[crux-commits] ports/contrib (3.7): r: a few changes to the build process

3 Jan 2023

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
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--rw-r--r--	root/root	usr/lib/R/library/spatial/ppdata/fig1b.dat
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--rw-r--r--	root/root	usr/lib/R/library/spatial/ppdata/fig2a.dat
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--rw-r--r--	root/root	usr/lib/R/library/spatial/ppdata/fig3a.dat
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--rw-r--r--	root/root	usr/lib/R/library/spatial/ppdata/grocery.dat
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 drwxr-xr-x	root/root	usr/lib/R/library/splines/
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 -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/
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 -rw-r--r--	root/root	usr/lib/R/library/stats4/html/R.css
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 -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
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-SHA256 (Pkgfile) = cac84e82c90a16aeb88bfd9c576452be26632e93380323c48c69b0816a721092
-SHA256 (.footprint) = 0c19dba114680e4654ddb67c7827365add2a2f23e840d04db655b33021daf385
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+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)
+..
+```

    

[crux-commits] ports/contrib (3.7): r: a few changes to the build process

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