commit: c9dc8c0bd3f814e3abc913d07fb0935a78797258 Author: Mark Wright <gienah <AT> gentoo <DOT> org> AuthorDate: Mon Jan 13 13:14:07 2020 +0000 Commit: Mark Wright <gienah <AT> gentoo <DOT> org> CommitDate: Mon Jan 13 13:14:07 2020 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c9dc8c0b
dev-lang/R: Bump to 3.6.2 Thanks to Neil for reporting, UlvHare for testing bug #702808. Fix bug #515428 pkg-config files with wrong LDFLAGS detected, thanks to patrick for reporting. Closes: https://bugs.gentoo.org/show_bug.cgi?id=702808 Closes: https://bugs.gentoo.org/show_bug.cgi?id=515428 Package-Manager: Portage-2.3.84, Repoman-2.3.20 Signed-off-by: Mark Wright <gienah <AT> gentoo.org> dev-lang/R/Manifest | 1 + dev-lang/R/R-3.6.2.ebuild | 207 +++++++++++++++++++++ .../R-3.6.2-no-LDFLAGS-in-libR-pkg-config.patch | 11 ++ dev-lang/R/files/R-3.6.2-no-gzip-doc.patch | 10 + 4 files changed, 229 insertions(+) diff --git a/dev-lang/R/Manifest b/dev-lang/R/Manifest index 32412abdb94..e02181ffa37 100644 --- a/dev-lang/R/Manifest +++ b/dev-lang/R/Manifest @@ -1,4 +1,5 @@ DIST R-3.4.1.tar.gz 30200109 BLAKE2B 03602e9a48759caee8ce047fa6273df7a54af089de4489e21953c0e3fc7bfdf720d924f1e0167d3dbf65f63ed42ac10dea8b45289b921cda1c0e6d25a0063ebb SHA512 19bd50c87dc001ef947c15c1760f27ac8986ff6b43c6d90d3093ae184e42963027ef06faf31ec57ac9e519af7a35a2f53f8ea23ef75d800ebbd02945cedc4651 DIST R-3.5.3.tar.gz 30205979 BLAKE2B 60dde4c1a7874df0b113630577d943d581d9e0844383a5cb7eda7f62470177d541704a888c33ded216f8b1f088cda493d7716693f5e2451effe3639ce2286dd1 SHA512 077cbd4bc9f19a3a2485afbd4d8e08e0754ddcb9a10164cbc8478f239d5ed0ffaf6796929f154cce1c8aea549c32d460049fc036dc326174d1dbb0a1ddb5f5ef DIST R-3.6.0.tar.gz 30449618 BLAKE2B 2fb2f1252f5ead97ab42eb1f71fa0be1e8aec2f6cce182956ec1c35b43b70b58f579faf5f3ca11efb8e9c24a9ed836b5b690cb23858249bc7f575aca4709bc3b SHA512 b2e17b909b6387abb964492e2e9370f913295ca7ac99bab0e965c43ed3c4635e27468c326fb2bca3c529b03c731b0170d9e777a194ad4d6c5a983c050223d8c8 +DIST R-3.6.2.tar.gz 33311930 BLAKE2B 53f344e80e017064a275c271d98be714e210193931a120e7ebc79ee6cf0ebc0c24c090acc25560998f26600c05305147816ab782632d99beaea83b3a9b5e2a21 SHA512 17513e9f4dd27c61c11f7aa45227aeeeefb375bf5d4e193b471724f379a1b2da33e127cbe91aa175cbbbb048b892047e2f610280585c8159242a6c94790b07f9 DIST R-78d6830e28ea90a046da79a9b4f70c39594bb6d6.bash_completion 13596 BLAKE2B 53338e4a1c4f68beb69247216e553dbcac47f660fbf032bfebf7a660e32d2cff5b11ed35411c52de7e1fd6e00bbf5b5ea19369a325fa0a38bd93d63dc3288cbd SHA512 9ccd19bb1b0c18a2f13035ccd6809447429e197e298fb4d1df808ef345d723b42f75a1b91c349f6dbb46e4a82e59ef33e11300c495d79b63d670d0c0f2b16a06 diff --git a/dev-lang/R/R-3.6.2.ebuild b/dev-lang/R/R-3.6.2.ebuild new file mode 100644 index 00000000000..b428a111271 --- /dev/null +++ b/dev-lang/R/R-3.6.2.ebuild @@ -0,0 +1,207 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +inherit bash-completion-r1 autotools eutils flag-o-matic fortran-2 multilib 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 ~arm64 ~hppa ~ia64 ~sparc ~x86 ~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:3= + net-libs/libtirpc + net-misc/curl + virtual/blas:0 + || ( sys-apps/coreutils 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: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 + "${FILESDIR}"/${PN}-3.6.2-no-LDFLAGS-in-libR-pkg-config.patch + "${FILESDIR}"/${PN}-3.6.2-no-gzip-doc.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 + eautoreconf +} + +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 ${P}" + R CMD javareconf + fi +} diff --git a/dev-lang/R/files/R-3.6.2-no-LDFLAGS-in-libR-pkg-config.patch b/dev-lang/R/files/R-3.6.2-no-LDFLAGS-in-libR-pkg-config.patch new file mode 100644 index 00000000000..2bcf50ccadb --- /dev/null +++ b/dev-lang/R/files/R-3.6.2-no-LDFLAGS-in-libR-pkg-config.patch @@ -0,0 +1,11 @@ +--- R-3.6.2-orig/src/unix/Makefile.in 2019-03-29 10:02:31.000000000 +1100 ++++ R-3.6.2/src/unix/Makefile.in 2020-01-13 22:39:14.506804106 +1100 +@@ -79,7 +79,7 @@ + -e "s:@rincludedir:$(rincludedir):" \ + -e "s:@rarch:$(R_ARCH):" \ + -e 's:@libsprivate:$(STATIC_LIBR_PC):' \ +- -e 's:@others:$(MAIN_LDFLAGS) $(LDFLAGS):' \ ++ -e 's:@others:$(MAIN_LDFLAGS):' \ + -e 's/@VERSION/$(VERSION)/' $(srcdir)/libR.pc.in \ + > "$(DESTDIR)$(libdir)/pkgconfig/libR.pc" + diff --git a/dev-lang/R/files/R-3.6.2-no-gzip-doc.patch b/dev-lang/R/files/R-3.6.2-no-gzip-doc.patch new file mode 100644 index 00000000000..c87b6178052 --- /dev/null +++ b/dev-lang/R/files/R-3.6.2-no-gzip-doc.patch @@ -0,0 +1,10 @@ +--- R-3.6.2-orig/doc/manual/Makefile.in 2019-03-29 10:02:40.000000000 +1100 ++++ R-3.6.2/doc/manual/Makefile.in 2020-01-13 22:17:31.324967094 +1100 +@@ -345,7 +345,6 @@ + @$(ECHO) "installing R info pages ..." + @for f in $(OBJECTS_INFO:.info=.info*); do \ + $(INSTALL_DATA) $${f} "$(DESTDIR)$(infodir)"; \ +- $(R_GZIPCMD) -f "$(DESTDIR)$(infodir)/$${f}"; \ + done + @$(ECHO) "updating '$(infodir)/dir' ..." + @for f in $(OBJECTS_INFO); do \
