Version bump

(Portage version: 2.2.8-prefix/cvs/Linux x86_64, signed Manifest commit with key 0x13CB1360)

6 files changed, 239 insertions, 11 deletions

diff --git a/dev-lang/R/ChangeLog b/dev-lang/R/ChangeLog
index ad367ccc4662..f00a9d4586ed 100644
--- a/dev-lang/R/ChangeLog
+++ b/dev-lang/R/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for dev-lang/R
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/dev-lang/R/ChangeLog,v 1.231 2014/03/02 21:33:49 dilfridge Exp $
+# $Header: /var/cvsroot/gentoo-x86/dev-lang/R/ChangeLog,v 1.232 2014/03/19 16:38:16 bicatali Exp $
+
+*R-3.0.3 (19 Mar 2014)
+
+  19 Mar 2014; Sébastien Fabbro <bicatali@gentoo.org> +R-3.0.3.ebuild,
+  R-3.0.1-r1.ebuild, files/R-2.11.1-parallel.patch,
+  files/R-2.13.1-zlib_header_fix.patch, files/R-3.0.0-rmath-shared.patch:
+  Version bump
 
   02 Mar 2014; Andreas K. Huettel <dilfridge@gentoo.org> R-3.0.2.ebuild:
   Add subslot dependency on dev-libs/icu
diff --git a/dev-lang/R/R-3.0.1-r1.ebuild b/dev-lang/R/R-3.0.1-r1.ebuild
index 3fc719be9820..81878716416f 100644
--- a/dev-lang/R/R-3.0.1-r1.ebuild
+++ b/dev-lang/R/R-3.0.1-r1.ebuild
@@ -1,10 +1,10 @@
-# Copyright 1999-2013 Gentoo Foundation
+# Copyright 1999-2014 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/dev-lang/R/R-3.0.1-r1.ebuild,v 1.2 2013/11/03 20:38:33 mattst88 Exp $
+# $Header: /var/cvsroot/gentoo-x86/dev-lang/R/R-3.0.1-r1.ebuild,v 1.3 2014/03/19 16:38:16 bicatali Exp $
 
 EAPI=5
 
-inherit bash-completion-r1 autotools eutils flag-o-matic fortran-2 multilib versionator toolchain-funcs
+inherit bash-completion-r1 autotools eutils flag-o-matic fortran-2 multilib versionator toolchain-funcs java-pkg-opt-2
 
 BCP=${PN}-20130129.bash_completion
 DESCRIPTION="Language and environment for statistical computing and graphics"
@@ -39,12 +39,13 @@ DEPEND="${CDEPEND}
 	doc? (
 			virtual/latex-base
 			dev-texlive/texlive-fontsrecommended
-		 )"
+		 )
+	java? ( >=virtual/jdk-1.5 )"
 
 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 )"
+	java? ( >=virtual/jdk-1.5 )"
 
 RESTRICT="minimal? ( test )"
 
@@ -56,6 +57,12 @@ pkg_setup() {
 		tc-has-openmp || die "Please enable openmp support in your compiler"
 	fi
 	fortran-2_pkg_setup
+
+	# Selects the build VM according to DEPEND and user preferences.
+	# Also sets VM specific addpredict and environment variables.
+	# Does nothing if java is disabled.
+	java-pkg-opt-2_pkg_setup
+
 	filter-ldflags -Wl,-Bdirect -Bdirect
 	# avoid using existing R installation
 	unset R_HOME
@@ -106,6 +113,8 @@ src_prepare() {
 	use perl && \
 		export PERL5LIB="${S}/share/perl:${PERL5LIB:+:}${PERL5LIB}"
 
+	java-pkg-opt-2_src_prepare
+
 	# don't search /usr/local
 	sed -i -e '/FLAGS=.*\/local\//c\: # removed by ebuild' configure.ac || die
 	# Fix for Darwin (OS X)
@@ -130,6 +139,11 @@ src_prepare() {
 }
 
 src_configure() {
+	# configure shouldn't run checks for java if disabled.
+	# Requires properly setup JVM or a addpredict hack for
+	# /proc/self/coredump_filter and possibly others.
+	# $(use_enable java)
+
 	econf \
 		--enable-byte-compiled-packages \
 		--enable-R-shlib \
diff --git a/dev-lang/R/R-3.0.3.ebuild b/dev-lang/R/R-3.0.3.ebuild
new file mode 100644
index 000000000000..190a2925d47f
--- /dev/null
+++ b/dev-lang/R/R-3.0.3.ebuild
@@ -0,0 +1,200 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/dev-lang/R/R-3.0.3.ebuild,v 1.1 2014/03/19 16:38:16 bicatali Exp $
+
+EAPI=5
+
+inherit bash-completion-r1 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/${BCP}.bz2 )"
+
+LICENSE="|| ( GPL-2 GPL-3 ) LGPL-2.1"
+SLOT="0"
+KEYWORDS="~amd64 ~hppa ~ia64 ~ppc ~ppc64 ~sparc ~x86 ~x86-fbsd ~amd64-linux ~x86-linux ~x64-macos"
+IUSE="bash-completion cairo doc icu java jpeg lapack minimal nls openmp perl png prefix profile readline static-libs tiff tk X"
+REQUIRED_USE="png? ( || ( cairo X ) ) jpeg? ( || ( cairo X ) ) tiff? ( || ( cairo X ) )"
+
+CDEPEND="
+	app-arch/bzip2:0=
+	app-arch/xz-utils:0=
+	app-text/ghostscript-gpl
+	dev-libs/libpcre:3=
+	virtual/blas:0
+	|| ( >=sys-apps/coreutils-8.15 sys-freebsd/freebsd-bin app-misc/realpath )
+	cairo? ( x11-libs/cairo[X] x11-libs/pango )
+	icu? ( dev-libs/icu:= )
+	jpeg? ( virtual/jpeg:0 )
+	lapack? ( virtual/lapack:0 )
+	perl? ( dev-lang/perl )
+	png? ( media-libs/libpng:0= )
+	readline? ( sys-libs/readline:0= )
+	tiff? ( media-libs/tiff:0= )
+	tk? ( dev-lang/tk:0= )
+	X? ( x11-libs/libXmu:0= x11-misc/xdg-utils )"
+
+DEPEND="${CDEPEND}
+	virtual/pkgconfig
+	doc? (
+		virtual/latex-base
+		dev-texlive/texlive-fontsrecommended
+	)"
+
+RDEPEND="${CDEPEND}
+	( || ( <sys-libs/zlib-1.2.5.1-r1:0= >=sys-libs/zlib-1.2.5.1-r2:0=[minizip] ) )
+	java? ( >=virtual/jre-1.5 )"
+
+RESTRICT="minimal? ( test )"
+
+R_DIR="${EROOT%/}/usr/$(get_libdir)/${PN}"
+
+pkg_setup() {
+	if use openmp; then
+		if [[ $(tc-getCC) == *gcc ]] && ! tc-has-openmp; then
+			ewarn "OpenMP is not available in your current selected gcc"
+			die "need openmp capable gcc"
+		fi
+		FORTRAN_NEED_OPENMP=1
+	fi
+	fortran-2_pkg_setup
+	filter-ldflags -Wl,-Bdirect -Bdirect
+	# avoid using existing R installation
+	unset R_HOME
+	# Temporary fix for bug #419761
+	if [[ ($(tc-getCC) == *gcc) && ($(gcc-version) == 4.7) ]]; then
+		append-flags -fno-ipa-cp-clone
+	fi
+}
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${PN}-2.11.1-parallel.patch \
+		"${FILESDIR}"/${PN}-2.13.1-zlib_header_fix.patch \
+		"${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
+}
+
+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) --variable=libdir 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) \
+		$(use_with tk tk-config "${EPREFIX}"/usr/lib/tkConfig.sh) \
+		$(use_with tk tcl-config "${EPREFIX}"/usr/lib/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/${PF}/html/manual
+	fi
+
+	cat > 99R <<-EOF
+		LDPATH=${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-2.11.1-parallel.patch b/dev-lang/R/files/R-2.11.1-parallel.patch
index 2be95349095a..c713d335badd 100644
--- a/dev-lang/R/files/R-2.11.1-parallel.patch
+++ b/dev-lang/R/files/R-2.11.1-parallel.patch
@@ -1,7 +1,8 @@
-Fix ocasional failure with parallel install (bug #322965)
-Patch by Sebastien Fabbro
+Fix ocasional failure with parallel install
+Gentoo bug: https://bugs.gentoo.org/show_bug.cgi?id=322965
+R bug: https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=14505
 
-https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=14505
+Patch by Sebastien Fabbro
 
 --- src/include/Makefile.in.orig	2010-06-15 18:18:54.000000000 +0000
 +++ src/include/Makefile.in	2010-06-15 18:19:48.000000000 +0000
diff --git a/dev-lang/R/files/R-2.13.1-zlib_header_fix.patch b/dev-lang/R/files/R-2.13.1-zlib_header_fix.patch
index 42e3b8a811c5..136acb26055f 100644
--- a/dev-lang/R/files/R-2.13.1-zlib_header_fix.patch
+++ b/dev-lang/R/files/R-2.13.1-zlib_header_fix.patch
@@ -1,6 +1,9 @@
-Update for zlib header changes 
+Update for zlib header changes for zlib > 1.2.5
 
-https://bugs.gentoo.org/show_bug.cgi?id=383431
+Gentoo bug: https://bugs.gentoo.org/show_bug.cgi?id=383431
+R bug: https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=14951
+
+Patch by Michael Schreckenbauer
 
 --- src/main/unzip.h.orig	2011-09-24 19:35:53.000000000 -0700
 +++ src/main/unzip.h	2011-09-24 19:37:06.000000000 -0700
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
index 4f8f3956d2c0..f53fb7910511 100644
--- a/dev-lang/R/files/R-3.0.0-rmath-shared.patch
+++ b/dev-lang/R/files/R-3.0.0-rmath-shared.patch
@@ -1,7 +1,10 @@
 Link with libm to fix unresolved symbols when linked with as-needed
 and add a soname to the standalone math library
+R bug: https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=14953
+
 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 @@