commit: 5a44f9d1cc382f7533212bd2d2662f3dcca3ad4b Author: Michael Orlitzky <mjo <AT> gentoo <DOT> org> AuthorDate: Tue Nov 22 19:21:34 2022 +0000 Commit: Michael Orlitzky <mjo <AT> gentoo <DOT> org> CommitDate: Tue Nov 22 21:40:45 2022 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=5a44f9d1
dev-lang/R: add 4.2.2 My upstream patches to the R_BROWSER and R_PDFVIEWER search order didn't land in this release, but we're already running eautoreconf, so we might as well include them. This lets us drop the dependency on xdg-utils, and remove the stanza (conditional on USE=X) that sets the default browser and viewer to xdg-open. We are also able to drop a patch to the test suite that was merged upstream. Closes: https://bugs.gentoo.org/458176 Closes: https://bugs.gentoo.org/879863 Signed-off-by: Michael Orlitzky <mjo <AT> gentoo.org> dev-lang/R/Manifest | 1 + dev-lang/R/R-4.2.2.ebuild | 246 +++++++++++++++++++++++ dev-lang/R/files/R-4.2.2-browser-pdf-prefs.patch | 95 +++++++++ 3 files changed, 342 insertions(+) diff --git a/dev-lang/R/Manifest b/dev-lang/R/Manifest index 8895d614d77a..b3d53118aec4 100644 --- a/dev-lang/R/Manifest +++ b/dev-lang/R/Manifest @@ -1,2 +1,3 @@ DIST R-4.2.1.tar.gz 37601544 BLAKE2B b898262a05c92e125c36a661a89be34b1698177832002f7aa21ccfcf0b30a06481e2154eea9e77a94b1ad8ca35c7bc4aead2be99b862dca7450acee1bec6a99f SHA512 c1baf46d22304c425dde79301183f80f99f2752300137b0b6f902c3e55e2419d5e9185c97de6e3c840a38f6345a6c334aa24161656d4a7f6fa01570390f1122f +DIST R-4.2.2.tar.gz 33987014 BLAKE2B 083d07b055308451e32133d378abc4aea7dd6da341554dca96ed5863fe2bc937aa3faa94bbd8d3620d3e6e020f806975cbc375ca28c599bd645267b97b2a49d4 SHA512 abbf1c7d016f8e1a9a0c4ad5dee2509a164449da34729f3e98d99ad8678ab398005fb8ed20288d4a6ed1e46ad4c70ad246f31a1a07aab99ba8fc6a5f02e1a309 DIST R-78d6830e28ea90a046da79a9b4f70c39594bb6d6.bash_completion 13596 BLAKE2B 53338e4a1c4f68beb69247216e553dbcac47f660fbf032bfebf7a660e32d2cff5b11ed35411c52de7e1fd6e00bbf5b5ea19369a325fa0a38bd93d63dc3288cbd SHA512 9ccd19bb1b0c18a2f13035ccd6809447429e197e298fb4d1df808ef345d723b42f75a1b91c349f6dbb46e4a82e59ef33e11300c495d79b63d670d0c0f2b16a06 diff --git a/dev-lang/R/R-4.2.2.ebuild b/dev-lang/R/R-4.2.2.ebuild new file mode 100644 index 000000000000..f7daf9d87167 --- /dev/null +++ b/dev-lang/R/R-4.2.2.ebuild @@ -0,0 +1,246 @@ +# Copyright 1999-2022 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 ~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 + "${FILESDIR}"/R-3.4.1-rmath-shared.patch + "${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 +) + +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 -j1 -C src/nmath/standalone DESTDIR="${D}" install + + if use doc; then + emake DESTDIR="${D}" install-info install-pdf + dosym ../manual /usr/share/doc/${PF}/html/manual + fi + + newenvd - 99R <<-_EOF_ + LDPATH="${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 ${P}" + R CMD javareconf + fi +} diff --git a/dev-lang/R/files/R-4.2.2-browser-pdf-prefs.patch b/dev-lang/R/files/R-4.2.2-browser-pdf-prefs.patch new file mode 100644 index 000000000000..b5a953cb6057 --- /dev/null +++ b/dev-lang/R/files/R-4.2.2-browser-pdf-prefs.patch @@ -0,0 +1,95 @@ +From 6e48ab8b5006f3fdd8ef08f3f86406a02eabdc80 Mon Sep 17 00:00:00 2001 +From: Michael Orlitzky <[email protected]> +Date: Mon, 12 Sep 2022 08:31:46 -0400 +Subject: [PATCH 1/3] m4/R.m4: prefer xdg-open for R_BROWSER and R_PDFVIEWER. + +The xdg-open utility (if it is present) will launch the user's +preferred browsr or PDF viewer when fed an HTML page or a PDF +document, respectively. It therefore makes sense to prefer it over +(for example) firefox, which may be installed but not the user's +preferred browser. +--- + m4/R.m4 | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/m4/R.m4 b/m4/R.m4 +index bdcfbea..c5052e7 100644 +--- a/m4/R.m4 ++++ b/m4/R.m4 +@@ -237,7 +237,7 @@ fi]) + ## xdg-open is the freedesktop.org interface to kfmclient/gnome-open + AC_DEFUN([R_PROG_BROWSER], + [if test -z "${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([${warn_pdfviewer}]) +-- +2.35.1 + +From 4e50ed9c976a4422a6d431d3d078164948f26bda Mon Sep 17 00:00:00 2001 +From: Michael Orlitzky <[email protected]> +Date: Mon, 12 Sep 2022 08:36:41 -0400 +Subject: [PATCH 2/3] m4/R.m4: add epiphany, lynx, and links to the R_BROWSER + search list. + +The epiphany browser is today one of the more popular ones, being the +"official" GNOME browser. And lynx and links are nice text-based +fallbacks. +--- + m4/R.m4 | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/m4/R.m4 b/m4/R.m4 +index c5052e7..e99b0f9 100644 +--- a/m4/R.m4 ++++ b/m4/R.m4 +@@ -237,7 +237,7 @@ fi]) + ## xdg-open is the freedesktop.org interface to kfmclient/gnome-open + AC_DEFUN([R_PROG_BROWSER], + [if test -z "${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 "${R_BROWSER}"; then + warn_browser="I could not determine a browser" +-- +2.35.1 + +From 719294ed2548f79ab6a5861662716d853284f4d7 Mon Sep 17 00:00:00 2001 +From: Michael Orlitzky <[email protected]> +Date: Mon, 12 Sep 2022 08:38:03 -0400 +Subject: [PATCH 3/3] m4/R.m4: add atril to the R_PDFVIEWER list. + +Atril is the PDF viewer for the MATE desktop, essentially a fork of +the gnome-2.x evince viewer. +--- + m4/R.m4 | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/m4/R.m4 b/m4/R.m4 +index e99b0f9..7e04ced 100644 +--- a/m4/R.m4 ++++ b/m4/R.m4 +@@ -255,7 +255,7 @@ AC_SUBST(R_BROWSER) + ## the FreeBSD acroread port. + AC_DEFUN([R_PROG_PDFVIEWER], + [AC_PATH_PROGS(R_PDFVIEWER, +- [${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 +
