From 57c2e006d0af9ab77ced676461d7100cade4a716 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Wed, 23 Nov 2022 01:07:24 +0000 Subject: gentoo auto-resync : 23:11:2022 - 01:07:24 --- dev-lang/Manifest.gz | Bin 19348 -> 19353 bytes dev-lang/R/Manifest | 3 + dev-lang/R/R-4.2.2.ebuild | 246 +++++++++++++++++++++++ dev-lang/R/files/R-4.2.2-browser-pdf-prefs.patch | 95 +++++++++ 4 files changed, 344 insertions(+) create mode 100644 dev-lang/R/R-4.2.2.ebuild create mode 100644 dev-lang/R/files/R-4.2.2-browser-pdf-prefs.patch (limited to 'dev-lang') diff --git a/dev-lang/Manifest.gz b/dev-lang/Manifest.gz index a86fa5f04cad..47b82b4453a3 100644 Binary files a/dev-lang/Manifest.gz and b/dev-lang/Manifest.gz differ diff --git a/dev-lang/R/Manifest b/dev-lang/R/Manifest index 187f82cf0452..7f8468347cb6 100644 --- a/dev-lang/R/Manifest +++ b/dev-lang/R/Manifest @@ -3,7 +3,10 @@ AUX R-3.4.1-rmath-shared.patch 899 BLAKE2B 0aba9c1c5417531647bed3829d53909e6f398 AUX R-3.6.2-no-LDFLAGS-in-libR-pkg-config.patch 469 BLAKE2B ee716b068316bbac0c07fe44bef739a491af5f4e90ba268cf7db428350763d498ab0b1bc9efa02ac885d0ac64aa5d076deaac094725766e340cbcd9d7e839b22 SHA512 cb7bc73fd0f1aa4159b25bc76318074662afddafdef8acc8caf20afb98da6c065c3bd0895c4a7a7f18a174d21d59c0f054a46aa513db1b5b622a110e7c54e171 AUX R-3.6.2-no-gzip-doc.patch 443 BLAKE2B 1154e9f67f08e1d8b286152bd093789a0b94b3a2422bdb54d1d1d03729bd892811e68121309c41ef4323ed31efcea82f3e265b37445e9870bbd88c5413311345 SHA512 99678dbf809761a2991cd5cbe6ff5ba8d1c3e9388f69d94b30726caae4eee29ae50ee74aa24e3851d41559f804381ec18a2cd818b97b5417bf7ae660c93ad2a6 AUX R-4.2.1-reg-packages-testfix.patch 950 BLAKE2B 99823d76d11c8d76755304bb28019526d3b06ee1747d7fe2773d26c3234e29fc847194ad58204c5eb8a231c3c1b4cee8b9d9df2f850e288fb08f0c6a29fe4bab SHA512 4ade0da830d3d223d7a308ca332cdbaba6a61c2f8d893ac21ff3a9fff3491bf72deb12f806dc9574e41c1352e3f3afc570c6a7dbcaa980b3dab1c330fe91d9b5 +AUX R-4.2.2-browser-pdf-prefs.patch 3653 BLAKE2B 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c47085197e990eecc6d316980dddcd2f6b2a5f5cfeae4a92b2de2ee5733de56f1aaa182f0c4e8b1b62207518123b60150685edb2ee5b734098121f09e6d963f6 SHA512 d959b84becffe57ac8d49aef9d2d7a294a7428972a8e4e438e26f99c09b4515db3723a09f7a75a6c5649c5cff38898fa13d2f894181060a8eaff1ee4a12dd07d 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 ${P}" + R CMD javareconf + fi +} diff --git a/dev-lang/R/files/R-4.2.2-browser-pdf-prefs.patch b/dev-lang/R/files/R-4.2.2-browser-pdf-prefs.patch new file mode 100644 index 000000000000..b5a953cb6057 --- /dev/null +++ b/dev-lang/R/files/R-4.2.2-browser-pdf-prefs.patch @@ -0,0 +1,95 @@ +From 6e48ab8b5006f3fdd8ef08f3f86406a02eabdc80 Mon Sep 17 00:00:00 2001 +From: Michael Orlitzky +Date: Mon, 12 Sep 2022 08:31:46 -0400 +Subject: [PATCH 1/3] m4/R.m4: prefer xdg-open for R_BROWSER and R_PDFVIEWER. + +The xdg-open utility (if it is present) will launch the user's +preferred browsr or PDF viewer when fed an HTML page or a PDF +document, respectively. It therefore makes sense to prefer it over +(for example) firefox, which may be installed but not the user's +preferred browser. +--- + m4/R.m4 | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/m4/R.m4 b/m4/R.m4 +index bdcfbea..c5052e7 100644 +--- a/m4/R.m4 ++++ b/m4/R.m4 +@@ -237,7 +237,7 @@ fi]) + ## xdg-open is the freedesktop.org interface to kfmclient/gnome-open + AC_DEFUN([R_PROG_BROWSER], + [if test -z "${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([${warn_pdfviewer}]) +-- +2.35.1 + +From 4e50ed9c976a4422a6d431d3d078164948f26bda Mon Sep 17 00:00:00 2001 +From: Michael Orlitzky +Date: Mon, 12 Sep 2022 08:36:41 -0400 +Subject: [PATCH 2/3] m4/R.m4: add epiphany, lynx, and links to the R_BROWSER + search list. + +The epiphany browser is today one of the more popular ones, being the +"official" GNOME browser. And lynx and links are nice text-based +fallbacks. +--- + m4/R.m4 | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/m4/R.m4 b/m4/R.m4 +index c5052e7..e99b0f9 100644 +--- a/m4/R.m4 ++++ b/m4/R.m4 +@@ -237,7 +237,7 @@ fi]) + ## xdg-open is the freedesktop.org interface to kfmclient/gnome-open + AC_DEFUN([R_PROG_BROWSER], + [if test -z "${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 "${R_BROWSER}"; then + warn_browser="I could not determine a browser" +-- +2.35.1 + +From 719294ed2548f79ab6a5861662716d853284f4d7 Mon Sep 17 00:00:00 2001 +From: Michael Orlitzky +Date: Mon, 12 Sep 2022 08:38:03 -0400 +Subject: [PATCH 3/3] m4/R.m4: add atril to the R_PDFVIEWER list. + +Atril is the PDF viewer for the MATE desktop, essentially a fork of +the gnome-2.x evince viewer. +--- + m4/R.m4 | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/m4/R.m4 b/m4/R.m4 +index e99b0f9..7e04ced 100644 +--- a/m4/R.m4 ++++ b/m4/R.m4 +@@ -255,7 +255,7 @@ AC_SUBST(R_BROWSER) + ## the FreeBSD acroread port. + AC_DEFUN([R_PROG_PDFVIEWER], + [AC_PATH_PROGS(R_PDFVIEWER, +- [${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 + -- cgit v1.2.3