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commit: 6b3b5b20fe9c71906a674908c8dd08d38706804b |
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Author: Michael Orlitzky <mjo <AT> gentoo <DOT> org> |
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AuthorDate: Mon Jul 12 14:07:28 2021 +0000 |
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Commit: Michael Orlitzky <mjo <AT> gentoo <DOT> org> |
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CommitDate: Mon Jul 12 14:11:40 2021 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=6b3b5b20 |
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|
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dev-lang/R: new version 4.1.0. |
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|
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New upstream version with a few other ebuild improvements: |
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|
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* Use https in HOMEPAGE. |
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* Remove workaround for upstream bug 17836. |
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* Add support (USE=lto) for link-time optimization. |
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* Remove an old gcc-4.x workaround. |
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|
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Closes: https://bugs.gentoo.org/792426 |
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Package-Manager: Portage-3.0.20, Repoman-3.0.2 |
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Signed-off-by: Michael Orlitzky <mjo <AT> gentoo.org> |
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|
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dev-lang/R/Manifest | 1 + |
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dev-lang/R/R-4.1.0.ebuild | 235 ++++++++++++++++++++++++++++++++++++++++++++++ |
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dev-lang/R/metadata.xml | 5 + |
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3 files changed, 241 insertions(+) |
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|
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diff --git a/dev-lang/R/Manifest b/dev-lang/R/Manifest |
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index 72da37844ea..e217fbc0125 100644 |
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--- a/dev-lang/R/Manifest |
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+++ b/dev-lang/R/Manifest |
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@@ -1,3 +1,4 @@ |
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DIST R-4.0.4.tar.gz 33687611 BLAKE2B 40cdfd98fe6c9193deb729d151631c2b0f935accf5ea6251704b633d2688278af1a5a67317152be023fb4a10315c64e473f58276bb0c3fadb1141c35391ad22e SHA512 811c4407a083eb776f92c3cbacb1dc7eada8890a8c27678c6c82bef9db52b1afaefeb408fbe11e46922740adee498f32e7ddf7451b3ab89cf60773737e47f8be |
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DIST R-4.0.5.tar.gz 32466444 BLAKE2B 5dbbd289f4fd6347b4109eecaf65b50b5793a83edddd2cb391c20473607f136d91a8e9f4ab9e453f6927d2ca9145762920424e3a1dcea89309afde56efd5d32c SHA512 6ff5b0f9cb6b17f66cde1f5585d1b33659dbae8919d34c2e593f68a0bff4d0425aa9704d99284d103702a9cd42f613311f3a87af6b939b1af65dcec80bf2ca8c |
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+DIST R-4.1.0.tar.gz 33714683 BLAKE2B 22ba966b5a29f153f3ce6cbc467e815c397e7c6aade0db62c7d2ae044056d9227da4dcb8fbf33e661548f4f434c328415e297c6b07b3932ef3f47358c2543f42 SHA512 41519bf06a1ebc2bb582e9a7c35d0e82e213312dec8147861a7f9b28ee750cd40dfbf02737602d05698641fcea6182b0da8131e83edacc358e98eca0a393b729 |
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DIST R-78d6830e28ea90a046da79a9b4f70c39594bb6d6.bash_completion 13596 BLAKE2B 53338e4a1c4f68beb69247216e553dbcac47f660fbf032bfebf7a660e32d2cff5b11ed35411c52de7e1fd6e00bbf5b5ea19369a325fa0a38bd93d63dc3288cbd SHA512 9ccd19bb1b0c18a2f13035ccd6809447429e197e298fb4d1df808ef345d723b42f75a1b91c349f6dbb46e4a82e59ef33e11300c495d79b63d670d0c0f2b16a06 |
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|
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diff --git a/dev-lang/R/R-4.1.0.ebuild b/dev-lang/R/R-4.1.0.ebuild |
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new file mode 100644 |
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index 00000000000..775e4cb5b02 |
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--- /dev/null |
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+++ b/dev-lang/R/R-4.1.0.ebuild |
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@@ -0,0 +1,235 @@ |
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+# Copyright 1999-2021 Gentoo Authors |
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+# Distributed under the terms of the GNU General Public License v2 |
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+ |
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+EAPI=7 |
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+ |
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+inherit bash-completion-r1 autotools flag-o-matic fortran-2 toolchain-funcs |
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+ |
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+# latest git commit for R bash completion: https://github.com/deepayan/rcompletion |
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+BCPV=78d6830e28ea90a046da79a9b4f70c39594bb6d6 |
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+ |
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+DESCRIPTION="Language and environment for statistical computing and graphics" |
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+HOMEPAGE="https://www.r-project.org/" |
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+SRC_URI=" |
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+ mirror://cran/src/base/R-4/${P}.tar.gz |
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+ https://raw.githubusercontent.com/deepayan/rcompletion/${BCPV}/bash_completion/R -> ${PN}-${BCPV}.bash_completion" |
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+ |
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+LICENSE="|| ( GPL-2 GPL-3 ) LGPL-2.1" |
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+SLOT="0" |
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+KEYWORDS="~amd64 ~arm64 ~hppa ~ia64 ~sparc ~x86 ~amd64-linux ~x86-linux" |
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+IUSE="cairo doc icu java jpeg lapack lto minimal nls openmp perl png prefix profile readline static-libs test tiff tk X" |
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+ |
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+REQUIRED_USE="png? ( || ( cairo X ) ) |
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+ jpeg? ( || ( cairo X ) ) |
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+ tiff? ( || ( cairo X ) ) |
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+" |
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+ |
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+# At least one package installation in the test suite requires TeX, |
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+# and will fail without it (bug #718056). |
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+BDEPEND="virtual/pkgconfig |
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+ doc? ( |
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+ virtual/latex-base |
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+ dev-texlive/texlive-fontsrecommended |
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+ ) |
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+ test? ( virtual/latex-base )" |
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+DEPEND=" |
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+ app-arch/bzip2:0= |
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+ app-arch/xz-utils:0= |
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+ app-text/ghostscript-gpl |
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+ dev-libs/libpcre2:= |
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+ net-libs/libtirpc |
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+ net-misc/curl |
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+ virtual/blas:0 |
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+ || ( sys-apps/coreutils app-misc/realpath ) |
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+ cairo? ( x11-libs/cairo:0=[X=] x11-libs/pango:0= ) |
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+ icu? ( dev-libs/icu:= ) |
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+ jpeg? ( virtual/jpeg:0 ) |
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+ lapack? ( virtual/lapack:0 ) |
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+ perl? ( dev-lang/perl ) |
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+ png? ( media-libs/libpng:0= ) |
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+ readline? ( sys-libs/readline:0= ) |
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+ tiff? ( media-libs/tiff:0= ) |
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+ tk? ( dev-lang/tk:0= ) |
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+ X? ( x11-libs/libXmu:0= x11-misc/xdg-utils )" |
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+ |
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+RDEPEND="${DEPEND} |
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+ sys-libs/zlib:0[minizip] |
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+ java? ( >=virtual/jre-1.8:* )" |
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+ |
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+RESTRICT="minimal? ( test ) |
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+ !test? ( test )" |
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+ |
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+PATCHES=( |
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+ "${FILESDIR}"/${PN}-3.4.1-parallel.patch |
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+ "${FILESDIR}"/${PN}-3.4.1-rmath-shared.patch |
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+ "${FILESDIR}"/${PN}-3.6.2-no-LDFLAGS-in-libR-pkg-config.patch |
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+ "${FILESDIR}"/${PN}-3.6.2-no-gzip-doc.patch |
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+) |
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+ |
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+pkg_pretend() { |
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+ [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp |
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+} |
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+ |
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+pkg_setup() { |
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+ if [[ ${MERGE_TYPE} != binary ]] && use openmp; then |
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+ FORTRAN_NEED_OPENMP=1 |
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+ fi |
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+ fortran-2_pkg_setup |
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+ filter-ldflags -Wl,-Bdirect -Bdirect |
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+ # avoid using existing R installation |
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+ unset R_HOME |
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+} |
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+ |
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+src_prepare() { |
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+ default |
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+ |
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+ # fix packages.html for doc (gentoo bug #205103) |
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+ sed -e "s:../../../library:../../../../$(get_libdir)/R/library:g" \ |
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+ -i src/library/tools/R/Rd.R || die |
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+ |
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+ # fix Rscript path when installed (gentoo bug #221061) |
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+ sed -e "s:-DR_HOME='\"\$(rhome)\"':-DR_HOME='\"${EROOT}/usr/$(get_libdir)/${PN}\"':" \ |
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+ -i src/unix/Makefile.in || die "sed unix Makefile failed" |
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+ |
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+ # fix HTML links to manual (gentoo bug #273957) |
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+ sed -e 's:\.\./manual/:manual/:g' \ |
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+ -i $(grep -Flr ../manual/ doc) || die "sed for HTML links failed" |
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+ |
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+ use lapack && \ |
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+ export LAPACK_LIBS="$($(tc-getPKG_CONFIG) --libs lapack)" |
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+ |
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+ if use X; then |
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+ export R_BROWSER="$(type -p xdg-open)" |
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+ export R_PDFVIEWER="$(type -p xdg-open)" |
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+ fi |
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+ use perl && \ |
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+ export PERL5LIB="${S}/share/perl:${PERL5LIB:+:}${PERL5LIB}" |
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+ |
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+ # don't search /usr/local |
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+ sed -i -e '/FLAGS=.*\/local\//c\: # removed by ebuild' configure.ac || die |
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+ # Fix for Darwin (OS X) |
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+ if use prefix; then |
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+ if [[ ${CHOST} == *-darwin* ]] ; then |
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+ sed -e 's:-install_name libR.dylib:-install_name ${libdir}/R/lib/libR.dylib:' \ |
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+ -e 's:-install_name libRlapack.dylib:-install_name ${libdir}/R/lib/libRlapack.dylib:' \ |
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+ -e 's:-install_name libRblas.dylib:-install_name ${libdir}/R/lib/libRblas.dylib:' \ |
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+ -e "/SHLIB_EXT/s/\.so/.dylib/" \ |
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+ -i configure.ac || die |
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+ # sort of "undo" 2.14.1-rmath-shared.patch |
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+ sed -e "s:-Wl,-soname=libRmath.so:-install_name ${EROOT}/usr/$(get_libdir)/libRmath.dylib:" \ |
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+ -i src/nmath/standalone/Makefile.in || die |
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+ else |
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+ append-ldflags -Wl,-rpath="${EROOT}/usr/$(get_libdir)/R/lib" |
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+ fi |
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+ fi |
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+ AT_M4DIR=m4 |
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+ eautoreconf |
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+} |
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+ |
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+src_configure() { |
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+ # --with-system-tre \ |
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+ # tre is patched from upstream |
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+ econf \ |
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+ --enable-byte-compiled-packages \ |
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+ --enable-R-shlib \ |
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+ --disable-R-framework \ |
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+ --with-blas="$($(tc-getPKG_CONFIG) --libs blas)" \ |
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+ rdocdir="${EPREFIX}/usr/share/doc/${PF}" \ |
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+ $(use_enable java) \ |
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+ $(use_enable lto lto R) |
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+ $(use_enable nls) \ |
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+ $(use_enable openmp) \ |
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+ $(use_enable profile R-profiling) \ |
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+ $(use_enable profile memory-profiling) \ |
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+ $(use_enable static-libs static) \ |
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+ $(use_enable static-libs R-static-lib) \ |
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+ $(use_with cairo) \ |
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+ $(use_with icu ICU) \ |
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+ $(use_with jpeg jpeglib) \ |
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+ $(use_with lapack) \ |
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+ $(use_with !minimal recommended-packages) \ |
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+ $(use_with png libpng) \ |
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+ $(use_with readline) \ |
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+ $(use_with tiff libtiff) \ |
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+ $(use_with tk tcltk) \ |
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+ $(use_with tk tk-config "${EPREFIX}"/usr/$(get_libdir)/tkConfig.sh) \ |
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+ $(use_with tk tcl-config "${EPREFIX}"/usr/$(get_libdir)/tclConfig.sh) \ |
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+ $(use_with X x) |
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+} |
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+ |
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+src_compile() { |
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+ export VARTEXFONTS="${T}/fonts" |
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+ emake AR="$(tc-getAR)" |
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+ emake -C src/nmath/standalone \ |
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+ shared $(use static-libs && echo static) AR="$(tc-getAR)" |
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+ use doc && emake info pdf |
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+} |
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+ |
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+src_install() { |
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+ default |
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+ emake -j1 -C src/nmath/standalone DESTDIR="${D}" install |
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+ |
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+ if use doc; then |
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+ emake DESTDIR="${D}" install-info install-pdf |
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+ dosym ../manual /usr/share/doc/${PF}/html/manual |
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+ fi |
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+ |
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+ cat > 99R <<-EOF |
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+ LDPATH=${EROOT}/usr/$(get_libdir)/${PN}/lib |
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+ R_HOME=${EROOT}/usr/$(get_libdir)/${PN} |
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+ EOF |
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+ doenvd 99R |
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+ newbashcomp "${DISTDIR}"/${PN}-${BCPV}.bash_completion ${PN} |
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+ # The buildsystem has a different understanding of install_names than |
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+ # we require. Since it builds modules like shared objects (wrong), many |
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+ # objects (all modules) get an incorrect install_name. Fixing the build |
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+ # system here is not really trivial. |
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+ if [[ ${CHOST} == *-darwin* ]] ; then |
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+ local mod |
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+ pushd "${ED}"/usr/$(get_libdir)/R > /dev/null |
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+ for mod in $(find . -name "*.dylib") ; do |
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+ mod=${mod#./} |
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+ install_name_tool -id "${EPREFIX}/usr/$(get_libdir)/R/${mod}" \ |
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+ "${mod}" |
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+ done |
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+ popd > /dev/null |
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+ fi |
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+ |
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+ # Users are encouraged to access some of the the R documentation |
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+ # interactively, through functions like "contributors()" that |
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+ # tries to open the "AUTHORS" file. Other files can be accessed |
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+ # by name with RShowDoc(), and the documentation for e.g. license() |
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+ # and RShowDoc() suggests a few of these names. Here we try to |
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+ # collect as many names as possible that a user might actually |
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+ # try to view through R, because if we don't decompress them, |
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+ # then R doesn't know what to do with 'em. Bug #556706. |
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+ INTERACTIVE_DOCS=( |
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+ AUTHORS |
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+ COPYING |
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+ FAQ |
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+ NEWS |
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+ THANKS |
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+ ) |
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+ |
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+ # Other data sources that are shipped as "documentation," but which |
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+ # need to be accessible via their original unmolested filenames. |
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+ INTERACTIVE_DATA=( |
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+ BioC_mirrors.csv |
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+ CRAN_mirrors.csv |
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+ KEYWORDS.db |
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+ NEWS.rds |
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+ ) |
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+ |
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+ NOCOMPRESS_DOCS=( "${INTERACTIVE_DOCS[@]}" "${INTERACTIVE_DATA[@]}" ) |
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+ |
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+ for f in "${NOCOMPRESS_DOCS[@]}"; do |
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+ docompress -x "/usr/share/doc/${PF}/${f}" |
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+ done |
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+} |
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+ |
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+pkg_postinst() { |
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+ if use java; then |
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+ einfo "Re-initializing java paths for ${P}" |
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+ R CMD javareconf |
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+ fi |
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+} |
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|
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diff --git a/dev-lang/R/metadata.xml b/dev-lang/R/metadata.xml |
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index 8972d9ed88c..e9bebc0e016 100644 |
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--- a/dev-lang/R/metadata.xml |
281 |
+++ b/dev-lang/R/metadata.xml |
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@@ -5,6 +5,11 @@ |
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<email>sci-mathematics@g.o</email> |
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<name>Gentoo Mathematics Project</name> |
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</maintainer> |
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+ <use> |
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+ <flag name="lto"> |
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+ Use link-time optimization for R and its recommended packages. |
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+ </flag> |
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+ </use> |
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<longdescription lang="en"> |
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R is GNU S, a system for statistical computation and graphics. It |
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consists of a language plus a run-time environment with graphics, a |