* [gentoo-commits] repo/gentoo:master commit in: dev-lang/R/files/, dev-lang/R/
@ 2017-01-05 19:26 Justin Lecher
0 siblings, 0 replies; 7+ messages in thread
From: Justin Lecher @ 2017-01-05 19:26 UTC (permalink / raw
To: gentoo-commits
commit: 17331c2f15ee02bc370d3e2e6a596d377552eb42
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Jan 5 19:25:46 2017 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Jan 5 19:26:13 2017 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=17331c2f
dev-lang/R: Backport patch for zlib-1.2.10 compatibility
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=604676
Package-Manager: Portage-2.3.3, Repoman-2.3.1
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
dev-lang/R/R-3.3.2.ebuild | 5 +++--
dev-lang/R/files/R-3.3.2-zlib-1.2.10-backport.patch | 20 ++++++++++++++++++++
2 files changed, 23 insertions(+), 2 deletions(-)
diff --git a/dev-lang/R/R-3.3.2.ebuild b/dev-lang/R/R-3.3.2.ebuild
index ceeeaf9..bc68f82 100644
--- a/dev-lang/R/R-3.3.2.ebuild
+++ b/dev-lang/R/R-3.3.2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -72,7 +72,8 @@ src_prepare() {
epatch \
"${FILESDIR}"/${PN}-2.11.1-parallel.patch \
"${FILESDIR}"/${PN}-2.13.1-zlib_header_fix.patch \
- "${FILESDIR}"/${PN}-3.0.0-rmath-shared.patch
+ "${FILESDIR}"/${PN}-3.0.0-rmath-shared.patch \
+ "${FILESDIR}"/${P}-zlib-1.2.10-backport.patch
# fix packages.html for doc (gentoo bug #205103)
sed -i \
diff --git a/dev-lang/R/files/R-3.3.2-zlib-1.2.10-backport.patch b/dev-lang/R/files/R-3.3.2-zlib-1.2.10-backport.patch
new file mode 100644
index 00000000..2cfb30d
--- /dev/null
+++ b/dev-lang/R/files/R-3.3.2-zlib-1.2.10-backport.patch
@@ -0,0 +1,20 @@
+Index: R.m4
+===================================================================
+--- m4/R.m4 (revision 71152)
++++ m4/R.m4 (revision 71889)
+@@ -3105,10 +3105,11 @@
+ #include <string.h>
+ #include <zlib.h>
+ int main() {
+-#ifdef ZLIB_VERSION
+-/* Work around Debian bug: it uses 1.2.3.4 even though there was no such
+- version on the master site zlib.net */
+- exit(strncmp(ZLIB_VERSION, "1.2.5", 5) < 0);
++#ifdef ZLIB_VERNUM
++ if (ZLIB_VERNUM < 0x1250) {
++ exit(1);
++ }
++ exit(0);
+ #else
+ exit(1);
+ #endif
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: dev-lang/R/files/, dev-lang/R/
@ 2022-09-15 15:51 Michael Orlitzky
0 siblings, 0 replies; 7+ messages in thread
From: Michael Orlitzky @ 2022-09-15 15:51 UTC (permalink / raw
To: gentoo-commits
commit: 6162fb237663bbe61114cf13951715c141d51bba
Author: Michael Orlitzky <mjo <AT> gentoo <DOT> org>
AuthorDate: Thu Sep 15 15:47:56 2022 +0000
Commit: Michael Orlitzky <mjo <AT> gentoo <DOT> org>
CommitDate: Thu Sep 15 15:49:34 2022 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=6162fb23
dev-lang/R: backport a fix for a broken test.
This isn't a critical fix by any means, but otherwise we're likely to
forget to re-enable this test when R-4.2.2 comes out.
Signed-off-by: Michael Orlitzky <mjo <AT> gentoo.org>
dev-lang/R/R-4.2.1.ebuild | 14 +++++-------
.../R/files/R-4.2.1-reg-packages-testfix.patch | 25 ++++++++++++++++++++++
2 files changed, 30 insertions(+), 9 deletions(-)
diff --git a/dev-lang/R/R-4.2.1.ebuild b/dev-lang/R/R-4.2.1.ebuild
index cfb2a07ff6bc..1ee01869a453 100644
--- a/dev-lang/R/R-4.2.1.ebuild
+++ b/dev-lang/R/R-4.2.1.ebuild
@@ -71,10 +71,11 @@ BDEPEND="
test? ( virtual/latex-base )"
PATCHES=(
- "${FILESDIR}"/${PN}-3.4.1-parallel.patch
- "${FILESDIR}"/${PN}-3.4.1-rmath-shared.patch
- "${FILESDIR}"/${PN}-3.6.2-no-LDFLAGS-in-libR-pkg-config.patch
- "${FILESDIR}"/${PN}-3.6.2-no-gzip-doc.patch
+ "${FILESDIR}"/R-3.4.1-parallel.patch
+ "${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-4.2.1-reg-packages-testfix.patch
)
pkg_pretend() {
@@ -108,11 +109,6 @@ src_prepare() {
sed -e 's:\.\./manual/:manual/:g' \
-i $(grep -Flr ../manual/ doc) || die "sed for HTML links failed"
- # Disable this test until it passes again,
- # https://bugs.r-project.org/show_bug.cgi?id=18338
- sed -e 's/ reg-packages.R / /' \
- -i tests/Makefile.common || die
-
use lapack &&
export LAPACK_LIBS="$($(tc-getPKG_CONFIG) --libs lapack)"
diff --git a/dev-lang/R/files/R-4.2.1-reg-packages-testfix.patch b/dev-lang/R/files/R-4.2.1-reg-packages-testfix.patch
new file mode 100644
index 000000000000..f5fe9667ad67
--- /dev/null
+++ b/dev-lang/R/files/R-4.2.1-reg-packages-testfix.patch
@@ -0,0 +1,25 @@
+diff --git a/tests/reg-packages.R b/tests/reg-packages.R
+index c9962ce..2d36d1e 100644
+--- a/tests/reg-packages.R
++++ b/tests/reg-packages.R
+@@ -260,7 +260,8 @@ stopifnot(exprs = {
+ (lenN <- length(print(iN <- grep("^[1-9][0-9]:", tlines)))) >= 2
+ iN - iw == seq_len(lenN) # these (3) lines come immediately after 'Warning',
+ ## and "related" to the some 'missing .. paren' above:
+- 8 <= print(iw - i) & iw - i <= 20 # see ~14
++ !is.na(ierr <- as.integer(substr(print(tlines[iN[1]]), 1, 2)))
++ 8 <= print(ierr - i) & ierr - i <= 14 # see 11
+ }) ## failed in R <= 4.1.1
+
+
+@@ -495,8 +496,8 @@ checkMatrix(ap, 4)
+
+
+ ## clean up
+-rmL <- c("myLib", if(has.symlink) "myLib_2", "myTst", file.path(pkgPath),
+- oldpkgdir, newpkgdir, repodir, backupPfiles)
++rmL <- c("myLib", if(has.symlink) "myLib_2", "myTst", "myTst2",
++ "PR17501.Rcheck")
+ if(do.cleanup) {
+ for(nm in rmL) unlink(nm, recursive = TRUE)
+ } else {
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: dev-lang/R/files/, dev-lang/R/
@ 2022-11-22 21:50 Michael Orlitzky
0 siblings, 0 replies; 7+ messages in thread
From: Michael Orlitzky @ 2022-11-22 21:50 UTC (permalink / raw
To: gentoo-commits
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 ${P}"
+ R CMD javareconf
+ fi
+}
diff --git a/dev-lang/R/files/R-4.2.2-browser-pdf-prefs.patch b/dev-lang/R/files/R-4.2.2-browser-pdf-prefs.patch
new file mode 100644
index 000000000000..b5a953cb6057
--- /dev/null
+++ b/dev-lang/R/files/R-4.2.2-browser-pdf-prefs.patch
@@ -0,0 +1,95 @@
+From 6e48ab8b5006f3fdd8ef08f3f86406a02eabdc80 Mon Sep 17 00:00:00 2001
+From: Michael Orlitzky <michael@orlitzky.com>
+Date: Mon, 12 Sep 2022 08:31:46 -0400
+Subject: [PATCH 1/3] m4/R.m4: prefer xdg-open for R_BROWSER and R_PDFVIEWER.
+
+The xdg-open utility (if it is present) will launch the user's
+preferred browsr or PDF viewer when fed an HTML page or a PDF
+document, respectively. It therefore makes sense to prefer it over
+(for example) firefox, which may be installed but not the user's
+preferred browser.
+---
+ m4/R.m4 | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/m4/R.m4 b/m4/R.m4
+index bdcfbea..c5052e7 100644
+--- a/m4/R.m4
++++ b/m4/R.m4
+@@ -237,7 +237,7 @@ fi])
+ ## xdg-open is the freedesktop.org interface to kfmclient/gnome-open
+ AC_DEFUN([R_PROG_BROWSER],
+ [if test -z "${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([${warn_pdfviewer}])
+--
+2.35.1
+
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: dev-lang/R/files/, dev-lang/R/
@ 2022-12-23 14:28 Michael Orlitzky
0 siblings, 0 replies; 7+ messages in thread
From: Michael Orlitzky @ 2022-12-23 14:28 UTC (permalink / raw
To: gentoo-commits
commit: 3371015e23a4c2fc0f6a8d566b80942c7bb15ed2
Author: Michael Orlitzky <mjo <AT> gentoo <DOT> org>
AuthorDate: Fri Dec 23 06:12:37 2022 +0000
Commit: Michael Orlitzky <mjo <AT> gentoo <DOT> org>
CommitDate: Fri Dec 23 14:23:36 2022 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3371015e
dev-lang/R: add upstream patch to fix USE="-readline" build.
Closes: https://bugs.gentoo.org/883395
Signed-off-by: Michael Orlitzky <mjo <AT> gentoo.org>
dev-lang/R/R-4.2.2.ebuild | 1 +
.../R/files/R-4.2.2-isspace-without-readline.patch | 22 ++++++++++++++++++++++
2 files changed, 23 insertions(+)
diff --git a/dev-lang/R/R-4.2.2.ebuild b/dev-lang/R/R-4.2.2.ebuild
index f7daf9d87167..b1adfb0f9f9a 100644
--- a/dev-lang/R/R-4.2.2.ebuild
+++ b/dev-lang/R/R-4.2.2.ebuild
@@ -76,6 +76,7 @@ PATCHES=(
"${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
)
pkg_pretend() {
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
new file mode 100644
index 000000000000..0b32bef1352b
--- /dev/null
+++ b/dev-lang/R/files/R-4.2.2-isspace-without-readline.patch
@@ -0,0 +1,22 @@
+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)
+ {
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: dev-lang/R/files/, dev-lang/R/
@ 2023-03-26 12:05 David Seifert
0 siblings, 0 replies; 7+ messages in thread
From: David Seifert @ 2023-03-26 12:05 UTC (permalink / raw
To: gentoo-commits
commit: 0f664a055fc55677cda7cdf18b0e5b62978d5b8c
Author: Alexandre Ferreira <alexandref75 <AT> gmail <DOT> com>
AuthorDate: Sun Mar 26 12:05:27 2023 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Mar 26 12:05:27 2023 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=0f664a05
dev-lang/R: add patch for curl 8
Closes: https://bugs.gentoo.org/902993
Signed-off-by: David Seifert <soap <AT> gentoo.org>
dev-lang/R/R-4.2.3.ebuild | 3 +-
dev-lang/R/files/R-4.2.3-curl-8.patch | 59 +++++++++++++++++++++++++++++++++++
2 files changed, 61 insertions(+), 1 deletion(-)
diff --git a/dev-lang/R/R-4.2.3.ebuild b/dev-lang/R/R-4.2.3.ebuild
index f07363fe354d..5fa0d6b05b51 100644
--- a/dev-lang/R/R-4.2.3.ebuild
+++ b/dev-lang/R/R-4.2.3.ebuild
@@ -76,7 +76,8 @@ PATCHES=(
"${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-4.2.2-parallel-rmath-h-install.patch
+ "${FILESDIR}"/R-4.2.3-curl-8.patch
)
pkg_pretend() {
diff --git a/dev-lang/R/files/R-4.2.3-curl-8.patch b/dev-lang/R/files/R-4.2.3-curl-8.patch
new file mode 100644
index 000000000000..92ee3b0d5702
--- /dev/null
+++ b/dev-lang/R/files/R-4.2.3-curl-8.patch
@@ -0,0 +1,59 @@
+https://bugs.gentoo.org/902993
+
+--- a/configure
++++ b/configure
+@@ -48533,7 +48533,7 @@
+ done
+
+ if test "x${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
+
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: dev-lang/R/files/, dev-lang/R/
@ 2023-05-11 9:23 David Seifert
0 siblings, 0 replies; 7+ messages in thread
From: David Seifert @ 2023-05-11 9:23 UTC (permalink / raw
To: gentoo-commits
commit: f8f5c9b4a76934fd2c2f4774aa63bf6a1a40ff6e
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Thu May 11 09:23:44 2023 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Thu May 11 09:23:44 2023 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=f8f5c9b4
dev-lang/R: drop 4.2.1, 4.2.2
Signed-off-by: David Seifert <soap <AT> gentoo.org>
dev-lang/R/Manifest | 2 -
dev-lang/R/R-4.2.1.ebuild | 250 ---------------------
dev-lang/R/R-4.2.2.ebuild | 248 --------------------
dev-lang/R/files/R-3.4.1-rmath-shared.patch | 21 --
.../R/files/R-4.2.1-reg-packages-testfix.patch | 25 ---
5 files changed, 546 deletions(-)
diff --git a/dev-lang/R/Manifest b/dev-lang/R/Manifest
index cb99b76da339..66ca1dcf1a07 100644
--- a/dev-lang/R/Manifest
+++ b/dev-lang/R/Manifest
@@ -1,5 +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-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-4.2.1.ebuild b/dev-lang/R/R-4.2.1.ebuild
deleted file mode 100644
index 0fda9d9aacd0..000000000000
--- a/dev-lang/R/R-4.2.1.ebuild
+++ /dev/null
@@ -1,250 +0,0 @@
-# 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
- x11-misc/xdg-utils
- )"
-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-4.2.1-reg-packages-testfix.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 $(grep -Flr ../manual/ doc) || die "sed for HTML links failed"
-
- use lapack &&
- export LAPACK_LIBS="$($(tc-getPKG_CONFIG) --libs lapack)"
-
- if use X; then
- export R_BROWSER="$(type -p xdg-open)"
- export R_PDFVIEWER="$(type -p xdg-open)"
- fi
- use perl &&
- export PERL5LIB="${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 ${P}"
- R CMD javareconf
- fi
-}
diff --git a/dev-lang/R/R-4.2.2.ebuild b/dev-lang/R/R-4.2.2.ebuild
deleted file mode 100644
index 0ccb36ebf04c..000000000000
--- a/dev-lang/R/R-4.2.2.ebuild
+++ /dev/null
@@ -1,248 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit bash-completion-r1 autotools flag-o-matic fortran-2 toolchain-funcs
-
-# latest git commit for R bash completion:
-# https://github.com/deepayan/rcompletion
-BCPV=78d6830e28ea90a046da79a9b4f70c39594bb6d6
-
-DESCRIPTION="Language and environment for statistical computing and graphics"
-HOMEPAGE="https://www.r-project.org/"
-SRC_URI="
- mirror://cran/src/base/R-4/${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
- "${FILESDIR}"/R-3.4.1-rmath-shared.patch
- "${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
- "${FILESDIR}"/R-4.2.2-isspace-without-readline.patch
- "${FILESDIR}/"R-4.2.2-parallel-rmath-h-install.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-3.4.1-rmath-shared.patch b/dev-lang/R/files/R-3.4.1-rmath-shared.patch
deleted file mode 100644
index 8bc6233de6df..000000000000
--- a/dev-lang/R/files/R-3.4.1-rmath-shared.patch
+++ /dev/null
@@ -1,21 +0,0 @@
---- a/src/nmath/standalone/Makefile.in 2017-07-05 23:20:26.098087600 +0000
-+++ b/src/nmath/standalone/Makefile.in 2017-07-05 23:21:55.087480310 +0000
-@@ -64,7 +64,8 @@
- Rexeclibdir_LTLIBRARIES = $(libRmath_la)
- libRmath_la_SOURCES = $(SOURCES)
- libRmath_la_OBJECTS = $(OBJECTS:.o=.lo)
--libRmath_la_LDFLAGS =
-+libRmath_la_LDFLAGS = -Wl,-soname=libRmath.so
-+libRmath_la_LIBADD = $(LIBM)
-
- CLEANFILES = Makedeps *.d *.o *.lo test check.log $(SOURCES)
- DISTCLEANFILES = Makefile $(Rexeclibdir_LIBRARIES) $(Rexeclibdir_LTLIBRARIES)
-@@ -127,7 +128,7 @@
-
- ## under peculiar circumstances, $(LIBM) here helps.
- $(libRmath_la): $(libRmath_la_OBJECTS)
-- $(DYLIB_LINK) -o $@ $(libRmath_la_LDFLAGS) $(libRmath_la_OBJECTS) $(LIBM)
-+ $(DYLIB_LINK) $(libRmath_la_LDFLAGS) $(libRmath_la_OBJECTS) $(libRmath_la_LIBADD) -o $@
-
- test: $(srcdir)/test.c
- $(CC) -o $@ $(ALL_CPPFLAGS) $(ALL_CFLAGS) $(srcdir)/test.c \
diff --git a/dev-lang/R/files/R-4.2.1-reg-packages-testfix.patch b/dev-lang/R/files/R-4.2.1-reg-packages-testfix.patch
deleted file mode 100644
index f5fe9667ad67..000000000000
--- a/dev-lang/R/files/R-4.2.1-reg-packages-testfix.patch
+++ /dev/null
@@ -1,25 +0,0 @@
-diff --git a/tests/reg-packages.R b/tests/reg-packages.R
-index c9962ce..2d36d1e 100644
---- a/tests/reg-packages.R
-+++ b/tests/reg-packages.R
-@@ -260,7 +260,8 @@ stopifnot(exprs = {
- (lenN <- length(print(iN <- grep("^[1-9][0-9]:", tlines)))) >= 2
- iN - iw == seq_len(lenN) # these (3) lines come immediately after 'Warning',
- ## and "related" to the some 'missing .. paren' above:
-- 8 <= print(iw - i) & iw - i <= 20 # see ~14
-+ !is.na(ierr <- as.integer(substr(print(tlines[iN[1]]), 1, 2)))
-+ 8 <= print(ierr - i) & ierr - i <= 14 # see 11
- }) ## failed in R <= 4.1.1
-
-
-@@ -495,8 +496,8 @@ checkMatrix(ap, 4)
-
-
- ## clean up
--rmL <- c("myLib", if(has.symlink) "myLib_2", "myTst", file.path(pkgPath),
-- oldpkgdir, newpkgdir, repodir, backupPfiles)
-+rmL <- c("myLib", if(has.symlink) "myLib_2", "myTst", "myTst2",
-+ "PR17501.Rcheck")
- if(do.cleanup) {
- for(nm in rmL) unlink(nm, recursive = TRUE)
- } else {
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: dev-lang/R/files/, dev-lang/R/
@ 2023-06-28 12:39 David Seifert
0 siblings, 0 replies; 7+ messages in thread
From: David Seifert @ 2023-06-28 12:39 UTC (permalink / raw
To: gentoo-commits
commit: e2ad71232800cc6604db4476a679fa06603b9b0e
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Wed Jun 28 12:39:04 2023 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Wed Jun 28 12:39:04 2023 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e2ad7123
dev-lang/R: rebase patches
Signed-off-by: David Seifert <soap <AT> gentoo.org>
dev-lang/R/R-4.3.0.ebuild | 6 +++---
...pkg-config.patch => R-4.3.0-no-LDFLAGS-in-libR-pkg-config.patch} | 0
.../files/{R-3.6.2-no-gzip-doc.patch => R-4.3.0-no-gzip-doc.patch} | 0
dev-lang/R/files/{R-3.4.1-parallel.patch => R-4.3.0-parallel.patch} | 0
4 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/dev-lang/R/R-4.3.0.ebuild b/dev-lang/R/R-4.3.0.ebuild
index ca6b74443472..e061cc99a441 100644
--- a/dev-lang/R/R-4.3.0.ebuild
+++ b/dev-lang/R/R-4.3.0.ebuild
@@ -71,9 +71,9 @@ BDEPEND="
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
+ "${FILESDIR}"/R-4.3.0-parallel.patch
+ "${FILESDIR}"/R-4.3.0-no-LDFLAGS-in-libR-pkg-config.patch
+ "${FILESDIR}"/R-4.3.0-no-gzip-doc.patch
)
pkg_pretend() {
diff --git a/dev-lang/R/files/R-3.6.2-no-LDFLAGS-in-libR-pkg-config.patch b/dev-lang/R/files/R-4.3.0-no-LDFLAGS-in-libR-pkg-config.patch
similarity index 100%
rename from dev-lang/R/files/R-3.6.2-no-LDFLAGS-in-libR-pkg-config.patch
rename to dev-lang/R/files/R-4.3.0-no-LDFLAGS-in-libR-pkg-config.patch
diff --git a/dev-lang/R/files/R-3.6.2-no-gzip-doc.patch b/dev-lang/R/files/R-4.3.0-no-gzip-doc.patch
similarity index 100%
rename from dev-lang/R/files/R-3.6.2-no-gzip-doc.patch
rename to dev-lang/R/files/R-4.3.0-no-gzip-doc.patch
diff --git a/dev-lang/R/files/R-3.4.1-parallel.patch b/dev-lang/R/files/R-4.3.0-parallel.patch
similarity index 100%
rename from dev-lang/R/files/R-3.4.1-parallel.patch
rename to dev-lang/R/files/R-4.3.0-parallel.patch
^ permalink raw reply related [flat|nested] 7+ messages in thread
end of thread, other threads:[~2023-06-28 12:39 UTC | newest]
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