R-3.3.2.ebuild 6097 BLAKE2B 61e6e9f500d6d5f12f8c97c63a183cd0a54c976a4725675cbe3b29f68ca082c8d18e7927132046a94945a692da132c7ab2822039d07abdeefe99c618c1107773 SHA512 0900d19c06a05baa83ab7fb0f802953aa9caab41bd59347e97dd23f6abb4a4f01af5c133db7a5c39a05d8296dc4cef8a8f8b4247c1967b784857ab0979d18ea3
 EBUILD R-3.4.1.ebuild 6305 BLAKE2B 825b0f75bdaa468e635d125f23a19ca694f5fcaf123476811dd4d556ff1126cfea3f0ba0022d6b11d77c2474ef25cbf76442ed33a60fe007798f337a6133194c SHA512 2e6f523d73c6847331f62cd3a1af9b46b67e96c7d610058df0f71c5a0fc49178332a03edc1f499a3c13d1ecf1ab6364e09d2bc8fa94bd8d38700d5489495ca32
 EBUILD R-3.5.1.ebuild 6302 BLAKE2B d2b6b0fa24f3f79c807c99bdcbf7f7898096455df955cd8c08ce8d01b78eac86d32d456c1684e0f7bb087778886c0caaf356d0e9437f22050c7f38dc7002be9e SHA512 41ea0238ff7d823519be6f6be57f4026097be3451a92ee344abcc2fcdd98a99e5bb262f97ef21c5896dd46c2ff672f0ce39c178b68a011341c2f4377850486be
+EBUILD R-3.5.3.ebuild 6310 BLAKE2B efde95796be8d70eccbbb6afc85913bb1dbfacaa0784696e60b20b7444910c803d9b00dfb2c56297a80009c421fbc256d76bcadb5ee34a868d318d20a8c6952a SHA512 3267578587e8ab38d2fe5b902e8ff95c254f618efcb1d77e143fff4af9157bcba607c774f784b87e3233912575ea53be04fd8946ae9faee610d5daae3dd849f0
 MISC metadata.xml 1140 BLAKE2B 774221eb531b4e80f0650b627b9ce53d9a2daf6342b1f19579d2d046e1c83aa497cc764870406b7ea3cf6cbae899cb6d460af92991d62bc6aea8da026a441822 SHA512 297c7e17998f92fb836b0599ce5221aee1ba1e7b1504edb348a602b695faf381d51f32f6118f5ef4bb353f02e92ffc5b3520b8d317d3e30a68a3cce0254fa6b1
diff --git a/dev-lang/R/R-3.5.3.ebuild b/dev-lang/R/R-3.5.3.ebuild
new file mode 100644
index 000000000000..39eee89799d1
--- /dev/null
+++ b/dev-lang/R/R-3.5.3.ebuild
@@ -0,0 +1,205 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit bash-completion-r1 autotools eutils flag-o-matic fortran-2 multilib 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-3/${P}.tar.gz
+	https://raw.githubusercontent.com/deepayan/rcompletion/${BCPV}/bash_completion/R -> ${PN}-${BCPV}.bash_completion"
+
+LICENSE="|| ( GPL-2 GPL-3 ) LGPL-2.1"
+SLOT="0"
+KEYWORDS="~amd64 ~ia64 ~sparc ~x86 ~x86-fbsd ~amd64-linux ~x86-linux ~x64-macos"
+IUSE="cairo doc icu java jpeg lapack minimal nls openmp perl png prefix profile readline static-libs tiff tk X"
+REQUIRED_USE="png? ( || ( cairo X ) ) jpeg? ( || ( cairo X ) ) tiff? ( || ( cairo X ) )"
+
+CDEPEND="
+	app-arch/bzip2:0=
+	app-arch/xz-utils:0=
+	app-text/ghostscript-gpl
+	>=dev-libs/libpcre-8.35:3=
+	net-libs/libtirpc
+	net-misc/curl
+	virtual/blas:0
+	|| ( >=sys-apps/coreutils-8.15 sys-freebsd/freebsd-bin 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 )"
+
+DEPEND="${CDEPEND}
+	virtual/pkgconfig
+	doc? (
+		virtual/latex-base
+		dev-texlive/texlive-fontsrecommended
+	)"
+
+RDEPEND="${CDEPEND}
+	>=sys-libs/zlib-1.2.5.1-r2:0[minizip]
+	java? ( >=virtual/jre-1.5 )"
+
+RESTRICT="minimal? ( test )"
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-3.4.1-parallel.patch
+	"${FILESDIR}"/${PN}-3.4.1-rmath-shared.patch
+)
+
+pkg_pretend() {
+	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
+}
+
+pkg_setup() {
+	if [[ ${MERGE_TYPE} != binary ]] && use openmp; then
+		if ! tc-check-openmp; then
+			ewarn "OpenMP is not available in your current selected compiler"
+			die "need openmp capable compiler"
+		fi
+		FORTRAN_NEED_OPENMP=1
+	fi
+	fortran-2_pkg_setup
+	filter-ldflags -Wl,-Bdirect -Bdirect
+	# avoid using existing R installation
+	unset R_HOME
+	# Temporary fix for bug #419761
+	if [[ ($(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)" \
+		--docdir="${EPREFIX}/usr/share/doc/${PF}" \
+		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
+	docompress -x /usr/share/doc/${PF}/{BioC_mirrors.csv,CRAN_mirrors.csv,KEYWORDS.db,NEWS.rds}
+}
+
+pkg_postinst() {
+	if use java; then
+		einfo "Re-initializing java paths for ${P}"
+		R CMD javareconf
+	fi
+}