Version bump

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

3 files changed, 35 insertions, 251 deletions

diff --git a/dev-lang/R/ChangeLog b/dev-lang/R/ChangeLog
index 857c1ad81ab1..d5b0120cc4b2 100644
--- a/dev-lang/R/ChangeLog
+++ b/dev-lang/R/ChangeLog
@@ -1,6 +1,12 @@
 # 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 1.234 2014/04/07 11:58:36 heroxbd Exp $
+# $Header: /var/cvsroot/gentoo-x86/dev-lang/R/ChangeLog,v 1.235 2014/04/15 19:00:08 bicatali Exp $
+
+*R-3.1.0 (15 Apr 2014)
+
+  15 Apr 2014; Sébastien Fabbro <bicatali@gentoo.org> +R-3.1.0.ebuild,
+  -R-3.0.1-r1.ebuild, -R-3.0.2.ebuild:
+  Version bump
 
   07 Apr 2014; Benda Xu <heroxbd@gentoo.org> R-3.0.2.ebuild, R-3.0.3.ebuild:
   bug 505904 by Robert McGehee: revert the blas library configure update for bug
diff --git a/dev-lang/R/R-3.0.1-r1.ebuild b/dev-lang/R/R-3.0.1-r1.ebuild
deleted file mode 100644
index 81878716416f..000000000000
--- a/dev-lang/R/R-3.0.1-r1.ebuild
+++ /dev/null
@@ -1,219 +0,0 @@
-# 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 1.3 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 java-pkg-opt-2
-
-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/${BCP}.bz2 )"
-
-LICENSE="|| ( GPL-2 GPL-3 ) LGPL-2.1"
-SLOT="0"
-KEYWORDS="~amd64 ~hppa ~ia64 ~ppc ~ppc64 ~sparc ~x86 ~x86-fbsd ~amd64-linux ~x86-linux ~x64-macos"
-IUSE="bash-completion cairo doc icu java jpeg lapack minimal nls openmp perl png prefix profile readline static-libs tiff tk X"
-REQUIRED_USE="png? ( || ( cairo X ) ) jpeg? ( || ( cairo X ) ) tiff? ( || ( cairo X ) )"
-
-CDEPEND="
-	app-arch/bzip2
-	app-text/ghostscript-gpl
-	dev-libs/libpcre
-	virtual/blas
-	cairo? ( x11-libs/cairo[X] x11-libs/pango )
-	icu? ( dev-libs/icu )
-	jpeg? ( virtual/jpeg:0 )
-	lapack? ( virtual/lapack )
-	perl? ( dev-lang/perl )
-	png? ( media-libs/libpng )
-	readline? ( sys-libs/readline )
-	tk? ( dev-lang/tk )
-	X? ( x11-libs/libXmu x11-misc/xdg-utils )"
-
-DEPEND="${CDEPEND}
-	virtual/pkgconfig
-	doc? (
-			virtual/latex-base
-			dev-texlive/texlive-fontsrecommended
-		 )
-	java? ( >=virtual/jdk-1.5 )"
-
-RDEPEND="${CDEPEND}
-	( || ( <sys-libs/zlib-1.2.5.1-r1 >=sys-libs/zlib-1.2.5.1-r2[minizip] ) )
-	app-arch/xz-utils
-	java? ( >=virtual/jdk-1.5 )"
-
-RESTRICT="minimal? ( test )"
-
-R_DIR="${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
-
-	# 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
-	# 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}"
-
-	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)
-	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() {
-	# 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.
-	# $(use_enable java)
-
-	econf \
-		--enable-byte-compiled-packages \
-		--enable-R-shlib \
-		--disable-R-framework \
-		--with-system-zlib \
-		--with-system-bzlib \
-		--with-system-pcre \
-		--with-system-xz \
-		--with-blas="$($(tc-getPKG_CONFIG) --libs blas)" \
-		--docdir="${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 -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/R-3.0.2.ebuild b/dev-lang/R/R-3.1.0.ebuild
index e2027d16e9a2..7f49a822024e 100644
--- a/dev-lang/R/R-3.0.2.ebuild
+++ b/dev-lang/R/R-3.1.0.ebuild
@@ -1,6 +1,6 @@
 # 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-3.0.2.ebuild,v 1.6 2014/04/07 11:58:36 heroxbd Exp $
+# $Header: /var/cvsroot/gentoo-x86/dev-lang/R/R-3.1.0.ebuild,v 1.1 2014/04/15 19:00:08 bicatali Exp $
 
 EAPI=5
 
@@ -20,31 +20,32 @@ IUSE="bash-completion cairo doc icu java jpeg lapack minimal nls openmp perl png
 REQUIRED_USE="png? ( || ( cairo X ) ) jpeg? ( || ( cairo X ) ) tiff? ( || ( cairo X ) )"
 
 CDEPEND="
-	app-arch/bzip2
+	app-arch/bzip2:0=
+	app-arch/xz-utils:0=
 	app-text/ghostscript-gpl
-	dev-libs/libpcre
-	virtual/blas
+	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 )
+	cairo? ( x11-libs/cairo:0=[X] x11-libs/pango:0= )
 	icu? ( dev-libs/icu:= )
 	jpeg? ( virtual/jpeg:0 )
-	lapack? ( virtual/lapack )
+	lapack? ( virtual/lapack:0 )
 	perl? ( dev-lang/perl )
-	png? ( media-libs/libpng )
-	readline? ( sys-libs/readline )
-	tk? ( dev-lang/tk )
-	X? ( x11-libs/libXmu x11-misc/xdg-utils )"
+	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
-		 )"
+		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
+	( || ( <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 )"
@@ -53,8 +54,11 @@ 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
-		tc-has-openmp || die "Please enable openmp support in your compiler"
 	fi
 	fortran-2_pkg_setup
 	filter-ldflags -Wl,-Bdirect -Bdirect
@@ -67,20 +71,10 @@ pkg_setup() {
 }
 
 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
+	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 \
@@ -131,6 +125,8 @@ src_prepare() {
 }
 
 src_configure() {
+	#	--with-system-tre \
+	# tre is patched from upstream
 	econf \
 		--enable-byte-compiled-packages \
 		--enable-R-shlib \
@@ -165,7 +161,8 @@ src_configure() {
 src_compile() {
 	export VARTEXFONTS="${T}/fonts"
 	emake AR="$(tc-getAR)"
-	emake -C src/nmath/standalone shared $(use static-libs && echo static) AR="$(tc-getAR)"
+	emake -C src/nmath/standalone \
+		shared $(use static-libs && echo static) AR="$(tc-getAR)"
 	use doc && emake info pdf
 }