Version bump

Package-Manager: portage-2.2.01.21688-prefix/cvs/Linux x86_64
Manifest-Sign-Key: 0x13CB1360

3 files changed, 216 insertions, 5 deletions

diff --git a/dev-lang/R/ChangeLog b/dev-lang/R/ChangeLog
index a4493e518605..122cec6b2ca1 100644
--- a/dev-lang/R/ChangeLog
+++ b/dev-lang/R/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for dev-lang/R
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/dev-lang/R/ChangeLog,v 1.212 2013/02/19 12:31:48 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/dev-lang/R/ChangeLog,v 1.213 2013/03/04 22:56:38 bicatali Exp $
+
+*R-2.15.3 (04 Mar 2013)
+
+  04 Mar 2013; Sébastien Fabbro <bicatali@gentoo.org> +R-2.15.3.ebuild:
+  Version bump
 
   19 Feb 2013; Justin Lecher <jlec@gentoo.org> R-2.10.1.ebuild,
   R-2.15.2.ebuild, metadata.xml:
diff --git a/dev-lang/R/Manifest b/dev-lang/R/Manifest
index 3933e51850cc..bea3ebc4b508 100644
--- a/dev-lang/R/Manifest
+++ b/dev-lang/R/Manifest
@@ -11,18 +11,20 @@ AUX R-2.15.2-cairo.patch 1141 SHA256 da114707c8319a3e553e38bce17bf3e172dda8a4f47
 DIST R-2.10.1.tar.gz 19705604 SHA256 5ca1780d9f47f2f4a9b52ba44fed9ee6e7d3547f18ed2c05192b0dbc56038e9d SHA512 aeedc0190c90b09fc2969f680ec0b8b8174ca224288d0d0c5536e19c63e28d92604ec2936015298b839cdbce349e5d4e9f759ef30d31fc3dccd2a67448e3b7d4 WHIRLPOOL 2252ad97059b6e7fbe4473280f681af1b57ff1a3c1c3151c499f71cc6b7f4d4fce0c5312389e79e61272f7b635cf31dcd1dd320525e627c08b97367c17ec3d58
 DIST R-2.15.2.tar.bz2 22374116 SHA256 57f929f0e3925d1ae9ae32010fb9a7cb02eed47ee998c0fdc8284cb8f167ffbc SHA512 2506654259fa72599c150ea6e43f5d57f57a5d2ed2771067a96bb2a232df9aa05213f327001c78a82beec88048cc102263b41e897392181d044db675818bfbff WHIRLPOOL 07e86aaac4362088bdf869a9bc25dadb3aaa3cab39b0ebc45d67c2deda0bbd46280cf70525e51ae2f433fa558a4098e5feff4fc34ca298f79f40dd9d4eb79674
 DIST R-2.15.2.tar.gz 24338934 SHA256 292837ae259b7668509b8a5d4ec8be0aa50c327cfe7a534bac419b4ca766d66d SHA512 86b07630cf9b69e9889a753297fd672a8fe89000c8b084908d6f1c90118cdb8b478681db37deefd5a5ddb3128169f60671201550bcd34689658b1f189398adac WHIRLPOOL 88fe31ce28115b0ca6961ad372c054618b199836131ca067f06139a0f6e4f23ff849f52d8653828e4245156d5377f4fbd08b866de44ea33b18b39c5694d08694
+DIST R-2.15.3.tar.gz 25409925 SHA256 c583a38f8dad3bc012c08116f4ba1eb2182cadfad4b0f8d7bd3cdba24bc255d6 SHA512 83389e792aecb52fcd129321c896558dd3bfaf0f6ac775b662d67bbea8a4ec86f22fab625cc20587a17f991ea39764a89fbea34c9f638e3134a095a4e3b2fa12 WHIRLPOOL 3c240f24c82db09fe2c9b4b33cb9ddbc57688940d6f6e3b76f67e0a440910f1aef23617f25219fd62ba83f730a4a8bae3ff32b9c27faad08fd8b95fce847ed6d
 DIST R-20120306.bash_completion.bz2 4325 SHA256 63003bcad2c35edc5e3329b72f85aaa0b8843b9ec424dc015b50212976372c3f SHA512 1bf874c58efb648aa96ac22b7c6c66444cb8f72b33cefa9eb28461043659476548873ec6dbd5a15bf893d6f87a7a7d18e4deb045759a1e74774d03cbb8f1f082 WHIRLPOOL 231742e9a886174b3f6bd62102d5b7cea1b050e786420f4e0cd4d9cec31ccb93fcc5a3115364776fbd00020d4e26398400e80cec126a41c5bd70677fd675c966
 DIST R-20130129.bash_completion.bz2 4209 SHA256 487e969b94563fec98ec58de7e6142e9361d4219088add0fca282b482a9e01b1 SHA512 910b26e16cfebe677f438abfa5f2652e582db143d91dbf0e7d4b1ea33462c7e5c89c3a3619c63ae98bba26b11a5adb16eda9d344f8cdbe4f0feabc546993c1a5 WHIRLPOOL 2368efaed37fcb6e010f6a234864631f68549bd8e3f733561170cc5b28f5557e546d8561246fb265a481a47991a262fec3acf6abc1dc3929a9357405e0d3c6fc
 DIST R.bash_completion.bz2 4019 SHA256 424790f7be27a0aad7b65289c97cb15d2ca9ee272f30f3e5c906217e487c7f85 SHA512 b11efb99a5dae1f434d2f8c70154a09dd3826126a034a102f905144650c3d77851ddeb206c247dd9365baca13cf95897708a62bd6f8bddc079e3b679a8470fe2 WHIRLPOOL eb8fb8bff43873b75b61bf92af817be7d2bc4eddb2bf51c13e51dc1bdcc0cb5b0bd3623cf73fe20867c8b734732c6c89523916bc8ed4fba2931e55c5a0f837b8
 EBUILD R-2.10.1.ebuild 4523 SHA256 31da6c5e6be39285b463247c44d46490c8b55314c90c6e5e8f259edb8d861f86 SHA512 c9664aecee491c43d9ad87259527b3835b70c1158eae3c374c8a4312fb96e0940edbf93c7ebc39c5a5d2b801075f6bf38f3e01b04f84adc496153efbb987f924 WHIRLPOOL 158c48b0fa24e2b1faa3adc75708cabaf7527f87f85c579c7de4e0450c973e64a38e5263b4232e0f92c391b9c763ef158a31183ba4afd8f5d96cc6ef9895e5e6
 EBUILD R-2.15.2-r2.ebuild 6365 SHA256 dcb5e88a9cc516b037f5aa777bc3ed2ca616aa403e425f95c82384b3e5c40a2e SHA512 df60fc90c40fd12ec17c274a186b3d6ccc5de30ff754bbb4ce7854271f8328a9bb46696aa63d393a1c26228379d8d8ab6ca080bd6a20cf02ccf91ccbcef9ac29 WHIRLPOOL 8334374beb16bcaac6910a8b4641b7e5fb81f9fce486ea6befc44be2aa88e55370b1333d1a13c1b65281ff2707cc0eddb07c8e024b1b46a231e5c7e15c3177a9
 EBUILD R-2.15.2.ebuild 6059 SHA256 5eed7c93ed61fcb7091a0584f60b9c9035bac1054c85e64fd779945c059476c9 SHA512 51da1c385a0cbb297c660a8250a9f2ae2d75d3ae51eed744e9d74918a7abe66f637c42249a1a510169174c347f233545422ce355afedc6a0da36c469abd2081d WHIRLPOOL 7295660140624e5d11252fa2bc955b74ce6517bd7d191f3c3018180f0f923c5f672d72c201624fde87086e03e8c4de2d40afec22bb7dc39cef60c62a1ba2ed31
-MISC ChangeLog 32329 SHA256 d378161dbd5c2fee2d5a5c5d7a223d3c9d78dede8934b2765499b4cdc76416f0 SHA512 cbaf2aead888a6fe33cfafbaa7f68f9d28f708bed5270cbf567ab626100368bbd0b047ac22c879b9e76840eb92f2788e88eb7d0204eb0786b97c84e7fa328755 WHIRLPOOL c27974b3a06a477aabfa610a72da40831eaca94139d661ddad939553bfddcc6bf48237200b0082ebc71db17f93cfe49b567fcaec0e0084673217efe7d1bbda01
+EBUILD R-2.15.3.ebuild 6210 SHA256 0188f05a869d13859dd35ef66892a66269702bde713f4b2d23ab5f8aef7a52df SHA512 bef2fc64c0256e7ba8e80f3aaec740784c03556facfaf611689869e22d277c44dab17a639232611e66560a4b16796a7ad2e460733e43d65ddcfb7e9a16fb9612 WHIRLPOOL 1034190fb5f530499680ad8611be28a8a154041d1d826e78e4d785e2415eb2cadfbd292b622bdf3949a4b758b856bb37fa52b6dee4dbdfda64cdfbdb1ab2700a
+MISC ChangeLog 32447 SHA256 afd74f2fed04b78886ddc88f6a34a745d9ba1b817805864d3d04bffd9cf2228e SHA512 85abe6a0a3b056b272ce3c58a924f3de3be01a874514bec9db0e65786a2378037ef5625a76bca1d6f53e0c089b24e575d068c6191a94b2abfdacdb5ab16cf3f2 WHIRLPOOL 8700baf9750c22620491c832925e128e2a946c172cf5920715c5598706fdfbcafd79bb5bcf73b63ae7f59e2c88a8c34edc386f47edd366d66afed92e6742a3a4
 MISC metadata.xml 1136 SHA256 7d7c013a77ad6ffc785202e05711d4127a77f64fe09ef919deffa80cc74f992a SHA512 761c3afcbfc76c6026cc6a6f89dae2502f495008851dcb070ee04990653ed6785f089d31a0ea3ada11ccf3d027d372256d04a0baf9ee5d2528e63a9ea4dee313 WHIRLPOOL b7bd0d3843543ff07d15e2d18ae56358477667cec9e78be266f2d983304537afd6c1bac0842e403ce62729248debe2fddfe345c66e022bf2716a47d7819fe041
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diff --git a/dev-lang/R/R-2.15.3.ebuild b/dev-lang/R/R-2.15.3.ebuild
new file mode 100644
index 000000000000..2e6cd4ed26f5
--- /dev/null
+++ b/dev-lang/R/R-2.15.3.ebuild
@@ -0,0 +1,204 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/dev-lang/R/R-2.15.3.ebuild,v 1.1 2013/03/04 22:56:38 bicatali Exp $
+
+EAPI=5
+
+inherit bash-completion-r1 autotools eutils flag-o-matic fortran-2 multilib versionator toolchain-funcs
+
+BCP=${PN}-20130129.bash_completion
+DESCRIPTION="Language and environment for statistical computing and graphics"
+HOMEPAGE="http://www.r-project.org/"
+SRC_URI="mirror://cran/src/base/R-2/${P}.tar.gz
+	bash-completion? ( http://dev.gentoo.org/~bicatali/distfiles/${BCP}.bz2 )"
+
+LICENSE="|| ( GPL-2 GPL-3 ) LGPL-2.1"
+SLOT="0"
+KEYWORDS="~alpha ~amd64 ~hppa ~ia64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-fbsd ~x86-linux ~x64-macos"
+IUSE="bash-completion cairo doc icu java jpeg lapack minimal nls openmp perl png prefix profile readline static-libs tiff tk X"
+REQUIRED_USE="png? ( || ( cairo X ) ) jpeg? ( || ( cairo X ) ) tiff? ( || ( cairo X ) )"
+
+CDEPEND="
+	app-arch/bzip2
+	app-text/ghostscript-gpl
+	dev-libs/libpcre
+	virtual/blas
+	cairo? ( x11-libs/cairo[X] x11-libs/pango )
+	icu? ( dev-libs/icu )
+	jpeg? ( virtual/jpeg )
+	lapack? ( virtual/lapack )
+	perl? ( dev-lang/perl )
+	png? ( media-libs/libpng )
+	readline? ( sys-libs/readline )
+	tk? ( dev-lang/tk )
+	X? ( x11-libs/libXmu x11-misc/xdg-utils )"
+
+DEPEND="${CDEPEND}
+	virtual/pkgconfig
+	doc? (
+			virtual/latex-base
+			dev-texlive/texlive-fontsrecommended
+		 )"
+
+RDEPEND="${CDEPEND}
+	( || ( <sys-libs/zlib-1.2.5.1-r1 >=sys-libs/zlib-1.2.5.1-r2[minizip] ) )
+	app-arch/xz-utils
+	java? ( >=virtual/jre-1.5 )"
+
+RESTRICT="minimal? ( test )"
+
+R_DIR="${EROOT%/}/usr/$(get_libdir)/${PN}"
+
+pkg_setup() {
+	if use openmp; then
+		FORTRAN_NEED_OPENMP=1
+		tc-has-openmp || die "Please enable openmp support in your compiler"
+	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() {
+	# gentoo bug #322965 (not applied upstream)
+	# https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=14505
+	epatch "${FILESDIR}"/${PN}-2.11.1-parallel.patch
+
+	# respect ldflags (not applied upstream)
+	# https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=14506
+	epatch "${FILESDIR}"/${PN}-2.12.1-ldflags.patch
+
+	# gentoo bug #383431
+	# https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=14951
+	epatch "${FILESDIR}"/${PN}-2.13.1-zlib_header_fix.patch
+
+	# https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=14953
+	epatch "${FILESDIR}"/${PN}-2.14.1-rmath-shared.patch
+
+	# fix packages.html for doc (gentoo bug #205103)
+	sed -i \
+		-e "s:../../../library:../../../../$(get_libdir)/R/library:g" \
+		src/library/tools/R/Rd.R || die
+
+	# fix Rscript path when installed (gentoo bug #221061)
+	sed -i \
+		-e "s:-DR_HOME='\"\$(rhome)\"':-DR_HOME='\"${R_DIR}\"':" \
+		src/unix/Makefile.in || die "sed unix Makefile failed"
+
+	# fix HTML links to manual (gentoo bug #273957)
+	sed -i \
+		-e 's:\.\./manual/:manual/:g' \
+		$(grep -Flr ../manual/ doc) || die "sed for HTML links failed"
+
+	use lapack && \
+		export LAPACK_LIBS="$($(tc-getPKG_CONFIG) --libs lapack)"
+
+	if use X; then
+		export R_BROWSER="$(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 -i \
+				-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/" \
+				configure.ac || die
+			# sort of "undo" 2.14.1-rmath-shared.patch
+			sed -i \
+				-e "s:-Wl,-soname=libRmath.so:-install_name ${EROOT%/}/usr/$(get_libdir)/libRmath.dylib:" \
+				src/nmath/standalone/Makefile.in || die
+		else
+			append-ldflags -Wl,-rpath="${EROOT%/}/usr/$(get_libdir)/R/lib"
+		fi
+	fi
+	AT_M4DIR=m4 eaclocal
+	eautoconf
+}
+
+src_configure() {
+	econf \
+		--enable-byte-compiled-packages \
+		--enable-R-shlib \
+		--disable-R-framework \
+		--with-system-zlib \
+		--with-system-bzlib \
+		--with-system-pcre \
+		--with-system-xz \
+		--with-blas="$($(tc-getPKG_CONFIG) --libs blas)" \
+		--docdir="${EPREFIX}/usr/share/doc/${PF}" \
+		rdocdir="${EPREFIX}/usr/share/doc/${PF}" \
+		$(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) \
+		$(use_with X x)
+}
+
+src_compile() {
+	export VARTEXFONTS="${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 -C src/nmath/standalone DESTDIR="${D}" install
+
+	if use doc; then
+		emake DESTDIR="${D}" install-info install-pdf
+		dosym ../manual /usr/share/doc/${PF}/html/manual
+	fi
+
+	cat > 99R <<-EOF
+		LDPATH=${R_DIR}/lib
+		R_HOME=${R_DIR}
+	EOF
+	doenvd 99R
+	use bash-completion && newbashcomp "${WORKDIR}"/${BCP} ${PN}
+	# The buildsystem has a different understanding of install_names than what
+	# 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/lib/R > /dev/null
+		for mod in $(find . -name "*.dylib") ; do
+			mod=${mod#./}
+			install_name_tool -id "${EPREFIX}/usr/lib/R/${mod}" \
+				"${mod}"
+		done
+		popd > /dev/null
+	fi
+}
+
+pkg_postinst() {
+	if use java; then
+		einfo "Re-initializing java paths for ${P}"
+		R CMD javareconf
+	fi
+}