Version bump.

Package-Manager: portage-2.1.11.59/cvs/Linux x86_64

4 files changed, 240 insertions, 12 deletions

diff --git a/dev-lang/R/ChangeLog b/dev-lang/R/ChangeLog
index 122cec6b2ca1..16000479f55a 100644
--- a/dev-lang/R/ChangeLog
+++ b/dev-lang/R/ChangeLog
@@ -1,6 +1,12 @@
 # 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 1.213 2013/03/04 22:56:38 bicatali Exp $
+# $Header: /var/cvsroot/gentoo-x86/dev-lang/R/ChangeLog,v 1.214 2013/04/04 22:10:01 calchan Exp $
+
+*R-3.0.0 (04 Apr 2013)
+
+  04 Apr 2013; Denis Dupeyron <calchan@gentoo.org> +R-3.0.0.ebuild,
+  +files/R-3.0.0-rmath-shared.patch:
+  Version bump.
 
 *R-2.15.3 (04 Mar 2013)
 
diff --git a/dev-lang/R/Manifest b/dev-lang/R/Manifest
index bea3ebc4b508..5018e23c4d34 100644
--- a/dev-lang/R/Manifest
+++ b/dev-lang/R/Manifest
@@ -1,6 +1,3 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
-
 AUX R-2.11.1-parallel.patch 633 SHA256 4ad6f007ffb390584de0c8a5935e98f98106f32394aac45c30c3fdfe77c00c70 SHA512 788eca6236dccaf3fd6a13387c167bf3b11625b32c5b658fb19b17521d8e2747170cfaa54eaca3a4703a89e1f9453399e013792f7f92e7e9d0adeafeefb7e6da WHIRLPOOL a8ebf8ea01406fe576d2f95d57efc1f3c42d9ba61f75bd1034f485c85e68576cdd1c46c5d0e3139b5de8da312c20e89c78d97395082b4ff821fde4248a1b2b58
 AUX R-2.12.1-ldflags.patch 639 SHA256 dee11fd510d31add8166230a7af61b7e700f2f4f122cbe0a07310d0017874933 SHA512 49b73cff79c1521e214f036390f32eed8c7d4afd39082eabb7e6c59e5d7136f399ff7227117e418d4445647d25259dce8eb208a1ebe5990bf4ad87cefa250338 WHIRLPOOL 98ec264ac6d68e64dcbce32f4688aa458ba6d300202b6f31cd7580de68c693f0fb6aecba40cd0f6736a0ef9ff346d04cd96af06716a25c4a84a72551085837ed
 AUX R-2.13.1-zlib_header_fix.patch 464 SHA256 161f0fff63db5cb2cb4894321759997e75463d784d5a7ba5105f74fe2ed73c40 SHA512 7d573f33f16a9cfe080976e32fae1cb0af50e02bef026814aa5d30ce5a37d79f0ddeb69cee817602de40968fc3d5aee2ee4681b15d4011afc61ad69a01705f17 WHIRLPOOL 30d34d6e3c3a39f395409f238f6469b0c096db5039df377c8668678aaf4968f704205202f5c4f63cf8c5e3607b15df83172af09178df7707e12e746151bf02aa
@@ -8,23 +5,19 @@ AUX R-2.14.1-rmath-shared.patch 986 SHA256 c05463dbf9ec5bba34cc987df4f6878154a73
 AUX R-2.14.1-tiff.patch 1711 SHA256 ff77e062a80eeb403dc98ffb0b6fedce28859f18082981891ae6e2a95cf61142 SHA512 cefa162324966999cc824b2167d39219c2dc7f72fedc1b61e4beda8d6016cb8dd0e732fb567f71aab18e03506e1fd16dc6743bd0142d4d0e4fcf87ba55f5f957 WHIRLPOOL 620d9db1533c22f95813da0690d0f4697c246d63d0a5ce5561e092dca8d467a9d40cad46fddc6eae8a1951a16b4889c341773ce31957fb0e8e734d6a0a2aed8f
 AUX R-2.14.1-warnings-buffer-overflow.patch 380 SHA256 e6b3e825ef837342c0a4bbfc05d7441d1ec5a98e31cf3bdb3d25000337a8538f SHA512 69fe4fa593a50ae9650ff868e729e3eeaba0f994cd31da853b0c1b7a50297d833a36c6f6078b093eb25e30dc5b1194de20d84ce59fab4aa65c4a32492532211f WHIRLPOOL 2046a434ba2cb6181ca4b4e09ddd69ba24fd457e0a4de876e52b8b2a84ac7a9a0f175def76ea663cfaa279ad6d6d7ab1096fd28819310a94cc451c856497f28f
 AUX R-2.15.2-cairo.patch 1141 SHA256 da114707c8319a3e553e38bce17bf3e172dda8a4f4791452a1d82da500b5439f SHA512 f37b8909f4fafef7ebc4dc0d82abaa62213bd7d5fcdd273c3effdcfc760ba6e66237ab043c8441bc010bde567b5303a59354ab8c0cc3658dfecdab821ea21ecc WHIRLPOOL 30ac3db661ea7e44252d443f766559c9d67023a5cc5f315aeb5718c498a94f4807d3d9b96aadedfbec7cac8884a012d1f76585ce3bad560a79c59ed0e8da63dd
+AUX R-3.0.0-rmath-shared.patch 1069 SHA256 fc5278e204bbd71ec5ac634e108295744d509ee50a61bb36e5fd268a854f9219 SHA512 63640d890346651f5f92664afffadc9614c1c4c6207d230df873d81fb9361827f0b9b96a46acd7d9bd3ee5d9f100bc0484c2dfa17c947c5707d6895fd46a6b74 WHIRLPOOL d68a3093b6a3a25b5e10a35e77a486ee78c5b19772764f7a3256e9020ff7ed1695dcb73e9819effbd0bc7a419fdca7d64f10e06064221b70701e8ae0a1b8cb26
 DIST R-2.10.1.tar.gz 19705604 SHA256 5ca1780d9f47f2f4a9b52ba44fed9ee6e7d3547f18ed2c05192b0dbc56038e9d SHA512 aeedc0190c90b09fc2969f680ec0b8b8174ca224288d0d0c5536e19c63e28d92604ec2936015298b839cdbce349e5d4e9f759ef30d31fc3dccd2a67448e3b7d4 WHIRLPOOL 2252ad97059b6e7fbe4473280f681af1b57ff1a3c1c3151c499f71cc6b7f4d4fce0c5312389e79e61272f7b635cf31dcd1dd320525e627c08b97367c17ec3d58
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 DIST R-20130129.bash_completion.bz2 4209 SHA256 487e969b94563fec98ec58de7e6142e9361d4219088add0fca282b482a9e01b1 SHA512 910b26e16cfebe677f438abfa5f2652e582db143d91dbf0e7d4b1ea33462c7e5c89c3a3619c63ae98bba26b11a5adb16eda9d344f8cdbe4f0feabc546993c1a5 WHIRLPOOL 2368efaed37fcb6e010f6a234864631f68549bd8e3f733561170cc5b28f5557e546d8561246fb265a481a47991a262fec3acf6abc1dc3929a9357405e0d3c6fc
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 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
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+EBUILD R-3.0.0.ebuild 6207 SHA256 e11f7ffdd7bb953865cde69a6c077e28609ee977529ce77900c59958dee4cb80 SHA512 3bdf0b5d1548013577bc1203f20ec58e9ffa6f25f9c5d01199bcd4f1e49852c09969dcba140fd9ea3ba1a3fee83cc0236daa723bdb45f87c8c0ca433910070cc WHIRLPOOL 8c7f90df3deffb0f8e07b26ba78c1c135eb5cd8502220f32ad3a3a28def1500d93448f76f0dc0f24d8b0d8cd9e6a06414e2099961265b23765586e75f49e6257
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diff --git a/dev-lang/R/R-3.0.0.ebuild b/dev-lang/R/R-3.0.0.ebuild
new file mode 100644
index 000000000000..d47eeffe0a90
--- /dev/null
+++ b/dev-lang/R/R-3.0.0.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-3.0.0.ebuild,v 1.1 2013/04/04 22:10:01 calchan Exp $
+
+EAPI=5
+
+inherit bash-completion-r1 autotools eutils flag-o-matic fortran-2 multilib versionator toolchain-funcs
+
+BCP=${PN}-20130129.bash_completion
+DESCRIPTION="Language and environment for statistical computing and graphics"
+HOMEPAGE="http://www.r-project.org/"
+SRC_URI="mirror://cran/src/base/R-3/${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}-3.0.0-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
+}
diff --git a/dev-lang/R/files/R-3.0.0-rmath-shared.patch b/dev-lang/R/files/R-3.0.0-rmath-shared.patch
new file mode 100644
index 000000000000..4f8f3956d2c0
--- /dev/null
+++ b/dev-lang/R/files/R-3.0.0-rmath-shared.patch
@@ -0,0 +1,25 @@
+Link with libm to fix unresolved symbols when linked with as-needed
+and add a soname to the standalone math library
+Patch by Sebastien Fabbro
+Adapted to R-3.0.0 by Denis Dupeyron
+--- src/nmath/standalone/Makefile.in.orig	2013-04-04 14:39:15.777544946 -0600
++++ src/nmath/standalone/Makefile.in	2013-04-04 14:40:51.256153179 -0600
+@@ -64,7 +64,8 @@
+ Rexeclibdir_LTLIBRARIES = $(libRmath_la)
+ libRmath_la_SOURCES = $(SOURCES)
+ libRmath_la_OBJECTS = $(OBJECTS:.o=.lo)
+-libRmath_la_LDFLAGS =
++libRmath_la_LDFLAGS = -Wl,-soname=libRmath.so
++libRmath_la_LIBADD = $(LIBM)
+ 
+ CLEANFILES = Makedeps *.d *.o *.lo test $(SOURCES)
+ DISTCLEANFILES = Makefile $(Rexeclibdir_LIBRARIES) $(Rexeclibdir_LTLIBRARIES)
+@@ -117,7 +118,7 @@
+ 
+ ## under peculiar circumstances, $(LIBM) here helps.
+ $(libRmath_la): $(libRmath_la_OBJECTS)
+-	$(DYLIB_LINK) -o $@ $(libRmath_la_LDFLAGS) $(libRmath_la_OBJECTS) $(LIBM)
++	$(DYLIB_LINK) $(libRmath_la_LDFLAGS) $(libRmath_la_OBJECTS) $(libRmath_la_LIBADD) -o $@
+ 
+ test: $(srcdir)/test.c
+ 	$(CC) -o $@ $(ALL_CPPFLAGS) $(ALL_CFLAGS) $(srcdir)/test.c \