commit: af2dc7c4efa9e3b453c745c0fb86e0c1e5be1421 Author: Sébastien Fabbro <bicatali <AT> gentoo <DOT> org> AuthorDate: Thu Jul 6 15:33:41 2017 +0000 Commit: Sebastien Fabbro <bicatali <AT> gentoo <DOT> org> CommitDate: Thu Jul 6 21:31:12 2017 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=af2dc7c4
dev-lang/R: version bump Package-Manager: Portage-2.3.6, Repoman-2.3.2 dev-lang/R/Manifest | 2 + dev-lang/R/R-3.4.1.ebuild | 204 ++++++++++++++++++++++++++++ dev-lang/R/files/R-3.4.1-parallel.patch | 11 ++ dev-lang/R/files/R-3.4.1-rmath-shared.patch | 21 +++ 4 files changed, 238 insertions(+) diff --git a/dev-lang/R/Manifest b/dev-lang/R/Manifest index 9ee4c158c3b..9403f0b02c9 100644 --- a/dev-lang/R/Manifest +++ b/dev-lang/R/Manifest @@ -2,3 +2,5 @@ DIST R-20130129.bash_completion.bz2 4209 SHA256 487e969b94563fec98ec58de7e6142e9 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 +DIST R-3.4.1.tar.gz 30200109 SHA256 02b1135d15ea969a3582caeb95594a05e830a6debcdb5b85ed2d5836a6a3fc78 SHA512 19bd50c87dc001ef947c15c1760f27ac8986ff6b43c6d90d3093ae184e42963027ef06faf31ec57ac9e519af7a35a2f53f8ea23ef75d800ebbd02945cedc4651 WHIRLPOOL 1396303a7ef7a0e8920af867e6b68e171152578231c9a7ad5020b494124922aae634c1ce6d0f2b2f8441481736b93c3abffe142f2af78dbb0dbc754c4faec3f1 +DIST R-78d6830e28ea90a046da79a9b4f70c39594bb6d6.bash_completion 13596 SHA256 7e452a23e0bd96b1076280448d130adab229b8ea37cd4531db77391868a31e97 SHA512 9ccd19bb1b0c18a2f13035ccd6809447429e197e298fb4d1df808ef345d723b42f75a1b91c349f6dbb46e4a82e59ef33e11300c495d79b63d670d0c0f2b16a06 WHIRLPOOL 49fd55e6a52d55f0aa15d3a117394793b6fba6f1b69a26911a2b2d7c40a65c8ec2246851edc3abb52849930c48e817ee62319ae8bc1db0a9b802c95fcb1554e0 diff --git a/dev-lang/R/R-3.4.1.ebuild b/dev-lang/R/R-3.4.1.ebuild new file mode 100644 index 00000000000..85556b03670 --- /dev/null +++ b/dev-lang/R/R-3.4.1.ebuild @@ -0,0 +1,204 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit bash-completion-r1 autotools eutils flag-o-matic fortran-2 multilib versionator toolchain-funcs + +# latest git commit for R bash completion: https://github.com/deepayan/rcompletion +BCPV=78d6830e28ea90a046da79a9b4f70c39594bb6d6 + +DESCRIPTION="Language and environment for statistical computing and graphics" +HOMEPAGE="http://www.r-project.org/"; +SRC_URI=" + mirror://cran/src/base/R-3/${P}.tar.gz + https://raw.githubusercontent.com/deepayan/rcompletion/${BCPV}/bash_completion/R -> ${PN}-${BCPV}.bash_completion" + +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= + net-misc/curl + 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 )" + +PATCHES=( + "${FILESDIR}"/${PN}-3.4.1-parallel.patch + "${FILESDIR}"/${PN}-3.4.1-rmath-shared.patch +) + +pkg_pretend() { + [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp +} + +pkg_setup() { + if [[ ${MERGE_TYPE} != binary ]] && use openmp; then + if ! tc-check-openmp; then + ewarn "OpenMP is not available in your current selected compiler" + die "need openmp capable compiler" + fi + FORTRAN_NEED_OPENMP=1 + fi + fortran-2_pkg_setup + filter-ldflags -Wl,-Bdirect -Bdirect + # avoid using existing R installation + unset R_HOME + # Temporary fix for bug #419761 + if [[ ($(tc-getCC) == *gcc) && ($(gcc-version) == 4.7) ]]; then + append-flags -fno-ipa-cp-clone + fi +} + +src_prepare() { + default + + # fix packages.html for doc (gentoo bug #205103) + sed -e "s:../../../library:../../../../$(get_libdir)/R/library:g" \ + -i src/library/tools/R/Rd.R || die + + # fix Rscript path when installed (gentoo bug #221061) + sed -e "s:-DR_HOME='\"\$(rhome)\"':-DR_HOME='\"${EROOT%/}/usr/$(get_libdir)/${PN}\"':" \ + -i src/unix/Makefile.in || die "sed unix Makefile failed" + + # fix HTML links to manual (gentoo bug #273957) + sed -e 's:\.\./manual/:manual/:g' \ + -i $(grep -Flr ../manual/ doc) || die "sed for HTML links failed" + + use lapack && \ + export LAPACK_LIBS="$($(tc-getPKG_CONFIG) --libs lapack)" + + if use X; then + export R_BROWSER="$(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 -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 -e "s:-Wl,-soname=libRmath.so:-install_name ${EROOT%/}/usr/$(get_libdir)/libRmath.dylib:" \ + -i 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/$(get_libdir)/tkConfig.sh) \ + $(use_with tk tcl-config "${EPREFIX}"/usr/$(get_libdir)/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)/${PN} + EOF + doenvd 99R + newbashcomp "${DISTDIR}"/${PN}-${BCPV}.bash_completion ${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/$(get_libdir)/R > /dev/null + for mod in $(find . -name "*.dylib") ; do + mod=${mod#./} + install_name_tool -id "${EPREFIX}/usr/$(get_libdir)/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 +} diff --git a/dev-lang/R/files/R-3.4.1-parallel.patch b/dev-lang/R/files/R-3.4.1-parallel.patch new file mode 100644 index 00000000000..6fac15b9ffb --- /dev/null +++ b/dev-lang/R/files/R-3.4.1-parallel.patch @@ -0,0 +1,11 @@ +--- a/src/include/Makefile.in 2017-07-05 23:09:09.682703655 +0000 ++++ b/src/include/Makefile.in 2017-07-05 23:06:56.533612308 +0000 +@@ -81,7 +81,7 @@ + Rmath.h0: $(srcdir)/Rmath.h0.in $(top_builddir)/config.status + @cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ + +-install: installdirs install-intl-@USE_INCLUDED_LIBINTL@ ++install: $(OBJ_HEADERS) installdirs install-intl-@USE_INCLUDED_LIBINTL@ + @for d in $(SUBDIRS); do \ + (cd $${d} && $(MAKE) $@) || exit 1; \ + done diff --git a/dev-lang/R/files/R-3.4.1-rmath-shared.patch b/dev-lang/R/files/R-3.4.1-rmath-shared.patch new file mode 100644 index 00000000000..8bc6233de6d --- /dev/null +++ b/dev-lang/R/files/R-3.4.1-rmath-shared.patch @@ -0,0 +1,21 @@ +--- a/src/nmath/standalone/Makefile.in 2017-07-05 23:20:26.098087600 +0000 ++++ b/src/nmath/standalone/Makefile.in 2017-07-05 23:21:55.087480310 +0000 +@@ -64,7 +64,8 @@ + Rexeclibdir_LTLIBRARIES = $(libRmath_la) + libRmath_la_SOURCES = $(SOURCES) + libRmath_la_OBJECTS = $(OBJECTS:.o=.lo) +-libRmath_la_LDFLAGS = ++libRmath_la_LDFLAGS = -Wl,-soname=libRmath.so ++libRmath_la_LIBADD = $(LIBM) + + CLEANFILES = Makedeps *.d *.o *.lo test check.log $(SOURCES) + DISTCLEANFILES = Makefile $(Rexeclibdir_LIBRARIES) $(Rexeclibdir_LTLIBRARIES) +@@ -127,7 +128,7 @@ + + ## under peculiar circumstances, $(LIBM) here helps. + $(libRmath_la): $(libRmath_la_OBJECTS) +- $(DYLIB_LINK) -o $@ $(libRmath_la_LDFLAGS) $(libRmath_la_OBJECTS) $(LIBM) ++ $(DYLIB_LINK) $(libRmath_la_LDFLAGS) $(libRmath_la_OBJECTS) $(libRmath_la_LIBADD) -o $@ + + test: $(srcdir)/test.c + $(CC) -o $@ $(ALL_CPPFLAGS) $(ALL_CFLAGS) $(srcdir)/test.c \
