dev-lang/R: bump to 3.2.2

Gentoo-Bug: 557600

Package-Manager: portage-2.2.20.1

2 files changed, 207 insertions, 0 deletions

diff --git a/dev-lang/R/Manifest b/dev-lang/R/Manifest
index d6134ee943d1..be5008e3cd4c 100644
--- a/dev-lang/R/Manifest
+++ b/dev-lang/R/Manifest
@@ -5,3 +5,4 @@ DIST R-3.1.0.tar.gz 28469975 SHA256 8a680390f84c58c01dcdefd682eaa0e90389f09e6d2f
 DIST R-3.1.1.tar.gz 28606569 SHA256 ce5c4d5e34414ce8f1ec2d5642861435fa1ddc4cd89bd336172bbe25a62c7a19 SHA512 a75d8b82645bd9486873669b802924448d591013076e3d7dc958502dc6f0dac7d7fb78f3921d34a1eac1383f141b6e800f4293f7fac09651e0176cf84c431af9 WHIRLPOOL ec05c70193a229cbaf15f3432853070c6666c3963a4e2719a6d8ff188bfc2cada0d1f2fe90a9dd6b43f46913138afed0be387ba73b7f9c4d87abc362cc8a5393
 DIST R-3.1.2.tar.gz 28655941 SHA256 bcd150afcae0e02f6efb5f35a6ab72432be82e849ec52ce0bb89d8c342a8fa7a SHA512 fee20cd94d14bd46cc36fb265ed4d64f44eaa3929dd13c62d29a5883fde607aba63e28a4b0f265ede63f78788996deaee36acf6a70cc0bc90a705c9782be01a1 WHIRLPOOL f02d543c0fd7e89e63aba844b7c0f651a9a6bb5dbfcd58bdb64b49d08335c3270383eb62291b9f2f20ef6ec9f39eef5cf77ae1af3109296f8b1898227cca99d1
 DIST R-3.2.0.tar.gz 29124927 SHA256 f5ae953f18ba6f3d55b46556bbbf73441350f9fd22625402b723a2b81ff64f35 SHA512 c6041c854251d51dd936d3a3632c2958a0437c58488f93e5ba810e957fb7f2276e3fe4f615fb4705f2fc5a66aa50a828b54b5e4e7b4358c7fd465c71531b9828 WHIRLPOOL e21a65b9197a202691dbe903b441caf7d8b92efdffb86dcccdbf09d080177cfd472a54d381df1cca749937434ffb9c08ac74198457e320353207cd00837e1086
+DIST R-3.2.2.tar.gz 29772864 SHA256 9c9152e74134b68b0f3a1c7083764adc1cb56fd8336bec003fd0ca550cd2461d SHA512 71ba470875262b9f00fb6970f209788df4dad30e0a28373b824b60d8bc6401afb7786e65387663c6490c7ddcd2bfd7f808a270a3e63238f3d7565d5f93607138 WHIRLPOOL fea59929ada1d67dafc6ad89409d18ad173af7990384033f490a00e0f794d9919aecf7cd37089d105fe03b9cf64d079e5d148622571cec3eb924c1c5bd00081e
diff --git a/dev-lang/R/R-3.2.2.ebuild b/dev-lang/R/R-3.2.2.ebuild
new file mode 100644
index 000000000000..12ad83ec2b0d
--- /dev/null
+++ b/dev-lang/R/R-3.2.2.ebuild
@@ -0,0 +1,206 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+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
+	http://dev.gentoo.org/~bicatali/distfiles/${BCP}.bz2"
+
+LICENSE="|| ( GPL-2 GPL-3 ) LGPL-2.1"
+SLOT="0"
+KEYWORDS="~amd64 ~hppa ~ia64 ~ppc ~ppc64 ~sparc ~x86 ~x86-fbsd ~amd64-linux ~x86-linux ~x64-macos"
+IUSE="cairo doc icu java jpeg lapack minimal nls openmp perl png prefix profile readline static-libs tiff tk X"
+REQUIRED_USE="png? ( || ( cairo X ) ) jpeg? ( || ( cairo X ) ) tiff? ( || ( cairo X ) )"
+
+CDEPEND="
+	app-arch/bzip2:0=
+	app-arch/xz-utils:0=
+	app-text/ghostscript-gpl
+	>=dev-libs/libpcre-8.35:3=
+	virtual/blas:0
+	|| ( >=sys-apps/coreutils-8.15 sys-freebsd/freebsd-bin app-misc/realpath )
+	cairo? ( x11-libs/cairo:0=[X] x11-libs/pango:0= )
+	icu? ( dev-libs/icu:= )
+	jpeg? ( virtual/jpeg:0 )
+	lapack? ( virtual/lapack:0 )
+	perl? ( dev-lang/perl )
+	png? ( media-libs/libpng:0= )
+	readline? ( sys-libs/readline:0= )
+	tiff? ( media-libs/tiff:0= )
+	tk? ( dev-lang/tk:0= )
+	X? ( x11-libs/libXmu:0= x11-misc/xdg-utils )"
+
+DEPEND="${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
+	AT_M4DIR=m4 eaclocal
+	eautoconf
+}
+
+src_configure() {
+	#	--with-system-tre \
+	# tre is patched from upstream
+	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) \
+		$(use_with tk tk-config "${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=${R_DIR}
+	EOF
+	doenvd 99R
+	newbashcomp "${WORKDIR}"/${BCP} ${PN}
+	# The buildsystem has a different understanding of install_names than
+	# 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}" \
+				"${mod}"
+		done
+		popd > /dev/null
+	fi
+	docompress -x /usr/share/doc/${PF}/NEWS.rds
+}
+
+pkg_postinst() {
+	if use java; then
+		einfo "Re-initializing java paths for ${P}"
+		R CMD javareconf
+	fi
+}