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authorTim Biermann <tbier@posteo.de>2023-01-03 13:35:52 +0000
committerTim Biermann <tbier@posteo.de>2023-01-03 13:35:52 +0000
commit1ff12a2781d8856dd2956e27423c4531d5d99491 (patch)
tree993a6a4b472691a564a72fc81020b2a5faaa32b9 /r
parentf6277c776c42c8eee1c46efb459c0d8d12983621 (diff)
downloadcontrib-1ff12a2781d8856dd2956e27423c4531d5d99491.tar.gz
contrib-1ff12a2781d8856dd2956e27423c4531d5d99491.tar.xz
r: a few changes to the build process
Diffstat (limited to 'r')
-rw-r--r--r/.footprint712
-rw-r--r--r/.signature9
-rw-r--r--r/Pkgfile60
-rw-r--r--r/R-4.2.2-browser-pdf-prefs.patch95
-rw-r--r--r/R-4.2.2-isspace-without-readline.patch22
-rw-r--r--r/R-4.2.2-parallel-rmath-h-install.patch23
-rw-r--r--r/README.md15
7 files changed, 207 insertions, 729 deletions
diff --git a/r/.footprint b/r/.footprint
index a18991586..b6b40854f 100644
--- a/r/.footprint
+++ b/r/.footprint
@@ -192,192 +192,12 @@ lrwxrwxrwx root/root usr/lib/R/etc/Renviron -> /etc/R/Renviron
lrwxrwxrwx root/root usr/lib/R/etc/javaconf -> /etc/R/javaconf
lrwxrwxrwx root/root usr/lib/R/etc/ldpaths -> /etc/R/ldpaths
lrwxrwxrwx root/root usr/lib/R/etc/repositories -> /etc/R/repositories
+lrwxrwxrwx root/root usr/lib/R/include -> ../../include/R
drwxr-xr-x root/root usr/lib/R/lib/
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@@ -1085,115 +561,6 @@ drwxr-xr-x root/root usr/lib/R/library/parallel/html/
-rw-r--r-- root/root usr/lib/R/library/parallel/html/R.css
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-drwxr-xr-x root/root usr/lib/R/library/rpart/doc/
--rw-r--r-- root/root usr/lib/R/library/rpart/doc/index.html
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--rw-r--r-- root/root usr/lib/R/library/rpart/doc/longintro.Rnw
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--rw-r--r-- root/root usr/lib/R/library/rpart/doc/usercode.R
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-drwxr-xr-x root/root usr/lib/R/library/rpart/libs/
--rwxr-xr-x root/root usr/lib/R/library/rpart/libs/rpart.so
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-drwxr-xr-x root/root usr/lib/R/library/spatial/
--rw-r--r-- root/root usr/lib/R/library/spatial/CITATION
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--rw-r--r-- root/root usr/lib/R/library/spatial/INDEX
-drwxr-xr-x root/root usr/lib/R/library/spatial/Meta/
--rw-r--r-- root/root usr/lib/R/library/spatial/Meta/Rd.rds
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-drwxr-xr-x root/root usr/lib/R/library/spatial/R/
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-drwxr-xr-x root/root usr/lib/R/library/spatial/help/
--rw-r--r-- root/root usr/lib/R/library/spatial/help/AnIndex
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-drwxr-xr-x root/root usr/lib/R/library/spatial/html/
--rw-r--r-- root/root usr/lib/R/library/spatial/html/00Index.html
--rw-r--r-- root/root usr/lib/R/library/spatial/html/R.css
-drwxr-xr-x root/root usr/lib/R/library/spatial/libs/
--rwxr-xr-x root/root usr/lib/R/library/spatial/libs/spatial.so
-drwxr-xr-x root/root usr/lib/R/library/spatial/po/
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-drwxr-xr-x root/root usr/lib/R/library/spatial/po/ko/
-drwxr-xr-x root/root usr/lib/R/library/spatial/po/pl/
-drwxr-xr-x root/root usr/lib/R/library/spatial/ppdata/
--rw-r--r-- root/root usr/lib/R/library/spatial/ppdata/agter.dat
--rw-r--r-- root/root usr/lib/R/library/spatial/ppdata/caveolae.dat
--rw-r--r-- root/root usr/lib/R/library/spatial/ppdata/cells.dat
--rw-r--r-- root/root usr/lib/R/library/spatial/ppdata/davis.dat
--rw-r--r-- root/root usr/lib/R/library/spatial/ppdata/drumlin.dat
--rw-r--r-- root/root usr/lib/R/library/spatial/ppdata/eagles.dat
--rw-r--r-- root/root usr/lib/R/library/spatial/ppdata/fig1b.dat
--rw-r--r-- root/root usr/lib/R/library/spatial/ppdata/fig1c.dat
--rw-r--r-- root/root usr/lib/R/library/spatial/ppdata/fig2a.dat
--rw-r--r-- root/root usr/lib/R/library/spatial/ppdata/fig2b.dat
--rw-r--r-- root/root usr/lib/R/library/spatial/ppdata/fig3a.dat
--rw-r--r-- root/root usr/lib/R/library/spatial/ppdata/fig3b.dat
--rw-r--r-- root/root usr/lib/R/library/spatial/ppdata/fig3c.dat
--rw-r--r-- root/root usr/lib/R/library/spatial/ppdata/grocery.dat
--rw-r--r-- root/root usr/lib/R/library/spatial/ppdata/hccells.dat
--rw-r--r-- root/root usr/lib/R/library/spatial/ppdata/nztrees.dat
--rw-r--r-- root/root usr/lib/R/library/spatial/ppdata/pairfn.dat
--rw-r--r-- root/root usr/lib/R/library/spatial/ppdata/pereg.dat
--rw-r--r-- root/root usr/lib/R/library/spatial/ppdata/pines.dat
--rw-r--r-- root/root usr/lib/R/library/spatial/ppdata/redwood.dat
--rw-r--r-- root/root usr/lib/R/library/spatial/ppdata/schools.dat
--rw-r--r-- root/root usr/lib/R/library/spatial/ppdata/stowns1.dat
--rw-r--r-- root/root usr/lib/R/library/spatial/ppdata/tokyo.dat
--rw-r--r-- root/root usr/lib/R/library/spatial/ppdata/towns.dat
drwxr-xr-x root/root usr/lib/R/library/splines/
-rw-r--r-- root/root usr/lib/R/library/splines/DESCRIPTION
-rw-r--r-- root/root usr/lib/R/library/splines/INDEX
@@ -1278,81 +645,6 @@ drwxr-xr-x root/root usr/lib/R/library/stats4/help/
drwxr-xr-x root/root usr/lib/R/library/stats4/html/
-rw-r--r-- root/root usr/lib/R/library/stats4/html/00Index.html
-rw-r--r-- root/root usr/lib/R/library/stats4/html/R.css
-drwxr-xr-x root/root usr/lib/R/library/survival/
--rw-r--r-- root/root usr/lib/R/library/survival/CITATION
--rw-r--r-- root/root usr/lib/R/library/survival/COPYRIGHTS
--rw-r--r-- root/root usr/lib/R/library/survival/DESCRIPTION
--rw-r--r-- root/root usr/lib/R/library/survival/INDEX
-drwxr-xr-x root/root usr/lib/R/library/survival/Meta/
--rw-r--r-- root/root usr/lib/R/library/survival/Meta/Rd.rds
--rw-r--r-- root/root usr/lib/R/library/survival/Meta/data.rds
--rw-r--r-- root/root usr/lib/R/library/survival/Meta/features.rds
--rw-r--r-- root/root usr/lib/R/library/survival/Meta/hsearch.rds
--rw-r--r-- root/root usr/lib/R/library/survival/Meta/links.rds
--rw-r--r-- root/root usr/lib/R/library/survival/Meta/nsInfo.rds
--rw-r--r-- root/root usr/lib/R/library/survival/Meta/package.rds
--rw-r--r-- root/root usr/lib/R/library/survival/Meta/vignette.rds
--rw-r--r-- root/root usr/lib/R/library/survival/NAMESPACE
-drwxr-xr-x root/root usr/lib/R/library/survival/R/
--rw-r--r-- root/root usr/lib/R/library/survival/R/survival
--rw-r--r-- root/root usr/lib/R/library/survival/R/survival.rdb
--rw-r--r-- root/root usr/lib/R/library/survival/R/survival.rdx
-drwxr-xr-x root/root usr/lib/R/library/survival/data/
--rw-r--r-- root/root usr/lib/R/library/survival/data/Rdata.rdb
--rw-r--r-- root/root usr/lib/R/library/survival/data/Rdata.rds
--rw-r--r-- root/root usr/lib/R/library/survival/data/Rdata.rdx
-drwxr-xr-x root/root usr/lib/R/library/survival/doc/
--rw-r--r-- root/root usr/lib/R/library/survival/doc/adjcurve.R
--rw-r--r-- root/root usr/lib/R/library/survival/doc/adjcurve.Rnw
--rw-r--r-- root/root usr/lib/R/library/survival/doc/adjcurve.pdf
--rw-r--r-- root/root usr/lib/R/library/survival/doc/approximate.R
--rw-r--r-- root/root usr/lib/R/library/survival/doc/approximate.Rnw
--rw-r--r-- root/root usr/lib/R/library/survival/doc/approximate.pdf
--rw-r--r-- root/root usr/lib/R/library/survival/doc/compete.R
--rw-r--r-- root/root usr/lib/R/library/survival/doc/compete.Rnw
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--rw-r--r-- root/root usr/lib/R/library/survival/doc/concordance.R
--rw-r--r-- root/root usr/lib/R/library/survival/doc/concordance.Rnw
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--rw-r--r-- root/root usr/lib/R/library/survival/doc/multi.Rnw
--rw-r--r-- root/root usr/lib/R/library/survival/doc/multi.pdf
--rw-r--r-- root/root usr/lib/R/library/survival/doc/other.Rnw
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--rw-r--r-- root/root usr/lib/R/library/survival/doc/population.R
--rw-r--r-- root/root usr/lib/R/library/survival/doc/population.Rnw
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--rw-r--r-- root/root usr/lib/R/library/survival/doc/survival.pdf
--rw-r--r-- root/root usr/lib/R/library/survival/doc/tiedtimes.R
--rw-r--r-- root/root usr/lib/R/library/survival/doc/tiedtimes.Rnw
--rw-r--r-- root/root usr/lib/R/library/survival/doc/tiedtimes.pdf
--rw-r--r-- root/root usr/lib/R/library/survival/doc/timedep.R
--rw-r--r-- root/root usr/lib/R/library/survival/doc/timedep.Rnw
--rw-r--r-- root/root usr/lib/R/library/survival/doc/timedep.pdf
--rw-r--r-- root/root usr/lib/R/library/survival/doc/validate.R
--rw-r--r-- root/root usr/lib/R/library/survival/doc/validate.Rnw
--rw-r--r-- root/root usr/lib/R/library/survival/doc/validate.pdf
-drwxr-xr-x root/root usr/lib/R/library/survival/help/
--rw-r--r-- root/root usr/lib/R/library/survival/help/AnIndex
--rw-r--r-- root/root usr/lib/R/library/survival/help/aliases.rds
-drwxr-xr-x root/root usr/lib/R/library/survival/help/figures/
--rw-r--r-- root/root usr/lib/R/library/survival/help/figures/logo.png
--rw-r--r-- root/root usr/lib/R/library/survival/help/paths.rds
--rw-r--r-- root/root usr/lib/R/library/survival/help/survival.rdb
--rw-r--r-- root/root usr/lib/R/library/survival/help/survival.rdx
-drwxr-xr-x root/root usr/lib/R/library/survival/html/
--rw-r--r-- root/root usr/lib/R/library/survival/html/00Index.html
--rw-r--r-- root/root usr/lib/R/library/survival/html/R.css
-drwxr-xr-x root/root usr/lib/R/library/survival/libs/
--rwxr-xr-x root/root usr/lib/R/library/survival/libs/survival.so
drwxr-xr-x root/root usr/lib/R/library/tcltk/
-rw-r--r-- root/root usr/lib/R/library/tcltk/DESCRIPTION
-rw-r--r-- root/root usr/lib/R/library/tcltk/INDEX
@@ -1516,7 +808,7 @@ drwxr-xr-x root/root usr/share/R/make/
-rw-r--r-- root/root usr/share/R/make/vars.mk
-rw-r--r-- root/root usr/share/R/make/winshlib.mk
drwxr-xr-x root/root usr/share/R/sh/
--rw-r--r-- root/root usr/share/R/sh/echo.sh
+-rwxr-xr-x root/root usr/share/R/sh/echo.sh
drwxr-xr-x root/root usr/share/applications/
-rw-r--r-- root/root usr/share/applications/r.desktop
drwxr-xr-x root/root usr/share/man/
diff --git a/r/.signature b/r/.signature
index 8ab8e38e0..7cd7b47b9 100644
--- a/r/.signature
+++ b/r/.signature
@@ -1,11 +1,14 @@
untrusted comment: verify with /etc/ports/contrib.pub
-RWSagIOpLGJF374+dbgD38FMxrgQ1lJgIQntQU3RqI04+cgW3tKb0y1SLKnFqK11kBXldJVm+BflFxAS8wbMaUcyUbhqloCT3AU=
-SHA256 (Pkgfile) = cac84e82c90a16aeb88bfd9c576452be26632e93380323c48c69b0816a721092
-SHA256 (.footprint) = 0c19dba114680e4654ddb67c7827365add2a2f23e840d04db655b33021daf385
+RWSagIOpLGJF39+Bc1P7HQaUqYnyquWW9fyjZTXo7x1/a4IYKq/unLJaSbKnOXUoHaLDZMbcbNtoTeaZBC1hSNoNylQ2osVFkwA=
+SHA256 (Pkgfile) = 6e7ca7dcaa9cdc9fe580a0ee7d2dd8e47505bd6220ae0a834ea94c14ec210181
+SHA256 (.footprint) = 665cccb2f203c0b448be4f31597184cdfa3a1062ce3ff85f2f1dbbf0f3a57ff4
SHA256 (R-4.2.2.tar.gz) = 0ff62b42ec51afa5713caee7c4fde7a0c45940ba39bef8c5c9487fef0c953df5
SHA256 (r.desktop) = 25b01ea93fa704884b65ba002d44d4e99725bd826997e8c73b6467df9f23c798
SHA256 (r.png) = 1580d06a737951f4f3c903cbd514247d9071fc6868eb9c2de94bb999cc195cb1
SHA256 (R.conf) = 01057f4dd3d0eca3e31090b2793ab17ed6648501513f6cfea36a0c609a55ac5e
+SHA256 (R-4.2.2-browser-pdf-prefs.patch) = 98ba658e6be56bafc5f831627894c4706406e2e8feb39f6a18e8b54b0ec62f2c
+SHA256 (R-4.2.2-isspace-without-readline.patch) = 9e2a9d728abfd0a4acc83ac8a287592435472336fd55bc5083fc0b1ac5f75448
+SHA256 (R-4.2.2-parallel-rmath-h-install.patch) = f406c35ec38d37ccce109492afc18e02ed8f5adb781af68628801fa40c3f1121
SHA256 (R-3.4.1-parallel.patch) = 7d08b75592f9452b1f92bfe148f9d24fd19ba9163cd16ee2dac753f2c1a891be
SHA256 (R-3.4.1-rmath-shared.patch) = 76a2d04b3a77884baa3cf84b25920f875e026b73c217c59b06aba2fae634f858
SHA256 (R-3.6.2-no-LDFLAGS-in-libR-pkg-config.patch) = 5611b1c168ff338a4164302fc265be150700ebbca49a33b55973810fe5519b6e
diff --git a/r/Pkgfile b/r/Pkgfile
index 4f9b993bc..79272bd7c 100644
--- a/r/Pkgfile
+++ b/r/Pkgfile
@@ -6,9 +6,11 @@
name=r
version=4.2.2
-release=1
+release=2
source=(https://cran.r-project.org/src/base/R-${version::1}/R-$version.tar.gz
r.desktop r.png R.conf
+ R-4.2.2-browser-pdf-prefs.patch
+ R-4.2.2-isspace-without-readline.patch R-4.2.2-parallel-rmath-h-install.patch
R-3.4.1-parallel.patch R-3.4.1-rmath-shared.patch
R-3.6.2-no-LDFLAGS-in-libR-pkg-config.patch)
@@ -19,22 +21,36 @@ build() {
patch -Np1 -i $SRC/R-3.4.1-parallel.patch
patch -Np1 -i $SRC/R-3.4.1-rmath-shared.patch
patch -Np1 -i $SRC/R-3.6.2-no-LDFLAGS-in-libR-pkg-config.patch
+ patch -Np1 -i $SRC/R-4.2.2-browser-pdf-prefs.patch
+ patch -Np1 -i $SRC/R-4.2.2-isspace-without-readline.patch
+ patch -Np1 -i $SRC/R-4.2.2-parallel-rmath-h-install.patch
# configuring R
prt-get isinst tk && PKGMK_R+=" --with-x=yes" || PKGMK_R+=" --with-x=no"
- prt-get isinst lapack && PKGMK_R+=" --with-lapack LAPACK_LIBS=$(pkg-config --libs lapack)"
+ prt-get isinst lapack && PKGMK_R+=" --with-lapack LAPACK_LIBS=$(pkgconf --libs lapack)"
# this needs a properly working java environment!
[[ -e $(whereis javac) ]] && PKGMK_R+=" --enable-java" || PKGMK_R+=" --disable-java"
# set the correct dir for texmf distribution
sed -i 's|$(rsharedir)/texmf|${datarootdir}/texmf|' share/Makefile.in
+ sed -i -e '/R_LIBS_SITE=/s/^/#/g' etc/Renviron.in
+ echo 'R_LIBS_SITE=${R_LIBS_SITE-'"'/usr/lib/R/library:/usr/share/R/library'"'}' >> etc/Renviron.in
+
+ export R_PDFVIEWER=/usr/bin/xdg-open
+ export R_PRINTCMD=lpr
+ export R_BROWSER=/usr/bin/xdg-open
+
unset R_HOME
+ export ldpath="/usr/lib/R/lib"
# version 3.6.2 needs at least the addition to FCFLAGS
export CFLAGS+=' -fPIC'
export CPPFLAGS+=' -fPIC'
export FCFLAGS+=' -fPIC'
+
+ CFLAGS+=" -ffat-lto-objects" \
+ CXXFLAGS+=" -ffat-lto-objects" \
./configure $PKGMK_R \
--prefix=/usr \
--libdir=/usr/lib \
@@ -44,32 +60,44 @@ build() {
rincludedir=/usr/include/R/ \
F77=gfortran \
LIBnn=lib \
- BLAS_LIBS=$(pkg-config --libs blas) \
- PKG_CONFIG=/usr/bin/pkg-config \
- --with-blas \
+ BLAS_LIBS=$(pkgconf --libs blas) \
+ PKG_CONFIG=/usr/bin/pkgconf \
+ --with-blas=openblas \
--enable-BLAS-shlib \
--enable-R-shlib \
--enable-byte-compiled-packages \
- --disable-nls
+ --enable-lto \
+ --enable-R-profiling \
+ --enable-memory-profiling \
+ --with-cairo \
+ --with-ICU \
+ --with-jpeglib \
+ --with-lapack \
+ --with-libpng \
+ --with-libtiff \
+ --with-system-tre \
+ --without-recommended-packages \
+ --disable-nls | tee CONFIGURE.log
+cat CONFIGURE.log | grep -A30 'R is now' - > CAPABILITIES
make
- # make nmath library
- pushd src/nmath/standalone
- make shared
- popd
+ make -C src/nmath/standalone shared
- # install R to $PKG
make DESTDIR=$PKG install
- # same for the nmath library
- pushd src/nmath/standalone
- make DESTDIR=$PKG install
- #popd
+ make -C src/nmath/standalone DESTDIR=$PKG install
+
+ chmod +x $PKG/usr/lib/R/bin/*
+ chmod +x $PKG/usr/share/R/sh/echo.sh
+ #chmod -x $PKG/usr/lib/R/library/mgcv/CITATION
- sed -i "s|$PKG ||" "$PKG/usr/bin/R"
+ sed -i "s|$PKG ||" $PKG/usr/bin/R
rm $PKG/usr/lib/R/bin/R
cd $PKG/usr/lib/R/bin
ln -s ../../../bin/R
+ cd $PKG/usr/lib/R
+ ln -s ../../include/R include
+
install -Dm644 $SRC/r.desktop \
$PKG/usr/share/applications/r.desktop
install -Dm644 $SRC/r.png \
diff --git a/r/R-4.2.2-browser-pdf-prefs.patch b/r/R-4.2.2-browser-pdf-prefs.patch
new file mode 100644
index 000000000..b5a953cb6
--- /dev/null
+++ b/r/R-4.2.2-browser-pdf-prefs.patch
@@ -0,0 +1,95 @@
+From 6e48ab8b5006f3fdd8ef08f3f86406a02eabdc80 Mon Sep 17 00:00:00 2001
+From: Michael Orlitzky <michael@orlitzky.com>
+Date: Mon, 12 Sep 2022 08:31:46 -0400
+Subject: [PATCH 1/3] m4/R.m4: prefer xdg-open for R_BROWSER and R_PDFVIEWER.
+
+The xdg-open utility (if it is present) will launch the user's
+preferred browsr or PDF viewer when fed an HTML page or a PDF
+document, respectively. It therefore makes sense to prefer it over
+(for example) firefox, which may be installed but not the user's
+preferred browser.
+---
+ m4/R.m4 | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/m4/R.m4 b/m4/R.m4
+index bdcfbea..c5052e7 100644
+--- a/m4/R.m4
++++ b/m4/R.m4
+@@ -237,7 +237,7 @@ fi])
+ ## xdg-open is the freedesktop.org interface to kfmclient/gnome-open
+ AC_DEFUN([R_PROG_BROWSER],
+ [if test -z "${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
+
diff --git a/r/R-4.2.2-isspace-without-readline.patch b/r/R-4.2.2-isspace-without-readline.patch
new file mode 100644
index 000000000..0b32bef13
--- /dev/null
+++ b/r/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)
+ {
diff --git a/r/R-4.2.2-parallel-rmath-h-install.patch b/r/R-4.2.2-parallel-rmath-h-install.patch
new file mode 100644
index 000000000..756ec8ff5
--- /dev/null
+++ b/r/R-4.2.2-parallel-rmath-h-install.patch
@@ -0,0 +1,23 @@
+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/r/README.md b/r/README.md
new file mode 100644
index 000000000..aa256ff0b
--- /dev/null
+++ b/r/README.md
@@ -0,0 +1,15 @@
+R
+=
+
+## In case installing additional libraries fails
+
+In my experience, for some reason, certain libraries try to link to an
+outdated version of certain other system libraries.
+
+Consider rebuilding all libraries from within a running R session.
+
+```
+$ r
+> update.packages(checkBuilt = TRUE, ask = FALSE)
+..
+```

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