commit 1ff12a2781d8856dd2956e27423c4531d5d99491 Author: Tim Biermann <tbier@posteo.de> Date: Tue Jan 3 13:35:52 2023 +0000 r: a few changes to the build process 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/ -rwxr-xr-x root/root usr/lib/R/lib/libR.so -rwxr-xr-x root/root usr/lib/R/lib/libRblas.so -rwxr-xr-x root/root usr/lib/R/lib/libRlapack.so drwxr-xr-x root/root usr/lib/R/library/ -drwxr-xr-x root/root usr/lib/R/library/KernSmooth/ --rw-r--r-- root/root usr/lib/R/library/KernSmooth/DESCRIPTION --rw-r--r-- root/root usr/lib/R/library/KernSmooth/INDEX 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-drwxr-xr-x root/root usr/lib/R/library/spatial/po/it/ -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 --rw-r--r-- root/root usr/lib/R/library/survival/doc/compete.pdf --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 --rw-r--r-- root/root usr/lib/R/library/survival/doc/concordance.pdf --rw-r--r-- root/root usr/lib/R/library/survival/doc/discrim.R --rw-r--r-- root/root usr/lib/R/library/survival/doc/discrim.Rnw --rw-r--r-- root/root usr/lib/R/library/survival/doc/discrim.pdf --rw-r--r-- root/root usr/lib/R/library/survival/doc/index.html --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 --rw-r--r-- root/root usr/lib/R/library/survival/doc/other.pdf --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 --rw-r--r-- root/root usr/lib/R/library/survival/doc/population.pdf --rw-r--r-- root/root usr/lib/R/library/survival/doc/splines.R --rw-r--r-- root/root usr/lib/R/library/survival/doc/splines.Rnw --rw-r--r-- root/root usr/lib/R/library/survival/doc/splines.pdf --rw-r--r-- root/root usr/lib/R/library/survival/doc/survival.R --rw-r--r-- root/root usr/lib/R/library/survival/doc/survival.Rnw --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) +.. +```