commit: bda3e8cccb530a8f31303bd14a9b8cef8a58832d
Author: Denis Dupeyron <calchan <AT> gentoo <DOT> org>
AuthorDate: Thu Dec 8 16:34:25 2016 +0000
Commit: Denis Dupeyron <calchan <AT> gentoo <DOT> org>
CommitDate: Thu Dec 8 16:34:25 2016 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=bda3e8cc
dev-lang/R: bump to 3.3.2, thanks to Neil Shephard (bug #598834)
Package-Manager: portage-2.3.3
dev-lang/R/Manifest | 1 +
dev-lang/R/R-3.3.2.ebuild | 201 ++++++++++++++++++++++++++++++++++++++++++++++
2 files changed, 202 insertions(+)
diff --git a/dev-lang/R/Manifest b/dev-lang/R/Manifest
index 39b08f5..9ee4c15 100644
--- a/dev-lang/R/Manifest
+++ b/dev-lang/R/Manifest
@@ -1,3 +1,4 @@
DIST R-20130129.bash_completion.bz2 4209 SHA256
487e969b94563fec98ec58de7e6142e9361d4219088add0fca282b482a9e01b1 SHA512
910b26e16cfebe677f438abfa5f2652e582db143d91dbf0e7d4b1ea33462c7e5c89c3a3619c63ae98bba26b11a5adb16eda9d344f8cdbe4f0feabc546993c1a5
WHIRLPOOL
2368efaed37fcb6e010f6a234864631f68549bd8e3f733561170cc5b28f5557e546d8561246fb265a481a47991a262fec3acf6abc1dc3929a9357405e0d3c6fc
DIST R-3.2.2.tar.gz 29772864 SHA256
9c9152e74134b68b0f3a1c7083764adc1cb56fd8336bec003fd0ca550cd2461d SHA512
71ba470875262b9f00fb6970f209788df4dad30e0a28373b824b60d8bc6401afb7786e65387663c6490c7ddcd2bfd7f808a270a3e63238f3d7565d5f93607138
WHIRLPOOL
fea59929ada1d67dafc6ad89409d18ad173af7990384033f490a00e0f794d9919aecf7cd37089d105fe03b9cf64d079e5d148622571cec3eb924c1c5bd00081e
DIST R-3.3.1.tar.gz 29848329 SHA256
3dc59ae5831f5380f83c169bac2103ad052efe0ecec4ffa74bde4d85a0fda9e2 SHA512
d0ff85e99b9ec9cac672aa30d7d1a854778c6a610bcc5336e8c60c8c74f20856f2bfeae085af793fad646ff45cb4677d9d6dcbaa18212591f72f00a02339f4cd
WHIRLPOOL
6e2edb60173a54c8b25d16201c24176b3ea837287e6d306c9d2e2c4578764b0d469d9c17228b6be67dda646a4272f30b331dbbc6238a6e851eb5320f04c7f151
+DIST R-3.3.2.tar.gz 29440670 SHA256
d294ad21e9f574fb4828ebb3a94b8cb34f4f304a41687a994be00dd41a4e514c SHA512
06a98687c0b180cb0bfd57440ea26088212d9f48948d503136475bf54b42d72cfec5bea7e333c0cedd60733bd614dd0f8c2eced7e24478b6c89f48e8d0c43482
WHIRLPOOL
a68112df87552cc6ca8cd6b78b99dda2a22b8f4cfcd87a4512d541d25ef21358ede1ba71b4d7e9f274bf4e4340de18355a777d9af2ed41c0a498fa11d91cf0d8
diff --git a/dev-lang/R/R-3.3.2.ebuild b/dev-lang/R/R-3.3.2.ebuild
new file mode 100644
index 00000000..ceeeaf9
--- /dev/null
+++ b/dev-lang/R/R-3.3.2.ebuild
@@ -0,0 +1,201 @@
+# Copyright 1999-2016 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
+ https://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-r2:0[minizip]
+ java? ( >=virtual/jre-1.5 )"
+
+RESTRICT="minimal? ( test )"
+
+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='\"${EROOT%/}/usr/$(get_libdir)/${PN}\"':"
\
+ 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-blas="$($(tc-getPKG_CONFIG) --libs blas)" \
+ --docdir="${EPREFIX}/usr/share/doc/${PF}" \
+ rdocdir="${EPREFIX}/usr/share/doc/${PF}" \
+ $(use_enable java) \
+ $(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/${PF}/html/manual
+ fi
+
+ cat > 99R <<-EOF
+ LDPATH=${EROOT%/}/usr/$(get_libdir)/${PN}/lib
+ R_HOME=${EROOT%/}/usr/$(get_libdir)/${PN}
+ EOF
+ doenvd 99R
+ newbashcomp "${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}/{BioC_mirrors.csv,CRAN_mirrors.csv,KEYWORDS.db,NEWS.rds}
+}
+
+pkg_postinst() {
+ if use java; then
+ einfo "Re-initializing java paths for ${P}"
+ R CMD javareconf
+ fi
+}
