diff options
| -rw-r--r-- | dev-lang/R/Manifest | 1 | ||||
| -rw-r--r-- | dev-lang/R/R-4.2.3.ebuild | 248 | ||||
| -rw-r--r-- | dev-lang/R/files/R-4.2.2-browser-pdf-prefs.patch | 95 | ||||
| -rw-r--r-- | dev-lang/R/files/R-4.2.2-isspace-without-readline.patch | 22 | ||||
| -rw-r--r-- | dev-lang/R/files/R-4.2.2-parallel-rmath-h-install.patch | 23 | ||||
| -rw-r--r-- | dev-lang/R/files/R-4.2.3-curl-8.patch | 59 |
6 files changed, 0 insertions, 448 deletions
diff --git a/dev-lang/R/Manifest b/dev-lang/R/Manifest index 66ca1dcf1a07..92c9fed1a39b 100644 --- a/dev-lang/R/Manifest +++ b/dev-lang/R/Manifest @@ -1,3 +1,2 @@ -DIST R-4.2.3.tar.gz 34010655 BLAKE2B 688403c693de348bdc404c0ebc2df08d3415db216f6017beca8c0408dc70830239ba26ff89f020a249c8af6471363ed742f52c816da84aac8161ec4a522df405 SHA512 060bb4e1d1f1a5a0383a3b4372ac9247c0a20285020da17cebeb40ddc54da12d5f369ea243ea04d2c6970986fe22b3f9c37fbdfb3405cd8aa4f2353091ea9c5c DIST R-4.3.0.tar.gz 34821768 BLAKE2B 3505c8357419355fddb8aadbf0952c492e3e38d649d6261478d6187c94ff71110089ec0933a31dd2f7258e58a1d0864a68cb4d7b6cdefc54e5add55d0d62db10 SHA512 7f9bc8360818d7fdf05e26a4213df01468669514a4c2ad62dee358f53dcfa05a71ee72241db91fed59574c26d7caee5d3e0717637e1666daec99446e42c07813 DIST R-78d6830e28ea90a046da79a9b4f70c39594bb6d6.bash_completion 13596 BLAKE2B 53338e4a1c4f68beb69247216e553dbcac47f660fbf032bfebf7a660e32d2cff5b11ed35411c52de7e1fd6e00bbf5b5ea19369a325fa0a38bd93d63dc3288cbd SHA512 9ccd19bb1b0c18a2f13035ccd6809447429e197e298fb4d1df808ef345d723b42f75a1b91c349f6dbb46e4a82e59ef33e11300c495d79b63d670d0c0f2b16a06 diff --git a/dev-lang/R/R-4.2.3.ebuild b/dev-lang/R/R-4.2.3.ebuild deleted file mode 100644 index 9f94b563f46b..000000000000 --- a/dev-lang/R/R-4.2.3.ebuild +++ /dev/null @@ -1,248 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -inherit bash-completion-r1 autotools flag-o-matic fortran-2 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="https://www.r-project.org/" -SRC_URI=" - mirror://cran/src/base/R-4/${P}.tar.gz - https://raw.githubusercontent.com/deepayan/rcompletion/${BCPV}/bash_completion/R -> ${PN}-${BCPV}.bash_completion" - -LICENSE="|| ( GPL-2 GPL-3 ) LGPL-2.1" -SLOT="0" -KEYWORDS="amd64 arm64 ~hppa ~ia64 ~loong sparc ~x86 ~amd64-linux ~x86-linux" -IUSE="cairo doc icu java jpeg lapack lto minimal nls openmp perl png prefix profile readline test tiff tk X" - -REQUIRED_USE=" - png? ( || ( cairo X ) ) - jpeg? ( || ( cairo X ) ) - tiff? ( || ( cairo X ) )" -RESTRICT=" - minimal? ( test ) - !test? ( test )" - -# At least one package installation in the test suite requires TeX, -# and will fail without it (bug #718056). -DEPEND=" - app-arch/bzip2 - app-arch/xz-utils - app-text/ghostscript-gpl - dev-libs/libpcre2:= - >=dev-libs/tre-0.8.0_p20210321[approx] - net-misc/curl - virtual/blas - sys-libs/zlib[minizip] - || ( - sys-apps/coreutils - app-misc/realpath - ) - cairo? ( - x11-libs/cairo:=[X=] - x11-libs/pango:= - ) - icu? ( dev-libs/icu:= ) - jpeg? ( media-libs/libjpeg-turbo:= ) - kernel_linux? ( net-libs/libtirpc ) - lapack? ( virtual/lapack ) - perl? ( dev-lang/perl ) - png? ( media-libs/libpng:= ) - readline? ( sys-libs/readline:= ) - tiff? ( media-libs/tiff:= ) - tk? ( dev-lang/tk:= ) - X? ( - x11-libs/libXmu - x11-libs/libXt - )" -RDEPEND="${DEPEND} - java? ( >=virtual/jre-1.8:* )" -BDEPEND=" - virtual/pkgconfig - doc? ( - virtual/latex-base - dev-texlive/texlive-fontsrecommended - ) - test? ( virtual/latex-base )" - -PATCHES=( - "${FILESDIR}"/R-3.4.1-parallel.patch - "${FILESDIR}"/R-3.6.2-no-LDFLAGS-in-libR-pkg-config.patch - "${FILESDIR}"/R-3.6.2-no-gzip-doc.patch - "${FILESDIR}"/R-4.2.2-browser-pdf-prefs.patch - "${FILESDIR}"/R-4.2.2-isspace-without-readline.patch - "${FILESDIR}"/R-4.2.2-parallel-rmath-h-install.patch - "${FILESDIR}"/R-4.2.3-curl-8.patch -) - -pkg_pretend() { - [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp -} - -pkg_setup() { - if [[ ${MERGE_TYPE} != binary ]] && use openmp; then - tc-check-openmp - FORTRAN_NEED_OPENMP=1 - fi - - fortran-2_pkg_setup - - # avoid using existing R installation - unset R_HOME -} - -src_prepare() { - default - - # fix packages.html for doc (gentoo bug #205103) - sed -e "s:../../../library:../../../../$(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='\"${EPREFIX}/usr/$(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 $(grep -Flr ../manual/ doc) || die "sed for HTML links failed" - - use lapack && - export LAPACK_LIBS="$($(tc-getPKG_CONFIG) --libs lapack)" - - use perl && - export PERL5LIB="${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 (macOS) - 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 ${EPREFIX}/usr/$(get_libdir)/libRmath.dylib:" \ - -i src/nmath/standalone/Makefile.in || die - else - append-ldflags -Wl,-rpath="${EPREFIX}/usr/$(get_libdir)/R/lib" - fi - fi - - AT_M4DIR=m4 eautoreconf -} - -src_configure() { - filter-ldflags -Wl,-Bdirect -Bdirect - - econf \ - --enable-byte-compiled-packages \ - --enable-R-shlib \ - --disable-R-framework \ - --disable-R-static-lib \ - --with-blas="$($(tc-getPKG_CONFIG) --libs blas)" \ - rdocdir="${EPREFIX}/usr/share/doc/${PF}" \ - --with-system-tre \ - $(use_enable java) \ - $(use_enable lto lto R) \ - $(use_enable nls) \ - $(use_enable openmp) \ - $(use_enable profile R-profiling) \ - $(use_enable profile memory-profiling) \ - $(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) \ - $(use_with tk tk-config "${ESYSROOT}"/usr/$(get_libdir)/tkConfig.sh) \ - $(use_with tk tcl-config "${ESYSROOT}"/usr/$(get_libdir)/tclConfig.sh) \ - $(use_with X x) -} - -src_compile() { - export VARTEXFONTS="${T}"/fonts - emake AR="$(tc-getAR)" - emake -C src/nmath/standalone shared AR="$(tc-getAR)" - use doc && emake info pdf -} - -src_install() { - default - emake -C src/nmath/standalone DESTDIR="${D}" install - - if use doc; then - emake DESTDIR="${D}" install-info install-pdf - dosym ../manual /usr/share/doc/${PF}/html/manual - fi - - newenvd - 99R <<-_EOF_ - LDPATH="${EPREFIX}/usr/$(get_libdir)/${PN}/lib" - R_HOME="${EPREFIX}/usr/$(get_libdir)/${PN}" - _EOF_ - - newbashcomp "${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 || die - for mod in $(find . -name "*.dylib") ; do - mod=${mod#./} - install_name_tool -id "${EPREFIX}/usr/$(get_libdir)/R/${mod}" "${mod}" - done - popd >/dev/null || die - fi - - # Users are encouraged to access some of the the R documentation - # interactively, through functions like "contributors()" that - # tries to open the "AUTHORS" file. Other files can be accessed - # by name with RShowDoc(), and the documentation for e.g. license() - # and RShowDoc() suggests a few of these names. Here we try to - # collect as many names as possible that a user might actually - # try to view through R, because if we don't decompress them, - # then R doesn't know what to do with 'em. Bug #556706. - local INTERACTIVE_DOCS=( - AUTHORS - COPYING - FAQ - NEWS - THANKS - ) - - # Other data sources that are shipped as "documentation," but which - # need to be accessible via their original unmolested filenames. - local INTERACTIVE_DATA=( - BioC_mirrors.csv - CRAN_mirrors.csv - KEYWORDS.db - NEWS.rds - ) - - local f NOCOMPRESS_DOCS=( "${INTERACTIVE_DOCS[@]}" "${INTERACTIVE_DATA[@]}" ) - for f in "${NOCOMPRESS_DOCS[@]}"; do - docompress -x /usr/share/doc/${PF}/${f} - done - - # Finally, an extra copy of this started showing up at some point... - rm "${ED}"/usr/$(get_libdir)/R/COPYING || die -} - -pkg_postinst() { - if use java; then - einfo "Re-initializing java paths for ${P}" - R CMD javareconf - fi -} diff --git a/dev-lang/R/files/R-4.2.2-browser-pdf-prefs.patch b/dev-lang/R/files/R-4.2.2-browser-pdf-prefs.patch deleted file mode 100644 index b5a953cb6057..000000000000 --- a/dev-lang/R/files/R-4.2.2-browser-pdf-prefs.patch +++ /dev/null @@ -1,95 +0,0 @@ -From 6e48ab8b5006f3fdd8ef08f3f86406a02eabdc80 Mon Sep 17 00:00:00 2001 -From: Michael Orlitzky <michael@orlitzky.com> -Date: Mon, 12 Sep 2022 08:31:46 -0400 -Subject: [PATCH 1/3] m4/R.m4: prefer xdg-open for R_BROWSER and R_PDFVIEWER. - -The xdg-open utility (if it is present) will launch the user's -preferred browsr or PDF viewer when fed an HTML page or a PDF -document, respectively. It therefore makes sense to prefer it over -(for example) firefox, which may be installed but not the user's -preferred browser. ---- - m4/R.m4 | 4 ++-- - 1 file changed, 2 insertions(+), 2 deletions(-) - -diff --git a/m4/R.m4 b/m4/R.m4 -index bdcfbea..c5052e7 100644 ---- a/m4/R.m4 -+++ b/m4/R.m4 -@@ -237,7 +237,7 @@ fi]) - ## xdg-open is the freedesktop.org interface to kfmclient/gnome-open - AC_DEFUN([R_PROG_BROWSER], - [if test -z "${R_BROWSER}"; then -- AC_PATH_PROGS(R_BROWSER, [firefox mozilla galeon opera xdg-open kfmclient gnome-moz-remote open]) -+ AC_PATH_PROGS(R_BROWSER, [xdg-open firefox mozilla galeon opera kfmclient gnome-moz-remote open]) - fi - if test -z "${R_BROWSER}"; then - warn_browser="I could not determine a browser" -@@ -255,7 +255,7 @@ AC_SUBST(R_BROWSER) - ## the FreeBSD acroread port. - AC_DEFUN([R_PROG_PDFVIEWER], - [AC_PATH_PROGS(R_PDFVIEWER, -- [${R_PDFVIEWER} acroread acroread4 xdg-open evince xpdf gv gnome-gv ggv okular kpdf open gpdf kghostview]) -+ [${R_PDFVIEWER} xdg-open acroread acroread4 evince xpdf gv gnome-gv ggv okular kpdf open gpdf kghostview]) - if test -z "${R_PDFVIEWER}"; then - warn_pdfviewer="I could not determine a PDF viewer" - AC_MSG_WARN([${warn_pdfviewer}]) --- -2.35.1 - -From 4e50ed9c976a4422a6d431d3d078164948f26bda Mon Sep 17 00:00:00 2001 -From: Michael Orlitzky <michael@orlitzky.com> -Date: Mon, 12 Sep 2022 08:36:41 -0400 -Subject: [PATCH 2/3] m4/R.m4: add epiphany, lynx, and links to the R_BROWSER - search list. - -The epiphany browser is today one of the more popular ones, being the -"official" GNOME browser. And lynx and links are nice text-based -fallbacks. ---- - m4/R.m4 | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/m4/R.m4 b/m4/R.m4 -index c5052e7..e99b0f9 100644 ---- a/m4/R.m4 -+++ b/m4/R.m4 -@@ -237,7 +237,7 @@ fi]) - ## xdg-open is the freedesktop.org interface to kfmclient/gnome-open - AC_DEFUN([R_PROG_BROWSER], - [if test -z "${R_BROWSER}"; then -- AC_PATH_PROGS(R_BROWSER, [xdg-open firefox mozilla galeon opera kfmclient gnome-moz-remote open]) -+ AC_PATH_PROGS(R_BROWSER, [xdg-open firefox mozilla epiphany galeon opera kfmclient gnome-moz-remote open lynx links]) - fi - if test -z "${R_BROWSER}"; then - warn_browser="I could not determine a browser" --- -2.35.1 - -From 719294ed2548f79ab6a5861662716d853284f4d7 Mon Sep 17 00:00:00 2001 -From: Michael Orlitzky <michael@orlitzky.com> -Date: Mon, 12 Sep 2022 08:38:03 -0400 -Subject: [PATCH 3/3] m4/R.m4: add atril to the R_PDFVIEWER list. - -Atril is the PDF viewer for the MATE desktop, essentially a fork of -the gnome-2.x evince viewer. ---- - m4/R.m4 | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/m4/R.m4 b/m4/R.m4 -index e99b0f9..7e04ced 100644 ---- a/m4/R.m4 -+++ b/m4/R.m4 -@@ -255,7 +255,7 @@ AC_SUBST(R_BROWSER) - ## the FreeBSD acroread port. - AC_DEFUN([R_PROG_PDFVIEWER], - [AC_PATH_PROGS(R_PDFVIEWER, -- [${R_PDFVIEWER} xdg-open acroread acroread4 evince xpdf gv gnome-gv ggv okular kpdf open gpdf kghostview]) -+ [${R_PDFVIEWER} xdg-open acroread acroread4 evince atril xpdf gv gnome-gv ggv okular kpdf open gpdf kghostview]) - if test -z "${R_PDFVIEWER}"; then - warn_pdfviewer="I could not determine a PDF viewer" - AC_MSG_WARN([${warn_pdfviewer}]) --- -2.35.1 - diff --git a/dev-lang/R/files/R-4.2.2-isspace-without-readline.patch b/dev-lang/R/files/R-4.2.2-isspace-without-readline.patch deleted file mode 100644 index 0b32bef1352b..000000000000 --- a/dev-lang/R/files/R-4.2.2-isspace-without-readline.patch +++ /dev/null @@ -1,22 +0,0 @@ -From 6e36141598b78add7fb841480260b0a57ae79330 Mon Sep 17 00:00:00 2001 -From: smeyer <smeyer@00db46b3-68df-0310-9c12-caf00c1e9a41> -Date: Wed, 26 Oct 2022 08:22:41 +0000 -Subject: [PATCH] avoid implicit declaration of 'isspace' --without-readline - -git-svn-id: https://svn.r-project.org/R/trunk@83178 00db46b3-68df-0310-9c12-caf00c1e9a41 ---- - src/unix/sys-std.c | 1 + - 1 file changed, 1 insertion(+) - -diff --git a/src/unix/sys-std.c b/src/unix/sys-std.c -index 7b93d63884a..f95ff0cf7b3 100644 ---- a/src/unix/sys-std.c -+++ b/src/unix/sys-std.c -@@ -1339,6 +1339,7 @@ Rstd_ShowFiles(int nfile, /* number of files */ - */ - - -+#include <ctype.h> /* for isspace */ - - int attribute_hidden Rstd_ChooseFile(int _new, char *buf, int len) - { diff --git a/dev-lang/R/files/R-4.2.2-parallel-rmath-h-install.patch b/dev-lang/R/files/R-4.2.2-parallel-rmath-h-install.patch deleted file mode 100644 index 756ec8ff5428..000000000000 --- a/dev-lang/R/files/R-4.2.2-parallel-rmath-h-install.patch +++ /dev/null @@ -1,23 +0,0 @@ -From ee1428e77095e52a7396fa7b455f63b7c5b9495b Mon Sep 17 00:00:00 2001 -From: kalibera <kalibera@00db46b3-68df-0310-9c12-caf00c1e9a41> -Date: Tue, 27 Dec 2022 11:21:33 +0000 -Subject: [PATCH] Declare dependency to ensure include dir exists (PR#17743). - -git-svn-id: https://svn.r-project.org/R/trunk@83504 00db46b3-68df-0310-9c12-caf00c1e9a41 ---- - src/nmath/standalone/Makefile.in | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/src/nmath/standalone/Makefile.in b/src/nmath/standalone/Makefile.in -index 68b45006155..946795a0439 100644 ---- a/src/nmath/standalone/Makefile.in -+++ b/src/nmath/standalone/Makefile.in -@@ -151,7 +151,7 @@ install-strip: installdirs install-header install-pc - fi - @!(test -f libRmath.a) || $(SHELL) $(top_srcdir)/tools/copy-if-change libRmath.a $(DESTDIR)$(libdir)/libRmath.a - --install-header: -+install-header: installdirs - @(cd ../../include; $(MAKE) Rmath.h) - @WANT_R_FRAMEWORK_FALSE@ @$(SHELL) $(top_srcdir)/tools/copy-if-change ../../include/Rmath.h $(DESTDIR)$(includedir)/Rmath.h - @WANT_R_FRAMEWORK_TRUE@ @$(SHELL) $(top_srcdir)/tools/copy-if-change ../../include/Rmath.h $(R_FRAMEWORK_DIR)/Versions/$(FW_VERSION)/Resources/include/Rmath.h diff --git a/dev-lang/R/files/R-4.2.3-curl-8.patch b/dev-lang/R/files/R-4.2.3-curl-8.patch deleted file mode 100644 index 92ee3b0d5702..000000000000 --- a/dev-lang/R/files/R-4.2.3-curl-8.patch +++ /dev/null @@ -1,59 +0,0 @@ -https://bugs.gentoo.org/902993 - ---- a/configure -+++ b/configure -@@ -48533,7 +48533,7 @@ - done - - if test "x${have_libcurl}" = "xyes"; then --{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking if libcurl is version 7 and >= 7.28.0" >&5 -+{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking if libcurl is version 7 and >= 7.28.0 or version 8" >&5 - printf %s "checking if libcurl is version 7 and >= 7.28.0... " >&6; } - if test ${r_cv_have_curl728+y} - then : -@@ -48551,8 +48551,10 @@ - int main(int argc, const char * argv[]) - { - #ifdef LIBCURL_VERSION_MAJOR --#if LIBCURL_VERSION_MAJOR > 7 -+#if LIBCURL_VERSION_MAJOR > 8 - exit(1); -+#elif LIBCURL_VERSION_MAJOR == 8 -+ exit(0); - #elif LIBCURL_VERSION_MAJOR == 7 && LIBCURL_VERSION_MINOR >= 28 - exit(0); - #else ---- a/m4/R.m4 -+++ b/m4/R.m4 -@@ -4300,15 +4300,17 @@ - AC_CHECK_HEADERS(curl/curl.h, [have_libcurl=yes], [have_libcurl=no]) - - if test "x${have_libcurl}" = "xyes"; then --AC_CACHE_CHECK([if libcurl is version 7 and >= 7.28.0], [r_cv_have_curl728], -+AC_CACHE_CHECK([if libcurl is version 7 and >= 7.28.0 or verion 8], [r_cv_have_curl728_8], - [AC_RUN_IFELSE([AC_LANG_SOURCE([[ - #include <stdlib.h> - #include <curl/curl.h> - int main(int argc, const char * argv[]) - { - #ifdef LIBCURL_VERSION_MAJOR --#if LIBCURL_VERSION_MAJOR > 7 -+#if LIBCURL_VERSION_MAJOR > 8 - exit(1); -+#elif LIBCURL_VERSION_MAJOR == 8 -+ exit(0); - #elif LIBCURL_VERSION_MAJOR == 7 && LIBCURL_VERSION_MINOR >= 28 - exit(0); - #else -@@ -4318,9 +4320,9 @@ - exit(1); - #endif - } --]])], [r_cv_have_curl728=yes], [r_cv_have_curl728=no], [r_cv_have_curl728=no])]) -+]])], [r_cv_have_curl728_8=yes], [r_cv_have_curl728_8=no], [r_cv_have_curl728_8=no])]) - fi --if test "x${r_cv_have_curl728}" = xno; then -+if test "x${r_cv_have_curl728_8}" = xno; then - have_libcurl=no - fi - |