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commit: af2dc7c4efa9e3b453c745c0fb86e0c1e5be1421 |
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Author: Sébastien Fabbro <bicatali <AT> gentoo <DOT> org> |
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AuthorDate: Thu Jul 6 15:33:41 2017 +0000 |
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Commit: Sebastien Fabbro <bicatali <AT> gentoo <DOT> org> |
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CommitDate: Thu Jul 6 21:31:12 2017 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=af2dc7c4 |
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|
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dev-lang/R: version bump |
9 |
|
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Package-Manager: Portage-2.3.6, Repoman-2.3.2 |
11 |
|
12 |
dev-lang/R/Manifest | 2 + |
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dev-lang/R/R-3.4.1.ebuild | 204 ++++++++++++++++++++++++++++ |
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dev-lang/R/files/R-3.4.1-parallel.patch | 11 ++ |
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dev-lang/R/files/R-3.4.1-rmath-shared.patch | 21 +++ |
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4 files changed, 238 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 9ee4c158c3b..9403f0b02c9 100644 |
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--- a/dev-lang/R/Manifest |
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+++ b/dev-lang/R/Manifest |
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@@ -2,3 +2,5 @@ DIST R-20130129.bash_completion.bz2 4209 SHA256 487e969b94563fec98ec58de7e6142e9 |
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DIST R-3.2.2.tar.gz 29772864 SHA256 9c9152e74134b68b0f3a1c7083764adc1cb56fd8336bec003fd0ca550cd2461d SHA512 71ba470875262b9f00fb6970f209788df4dad30e0a28373b824b60d8bc6401afb7786e65387663c6490c7ddcd2bfd7f808a270a3e63238f3d7565d5f93607138 WHIRLPOOL fea59929ada1d67dafc6ad89409d18ad173af7990384033f490a00e0f794d9919aecf7cd37089d105fe03b9cf64d079e5d148622571cec3eb924c1c5bd00081e |
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DIST R-3.3.1.tar.gz 29848329 SHA256 3dc59ae5831f5380f83c169bac2103ad052efe0ecec4ffa74bde4d85a0fda9e2 SHA512 d0ff85e99b9ec9cac672aa30d7d1a854778c6a610bcc5336e8c60c8c74f20856f2bfeae085af793fad646ff45cb4677d9d6dcbaa18212591f72f00a02339f4cd WHIRLPOOL 6e2edb60173a54c8b25d16201c24176b3ea837287e6d306c9d2e2c4578764b0d469d9c17228b6be67dda646a4272f30b331dbbc6238a6e851eb5320f04c7f151 |
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DIST R-3.3.2.tar.gz 29440670 SHA256 d294ad21e9f574fb4828ebb3a94b8cb34f4f304a41687a994be00dd41a4e514c SHA512 06a98687c0b180cb0bfd57440ea26088212d9f48948d503136475bf54b42d72cfec5bea7e333c0cedd60733bd614dd0f8c2eced7e24478b6c89f48e8d0c43482 WHIRLPOOL a68112df87552cc6ca8cd6b78b99dda2a22b8f4cfcd87a4512d541d25ef21358ede1ba71b4d7e9f274bf4e4340de18355a777d9af2ed41c0a498fa11d91cf0d8 |
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+DIST R-3.4.1.tar.gz 30200109 SHA256 02b1135d15ea969a3582caeb95594a05e830a6debcdb5b85ed2d5836a6a3fc78 SHA512 19bd50c87dc001ef947c15c1760f27ac8986ff6b43c6d90d3093ae184e42963027ef06faf31ec57ac9e519af7a35a2f53f8ea23ef75d800ebbd02945cedc4651 WHIRLPOOL 1396303a7ef7a0e8920af867e6b68e171152578231c9a7ad5020b494124922aae634c1ce6d0f2b2f8441481736b93c3abffe142f2af78dbb0dbc754c4faec3f1 |
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+DIST R-78d6830e28ea90a046da79a9b4f70c39594bb6d6.bash_completion 13596 SHA256 7e452a23e0bd96b1076280448d130adab229b8ea37cd4531db77391868a31e97 SHA512 9ccd19bb1b0c18a2f13035ccd6809447429e197e298fb4d1df808ef345d723b42f75a1b91c349f6dbb46e4a82e59ef33e11300c495d79b63d670d0c0f2b16a06 WHIRLPOOL 49fd55e6a52d55f0aa15d3a117394793b6fba6f1b69a26911a2b2d7c40a65c8ec2246851edc3abb52849930c48e817ee62319ae8bc1db0a9b802c95fcb1554e0 |
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|
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diff --git a/dev-lang/R/R-3.4.1.ebuild b/dev-lang/R/R-3.4.1.ebuild |
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new file mode 100644 |
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index 00000000000..85556b03670 |
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--- /dev/null |
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+++ b/dev-lang/R/R-3.4.1.ebuild |
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@@ -0,0 +1,204 @@ |
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+# Copyright 1999-2017 Gentoo Foundation |
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+# Distributed under the terms of the GNU General Public License v2 |
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+ |
38 |
+EAPI=6 |
39 |
+ |
40 |
+inherit bash-completion-r1 autotools eutils flag-o-matic fortran-2 multilib versionator 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="http://www.r-project.org/" |
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+SRC_URI=" |
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+ mirror://cran/src/base/R-3/${P}.tar.gz |
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+ https://raw.githubusercontent.com/deepayan/rcompletion/${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 ~hppa ~ia64 ~ppc ~ppc64 ~sparc ~x86 ~x86-fbsd ~amd64-linux ~x86-linux ~x64-macos" |
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+IUSE="cairo doc icu java jpeg lapack minimal nls openmp perl png prefix profile readline static-libs tiff tk X" |
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+REQUIRED_USE="png? ( || ( cairo X ) ) jpeg? ( || ( cairo X ) ) tiff? ( || ( cairo X ) )" |
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+ |
57 |
+CDEPEND=" |
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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/libpcre-8.35:3= |
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+ net-misc/curl |
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+ virtual/blas:0 |
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+ || ( >=sys-apps/coreutils-8.15 sys-freebsd/freebsd-bin 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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+DEPEND="${CDEPEND} |
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+ virtual/pkgconfig |
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+ doc? ( |
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+ virtual/latex-base |
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+ dev-texlive/texlive-fontsrecommended |
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+ )" |
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+ |
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+RDEPEND="${CDEPEND} |
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+ >=sys-libs/zlib-1.2.5.1-r2:0[minizip] |
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+ java? ( >=virtual/jre-1.5 )" |
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+ |
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+RESTRICT="minimal? ( 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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+) |
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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 [[ ${MERGE_TYPE} != binary ]] && use openmp; then |
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+ if ! tc-check-openmp; then |
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+ ewarn "OpenMP is not available in your current selected compiler" |
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+ die "need openmp capable compiler" |
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+ fi |
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+ FORTRAN_NEED_OPENMP=1 |
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+ fi |
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+ fortran-2_pkg_setup |
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+ filter-ldflags -Wl,-Bdirect -Bdirect |
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+ # avoid using existing R installation |
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+ unset R_HOME |
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+ # Temporary fix for bug #419761 |
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+ if [[ ($(tc-getCC) == *gcc) && ($(gcc-version) == 4.7) ]]; then |
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+ append-flags -fno-ipa-cp-clone |
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+ fi |
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+} |
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+ |
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+src_prepare() { |
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+ default |
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+ |
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+ # fix packages.html for doc (gentoo bug #205103) |
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+ sed -e "s:../../../library:../../../../$(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 eaclocal |
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+ eautoconf |
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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)" \ |
170 |
+ --docdir="${EPREFIX}/usr/share/doc/${PF}" \ |
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+ rdocdir="${EPREFIX}/usr/share/doc/${PF}" \ |
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+ $(use_enable java) \ |
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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 \ |
197 |
+ shared $(use static-libs && echo static) AR="$(tc-getAR)" |
198 |
+ use doc && emake info pdf |
199 |
+} |
200 |
+ |
201 |
+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 |
218 |
+ # objects (all modules) get an incorrect install_name. Fixing the build |
219 |
+ # 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/${mod}" \ |
226 |
+ "${mod}" |
227 |
+ done |
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+ popd > /dev/null |
229 |
+ fi |
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+ docompress -x /usr/share/doc/${PF}/{BioC_mirrors.csv,CRAN_mirrors.csv,KEYWORDS.db,NEWS.rds} |
231 |
+} |
232 |
+ |
233 |
+pkg_postinst() { |
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+ if use java; then |
235 |
+ einfo "Re-initializing java paths for ${P}" |
236 |
+ R CMD javareconf |
237 |
+ fi |
238 |
+} |
239 |
|
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diff --git a/dev-lang/R/files/R-3.4.1-parallel.patch b/dev-lang/R/files/R-3.4.1-parallel.patch |
241 |
new file mode 100644 |
242 |
index 00000000000..6fac15b9ffb |
243 |
--- /dev/null |
244 |
+++ b/dev-lang/R/files/R-3.4.1-parallel.patch |
245 |
@@ -0,0 +1,11 @@ |
246 |
+--- a/src/include/Makefile.in 2017-07-05 23:09:09.682703655 +0000 |
247 |
++++ b/src/include/Makefile.in 2017-07-05 23:06:56.533612308 +0000 |
248 |
+@@ -81,7 +81,7 @@ |
249 |
+ Rmath.h0: $(srcdir)/Rmath.h0.in $(top_builddir)/config.status |
250 |
+ @cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ |
251 |
+ |
252 |
+-install: installdirs install-intl-@USE_INCLUDED_LIBINTL@ |
253 |
++install: $(OBJ_HEADERS) installdirs install-intl-@USE_INCLUDED_LIBINTL@ |
254 |
+ @for d in $(SUBDIRS); do \ |
255 |
+ (cd $${d} && $(MAKE) $@) || exit 1; \ |
256 |
+ done |
257 |
|
258 |
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 |
259 |
new file mode 100644 |
260 |
index 00000000000..8bc6233de6d |
261 |
--- /dev/null |
262 |
+++ b/dev-lang/R/files/R-3.4.1-rmath-shared.patch |
263 |
@@ -0,0 +1,21 @@ |
264 |
+--- a/src/nmath/standalone/Makefile.in 2017-07-05 23:20:26.098087600 +0000 |
265 |
++++ b/src/nmath/standalone/Makefile.in 2017-07-05 23:21:55.087480310 +0000 |
266 |
+@@ -64,7 +64,8 @@ |
267 |
+ Rexeclibdir_LTLIBRARIES = $(libRmath_la) |
268 |
+ libRmath_la_SOURCES = $(SOURCES) |
269 |
+ libRmath_la_OBJECTS = $(OBJECTS:.o=.lo) |
270 |
+-libRmath_la_LDFLAGS = |
271 |
++libRmath_la_LDFLAGS = -Wl,-soname=libRmath.so |
272 |
++libRmath_la_LIBADD = $(LIBM) |
273 |
+ |
274 |
+ CLEANFILES = Makedeps *.d *.o *.lo test check.log $(SOURCES) |
275 |
+ DISTCLEANFILES = Makefile $(Rexeclibdir_LIBRARIES) $(Rexeclibdir_LTLIBRARIES) |
276 |
+@@ -127,7 +128,7 @@ |
277 |
+ |
278 |
+ ## under peculiar circumstances, $(LIBM) here helps. |
279 |
+ $(libRmath_la): $(libRmath_la_OBJECTS) |
280 |
+- $(DYLIB_LINK) -o $@ $(libRmath_la_LDFLAGS) $(libRmath_la_OBJECTS) $(LIBM) |
281 |
++ $(DYLIB_LINK) $(libRmath_la_LDFLAGS) $(libRmath_la_OBJECTS) $(libRmath_la_LIBADD) -o $@ |
282 |
+ |
283 |
+ test: $(srcdir)/test.c |
284 |
+ $(CC) -o $@ $(ALL_CPPFLAGS) $(ALL_CFLAGS) $(srcdir)/test.c \ |