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authorV3n3RiX <venerix@koprulu.sector>2022-11-23 01:07:24 +0000
committerV3n3RiX <venerix@koprulu.sector>2022-11-23 01:07:24 +0000
commit57c2e006d0af9ab77ced676461d7100cade4a716 (patch)
treefedd61a96505af97dea0e78425b1b7a70b813a46 /dev-lang/R
parent664924d8659185e3b43f99ee8a0b88177efb93dc (diff)
gentoo auto-resync : 23:11:2022 - 01:07:24
Diffstat (limited to 'dev-lang/R')
-rw-r--r--dev-lang/R/Manifest3
-rw-r--r--dev-lang/R/R-4.2.2.ebuild246
-rw-r--r--dev-lang/R/files/R-4.2.2-browser-pdf-prefs.patch95
3 files changed, 344 insertions, 0 deletions
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 5083e6b99e0ae41a96193f92fbf2daec04a797996ceec68eb83973377173079e4101c07f594b507f29ba4d4d42c8fe22174847376df26f77bfe156bbd3705827 SHA512 06124b7f67c6cd29b2630239e62a73b2ecb13c34cc683a1f9152d492f9608f87f6da325a418869699e11e1bc4813c5c1a5ea95cc59d462d74c8e474e61f6fc3d
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
EBUILD R-4.2.1.ebuild 7216 BLAKE2B 2aaa42ab58b3408d544d6902ae4629a473aacf04802474296aad08a4c489cfa3312ca7a4464b3679f6670015356d0a54a1a0d9e55dcaf53638a0c9a3ae89e158 SHA512 7100728db02324e66ca3d2b7c597abdeddedabfde503dd62770dfc1912b9eff0f6dc3ace463fbab5c9141d5fb8ba303ee0dab200cdcdd82df8d9940cad8923be
+EBUILD R-4.2.2.ebuild 7096 BLAKE2B d57411cb7f555c05ab98a2e6c81b98deee31cbd8e6414e4ef06573513f6005476455fc1c0d860b9cd3363e19e8161e1273f04995382978dae769babaa92e5322 SHA512 47e0ace8deef07f0c7f50b07740c9318f4216a6d0ff2d9b9acca98f14090113c3adebc71ed8deb56040372c8265756833b8dff99098681047a223018e4dd53ba
MISC metadata.xml 1344 BLAKE2B 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 ${P}"
+ R CMD javareconf
+ fi
+}
diff --git a/dev-lang/R/files/R-4.2.2-browser-pdf-prefs.patch b/dev-lang/R/files/R-4.2.2-browser-pdf-prefs.patch
new file mode 100644
index 000000000000..b5a953cb6057
--- /dev/null
+++ b/dev-lang/R/files/R-4.2.2-browser-pdf-prefs.patch
@@ -0,0 +1,95 @@
+From 6e48ab8b5006f3fdd8ef08f3f86406a02eabdc80 Mon Sep 17 00:00:00 2001
+From: Michael Orlitzky <michael@orlitzky.com>
+Date: Mon, 12 Sep 2022 08:31:46 -0400
+Subject: [PATCH 1/3] m4/R.m4: prefer xdg-open for R_BROWSER and R_PDFVIEWER.
+
+The xdg-open utility (if it is present) will launch the user's
+preferred browsr or PDF viewer when fed an HTML page or a PDF
+document, respectively. It therefore makes sense to prefer it over
+(for example) firefox, which may be installed but not the user's
+preferred browser.
+---
+ m4/R.m4 | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/m4/R.m4 b/m4/R.m4
+index bdcfbea..c5052e7 100644
+--- a/m4/R.m4
++++ b/m4/R.m4
+@@ -237,7 +237,7 @@ fi])
+ ## xdg-open is the freedesktop.org interface to kfmclient/gnome-open
+ AC_DEFUN([R_PROG_BROWSER],
+ [if test -z "${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
+