Use R blas internals to pass tests for stable candidate (it does work with other blas than blas-reference), remove old

(Portage version: 2.2.6.22374-prefix/cvs/Linux x86_64, signed Manifest commit with key 0x13CB1360)

9 files changed, 21 insertions, 514 deletions

diff --git a/dev-lang/R/ChangeLog b/dev-lang/R/ChangeLog
index 22ddef4dd743..a9af427d139a 100644
--- a/dev-lang/R/ChangeLog
+++ b/dev-lang/R/ChangeLog
@@ -1,6 +1,15 @@
 # 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 1.217 2013/08/27 15:03:04 kensington Exp $
+# $Header: /var/cvsroot/gentoo-x86/dev-lang/R/ChangeLog,v 1.218 2013/09/24 16:13:24 bicatali Exp $
+
+*R-3.0.1-r1 (24 Sep 2013)
+
+  24 Sep 2013; Sébastien Fabbro <bicatali@gentoo.org> +R-3.0.1-r1.ebuild,
+  -R-2.15.2-r2.ebuild, -R-2.15.2.ebuild, -R-3.0.0.ebuild,
+  -files/R-2.14.1-tiff.patch, -files/R-2.14.1-warnings-buffer-overflow.patch,
+  -files/R-2.15.2-cairo.patch, R-3.0.1.ebuild, metadata.xml:
+  Use R blas internals to pass tests for stable candidate (it does work with
+  other blas than blas-reference), remove old
 
   27 Aug 2013; Michael Palimaka <kensington@gentoo.org> R-2.10.1.ebuild,
   R-2.15.2-r2.ebuild, R-2.15.2.ebuild, R-2.15.3.ebuild, R-3.0.0.ebuild,
diff --git a/dev-lang/R/R-2.15.2-r2.ebuild b/dev-lang/R/R-2.15.2-r2.ebuild
deleted file mode 100644
index 651ecd3b46c3..000000000000
--- a/dev-lang/R/R-2.15.2-r2.ebuild
+++ /dev/null
@@ -1,208 +0,0 @@
-# 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-2.15.2-r2.ebuild,v 1.3 2013/08/27 15:03:04 kensington 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
-SRC_URI="http://dev.gentoo.org/~bicatali/distfiles/${P}.tar.bz2
-	bash-completion? ( http://dev.gentoo.org/~bicatali/distfiles/${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: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="${CDEPEND}
-	virtual/pkgconfig
-	doc? (
-			virtual/latex-base
-			dev-texlive/texlive-fontsrecommended
-		 )"
-
-RDEPEND="${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}"/${PN}-2.14.1-rmath-shared.patch
-
-	# fix cairo plots (gentoo bug #453048)
-	epatch "${FILESDIR}"/${PN}-2.15.2-cairo.patch
-
-	# fix packages.html for doc (gentoo bug #205103)
-	sed -i \
-		-e "s:../../../library:../../../../$(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/R-2.15.2.ebuild b/dev-lang/R/R-2.15.2.ebuild
deleted file mode 100644
index aaddb73d3bd5..000000000000
--- a/dev-lang/R/R-2.15.2.ebuild
+++ /dev/null
@@ -1,200 +0,0 @@
-# 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-2.15.2.ebuild,v 1.3 2013/08/27 15:03:04 kensington Exp $
-
-EAPI=4
-
-inherit bash-completion-r1 autotools eutils flag-o-matic fortran-2 multilib versionator toolchain-funcs
-
-BCP=${PN}-20120306.bash_completion
-DESCRIPTION="Language and environment for statistical computing and graphics"
-HOMEPAGE="http://www.r-project.org/"
-SRC_URI="mirror://cran/src/base/R-2/${P}.tar.gz
-	bash-completion? ( http://dev.gentoo.org/~bicatali/distfiles/${BCP}.bz2 )"
-
-LICENSE="|| ( GPL-2 GPL-3 ) LGPL-2.1"
-SLOT="0"
-KEYWORDS="~alpha ~amd64 ~hppa ~ia64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-fbsd ~x86-linux ~x64-macos"
-IUSE="bash-completion cairo doc icu java jpeg lapack minimal nls openmp perl png profile readline static-libs tiff tk X"
-REQUIRED_USE="png? ( || ( cairo X ) ) jpeg? ( || ( cairo X ) ) tiff? ( || ( cairo X ) )"
-
-CDEPEND="app-arch/bzip2
-	app-text/ghostscript-gpl
-	dev-libs/libpcre
-	virtual/blas
-	virtual/fortran
-	cairo? ( x11-libs/cairo[X] x11-libs/pango )
-	icu? ( dev-libs/icu )
-	jpeg? ( virtual/jpeg:0 )
-	lapack? ( virtual/lapack )
-	perl? ( dev-lang/perl )
-	png? ( media-libs/libpng )
-	readline? ( sys-libs/readline )
-	tk? ( dev-lang/tk )
-	X? ( x11-libs/libXmu x11-misc/xdg-utils )"
-
-DEPEND="${CDEPEND}
-	virtual/pkgconfig
-	doc? (
-			virtual/latex-base
-			dev-texlive/texlive-fontsrecommended
-		 )"
-
-RDEPEND="${CDEPEND}
-	( || ( <sys-libs/zlib-1.2.5.1-r1 >=sys-libs/zlib-1.2.5.1-r2[minizip] ) )
-	app-arch/xz-utils
-	java? ( >=virtual/jre-1.5 )"
-
-RESTRICT="minimal? ( test )"
-
-R_DIR="${EPREFIX}/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 [[ ${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 "s:-Wl,-soname=libRmath.so:-install_name ${EPREFIX}/usr/$(get_libdir)/libRmath.dylib:" \
-			-i src/nmath/standalone/Makefile.in || die
-	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
-	emake -C src/nmath/standalone shared $(use static-libs && echo static)
-	use doc && emake info pdf
-}
-
-src_install() {
-	default
-	emake -C src/nmath/standalone DESTDIR="${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/R-3.0.0.ebuild b/dev-lang/R/R-3.0.1-r1.ebuild
index 15f92b2f6326..7a7d3604a000 100644
--- a/dev-lang/R/R-3.0.0.ebuild
+++ b/dev-lang/R/R-3.0.1-r1.ebuild
@@ -1,6 +1,6 @@
 # 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 1.3 2013/08/27 15:03:04 kensington Exp $
+# $Header: /var/cvsroot/gentoo-x86/dev-lang/R/R-3.0.1-r1.ebuild,v 1.1 2013/09/24 16:13:24 bicatali Exp $
 
 EAPI=5
 
@@ -9,7 +9,8 @@ inherit bash-completion-r1 autotools eutils flag-o-matic fortran-2 multilib vers
 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
+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"
diff --git a/dev-lang/R/R-3.0.1.ebuild b/dev-lang/R/R-3.0.1.ebuild
index e2af154b62e1..cb0803a0cc52 100644
--- a/dev-lang/R/R-3.0.1.ebuild
+++ b/dev-lang/R/R-3.0.1.ebuild
@@ -1,6 +1,6 @@
 # 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-3.0.1.ebuild,v 1.2 2013/08/27 15:03:04 kensington Exp $
+# $Header: /var/cvsroot/gentoo-x86/dev-lang/R/R-3.0.1.ebuild,v 1.3 2013/09/24 16:13:24 bicatali Exp $
 
 EAPI=5
 
@@ -138,7 +138,7 @@ src_configure() {
 		--with-system-bzlib \
 		--with-system-pcre \
 		--with-system-xz \
-		--with-blas="$($(tc-getPKG_CONFIG) --libs blas)" \
+		--without-blas \
 		--docdir="${EPREFIX}/usr/share/doc/${PF}" \
 		rdocdir="${EPREFIX}/usr/share/doc/${PF}" \
 		$(use_enable nls) \
diff --git a/dev-lang/R/files/R-2.14.1-tiff.patch b/dev-lang/R/files/R-2.14.1-tiff.patch
deleted file mode 100644
index f815285557f3..000000000000
--- a/dev-lang/R/files/R-2.14.1-tiff.patch
+++ /dev/null
@@ -1,47 +0,0 @@
-Add a --with-libtiff to avoid broken implicit dependencies
-Patch by Sebastien Fabbro
-
---- configure.ac.orig	2012-01-02 17:01:24.000000000 +0000
-+++ configure.ac	2012-01-02 17:04:21.000000000 +0000
-@@ -396,6 +396,10 @@
- [AS_HELP_STRING([--with-jpeglib],[use jpeglib library (if available) @<:@yes@:>@])],
- [R_ARG_USE(jpeglib)],
- [use_jpeglib=yes])
-+AC_ARG_WITH([libtiff],
-+[AS_HELP_STRING([--with-libtiff],[use libtiff library (if available) @<:@yes@:>@])],
-+[R_ARG_USE(libtiff)],
-+[use_libtiff=yes])
- AC_ARG_WITH([system-zlib],
- [AS_HELP_STRING([--with-system-zlib],[use system zlib library (if available) @<:@no@:>@])],
- [R_ARG_USE_SYSTEM(zlib)],
---- m4/R.m4.orig	2012-01-02 17:05:22.000000000 +0000
-+++ m4/R.m4	2012-01-02 17:08:08.000000000 +0000
-@@ -2005,16 +2005,18 @@
- 	      [Define if you have the PNG headers and libraries.])
-   fi
- fi
--AC_CHECK_HEADERS(tiffio.h)
--# may need to resolve jpeg routines
--AC_CHECK_LIB(tiff, TIFFOpen, [have_tiff=yes], [have_tiff=no], [${BITMAP_LIBS}])
--if test "x${ac_cv_header_tiffio_h}" = xyes ; then
--  if test "x${have_tiff}" = xyes; then
--    AC_DEFINE(HAVE_TIFF, 1, [Define this if libtiff is available.])
--    BITMAP_LIBS="-ltiff ${BITMAP_LIBS}"
--  else
--    have_tiff=no
--  fi
-+if test "${use_libtiff}" = yes; then
-+   AC_CHECK_HEADERS(tiffio.h)
-+   # may need to resolve jpeg routines
-+   AC_CHECK_LIB(tiff, TIFFOpen, [have_tiff=yes], [have_tiff=no], [${BITMAP_LIBS}])
-+   if test "x${ac_cv_header_tiffio_h}" = xyes ; then
-+     if test "x${have_tiff}" = xyes; then
-+      AC_DEFINE(HAVE_TIFF, 1, [Define this if libtiff is available.])
-+      BITMAP_LIBS="-ltiff ${BITMAP_LIBS}"
-+     else
-+	have_tiff=no
-+     fi
-+   fi
- fi
- AC_SUBST(BITMAP_LIBS)
- ])# R_BITMAPS
diff --git a/dev-lang/R/files/R-2.14.1-warnings-buffer-overflow.patch b/dev-lang/R/files/R-2.14.1-warnings-buffer-overflow.patch
deleted file mode 100644
index 9a5caf244f36..000000000000
--- a/dev-lang/R/files/R-2.14.1-warnings-buffer-overflow.patch
+++ /dev/null
@@ -1,12 +0,0 @@
---- src/main/main.c.orig	2012-02-23 21:57:10.478788427 +0100
-+++ src/main/main.c	2012-02-23 21:56:12.186789729 +0100
-@@ -674,7 +674,7 @@
- #ifdef ENABLE_NLS
-     char localedir[PATH_MAX+20];
- #endif
--    char deferred_warnings[6][250];
-+    char deferred_warnings[11][250];
-     volatile int ndeferred_warnings = 0;
- 
-     InitConnections(); /* needed to get any output at all */
-
diff --git a/dev-lang/R/files/R-2.15.2-cairo.patch b/dev-lang/R/files/R-2.15.2-cairo.patch
deleted file mode 100644
index 3a02b28ead9d..000000000000
--- a/dev-lang/R/files/R-2.15.2-cairo.patch
+++ /dev/null
@@ -1,36 +0,0 @@
---- src/modules/X11/devX11.c	(révision 61681)
-+++ src/modules/X11/devX11.c	(révision 61682)
-@@ -244,6 +244,7 @@ 
- {
-     if(inclose || !xd || !xd->buffered || xd->holdlevel > 0) return;
-     cairo_paint(xd->xcc);
-+    cairo_surface_flush(xd->xcs);
-     if (xd->type == WINDOW) XDefineCursor(display, xd->window, arrow_cursor);
-     XSync(display, 0);
-     xd->last = currentTime();
-@@ -753,8 +754,10 @@ 
- #ifdef HAVE_WORKING_CAIRO
- 	    pX11Desc xd = (pX11Desc) dd->deviceSpecific;
- 	    /* We can use the buffered copy where we have it */ 
--	    if(xd->buffered == 1) cairo_paint(xd->xcc);
--	    else if (xd->buffered > 1)
-+	    if(xd->buffered == 1) {
-+		cairo_paint(xd->xcc);
-+		cairo_surface_flush(xd->xcs);
-+	    } else if (xd->buffered > 1)
- 		/* rely on timer to repaint eventually */
- 		xd->last_activity = currentTime();
- 	    else
-@@ -2691,7 +2694,11 @@ 
- 		Cairo_update(xd);
- 	    return;
- 	}
--	if(xd->buffered) cairo_paint(xd->xcc);
-+	if(xd->buffered) {
-+	    cairo_paint(xd->xcc);
-+	    cairo_surface_flush(xd->xcs);
-+	}
-+	
- #endif
- 	if(xd->type==WINDOW) XDefineCursor(display, xd->window, arrow_cursor);
- 	XSync(display, 0);
diff --git a/dev-lang/R/metadata.xml b/dev-lang/R/metadata.xml
index 1deadcbddd09..5d205a8da7fb 100644
--- a/dev-lang/R/metadata.xml
+++ b/dev-lang/R/metadata.xml
@@ -1,12 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-  <herd>sci-mathematics</herd>
-  <maintainer>
-    <email>calchan@gentoo.org</email>
-    <name>Denis Dupeyron</name>
-  </maintainer>
-  <longdescription lang="en">
+<herd>sci-mathematics</herd>
+<maintainer>
+  <email>calchan@gentoo.org</email>
+  <name>Denis Dupeyron</name>
+</maintainer>
+<longdescription lang="en">
   R is GNU S, a system for statistical computation and graphics. It
   consists of a language plus a run-time environment with graphics, a
   debugger, access to certain system functions, and the ability to run