fix math/R missing fonts on plots (Was: Re: graphics/cairo + math/R font issues)

2020-07-16 Thread Nam Nguyen 
Zé Loff writes:

> Although changing the default font can be easily done -- adding a
> default site-wide configuration file could be a possible workaround to
> make the port work properly again -- this appears not to be the case
> with the math/greek symbols font, which seems to be harder to replace,
> so just changing fonts isn't a proper fix.
>
> However, all works properly if R is instructed to forget about cairo and
> just use the "Xlib" device as a default (as is done on macOS, precisely
> due to issues with pango).  Ingo: do you think we should patch the port
> to do this, until the pango/type 1 issues are solvable

>> 3. Fonts don't render in the Plots window. Not sure why. Help
>> appreciated.
>
> pango/harfbuzz fallout, probably.  Pango stopped supporting Type 1
> fonts.  I have the same issue with R itself.  My solution it to add
>
>   options.X11(family = "DejaVu Sans")
>
> or some other TrueType family.

I was preparing an editors/TeXmacs update and noticed that the R plugin
had graphs with missing glyphs.

Here is a diff for R to do what Ze Loff suggested in these two
threads[2][3]. Fix taken from [1]. sthen@ described the root cause in
[2] but consider this workaround.

This diff:
- changes the site-wide config
  (/usr/local/lib/R/library/base/R/Rprofile) to use DejaVu Sans by
  default.
- updates README to document that the font can be changed
- bumps REVISION
sources:
[1] 
https://stackoverflow.com/questions/1189759/expert-r-users-whats-in-your-rprofile
[2] https://marc.info/?l=openbsd-ports=157830898518255=2
[3] https://marc.info/?l=openbsd-ports=159342491019196=2

I was able to run these two test plots with the TeXmacs R plugin,
math/rstudio and with R itself.

test 1:
demo(plotmath)
mash enter a few times

test 2:
qnorm(1/2,mean=0,sd=1)
x<-1:100
y<-rnorm(x)
plot(x,y)

Feedback and tests are welcome.

Index: Makefile
===
RCS file: /cvs/ports/math/R/Makefile,v
retrieving revision 1.118
diff -u -p -u -p -r1.118 Makefile
--- Makefile23 Jun 2020 18:54:24 -  1.118
+++ Makefile16 Jul 2020 06:20:25 -
@@ -2,6 +2,7 @@
 
 COMMENT=   powerful math/statistics/graphics language
 DISTNAME=  R-4.0.2
+REVISION=  0
 
 SO_VERSION=37.0
 .for _lib in R Rblas Rlapack
Index: patches/patch-src_library_profile_Common_R
===
RCS file: patches/patch-src_library_profile_Common_R
diff -N patches/patch-src_library_profile_Common_R
--- /dev/null   1 Jan 1970 00:00:00 -
+++ patches/patch-src_library_profile_Common_R  16 Jul 2020 06:20:25 -
@@ -0,0 +1,17 @@
+$OpenBSD$
+
+add default font to fix missing font on plots. see:
+https://stackoverflow.com/questions/1189759/expert-r-users-whats-in-your-rprofile
+
+Index: src/library/profile/Common.R
+--- src/library/profile/Common.R.orig
 src/library/profile/Common.R
+@@ -35,6 +35,8 @@ options(show.error.messages = TRUE)
+ options(scipen = 0)
+ options(max.print = 9)# max. #{entries} in internal printMatrix()
+ options(add.smooth = TRUE)# currently only used in 'plot.lm'
++setHook(packageEvent("grDevices", "onLoad"),
++function(...) grDevices::X11.options(family = "DejaVu Sans"))
+ 
+ if(isFALSE(as.logical(Sys.getenv("_R_OPTIONS_STRINGS_AS_FACTORS_",
+  "FALSE" {
Index: pkg/README
===
RCS file: /cvs/ports/math/R/pkg/README,v
retrieving revision 1.10
diff -u -p -u -p -r1.10 README
--- pkg/README  18 May 2020 05:26:13 -  1.10
+++ pkg/README  16 Jul 2020 06:20:25 -
@@ -16,3 +16,9 @@ Running:
 
 as root, will update both ${TRUEPREFIX}/lib/R/etc/Makeconf and
 ${TRUEPREFIX}/lib/R/etc/ldpaths with the right settings.
+
+Changing fonts
+==
+Fonts on plots can be customized.
+
+> X11.options(family = "DejaVu Sans")

Re: Fix math/R

2012-01-23 Thread Benjamin Nadland 
On Sun, Jan 22, 2012 at 06:47:28PM +0100, David Coppa wrote:
 On Thu, Jan 19, 2012 at 5:22 PM, David Coppa dco...@openbsd.org wrote:
  Hi,
 
  This diff fixes R's problem with pthread undefined symbols, as
  reported here:
 
  http://marc.info/?l=openbsd-portsm=132196919327917
 
  and here:
 
  http://marc.info/?l=openbsd-portsm=132187529729922
 
  It also fixes libpthread linkage (-lpthread - -pthread) and
  an incorrect usage of the --export-dynamic linker flag (it's
  '-Wl,--export-dynamic', not '-Wl,-export-dynamic'.
 
  Tested on sparc64 and amd64.
  Ok?
 
 Ping!

It seems my last message did not get through, sorry.

This fixes my problems on i386. Thanks.

Re: Fix math/R

2012-01-23 Thread Benjamin Nadland 
On Thu, Jan 19, 2012 at 09:22:03AM -0700, David Coppa wrote:
 Hi,
 
 This diff fixes R's problem with pthread undefined symbols, as
 reported here:
 
 http://marc.info/?l=openbsd-portsm=132196919327917
 
 and here:
 
 http://marc.info/?l=openbsd-portsm=132187529729922
 
 It also fixes libpthread linkage (-lpthread - -pthread) and
 an incorrect usage of the --export-dynamic linker flag (it's
 '-Wl,--export-dynamic', not '-Wl,-export-dynamic'.
 
 Tested on sparc64 and amd64.

Tested on i386. Works fine, thanks!

Re: Fix math/R

2012-01-22 Thread David Coppa 
On Thu, Jan 19, 2012 at 5:22 PM, David Coppa dco...@openbsd.org wrote:
 Hi,

 This diff fixes R's problem with pthread undefined symbols, as
 reported here:

 http://marc.info/?l=openbsd-portsm=132196919327917

 and here:

 http://marc.info/?l=openbsd-portsm=132187529729922

 It also fixes libpthread linkage (-lpthread - -pthread) and
 an incorrect usage of the --export-dynamic linker flag (it's
 '-Wl,--export-dynamic', not '-Wl,-export-dynamic'.

 Tested on sparc64 and amd64.
 Ok?

Ping!

 Index: Makefile
 ===
 RCS file: /cvs/ports/math/R/Makefile,v
 retrieving revision 1.44
 diff -u -p -r1.44 Makefile
 --- Makefile    3 Nov 2011 20:28:09 -       1.44
 +++ Makefile    19 Jan 2012 16:10:45 -
 @@ -4,7 +4,7 @@ SHARED_ONLY=    Yes

  COMMENT=       clone of S, a powerful math/statistics/graphics language
  DISTNAME=      R-2.8.1
 -REVISION=      6
 +REVISION=      7
  SHARED_LIBS=   Rlapack 29.0 \
                Rblas   29.0

 @@ -20,8 +20,8 @@ PERMIT_DISTFILES_FTP= Yes
  WANTLIB=       GL ICE SM X11 Xext Xmu Xrender Xss Xt \
                bz2 c cairo expat fontconfig freetype glib-2.0 \
                gmodule-2.0 gobject-2.0 gthread-2.0 jpeg m ncurses pango-1.0 \
 -               pangocairo-1.0 pangoft2-1.0 pcre pixman-1 png  pthread-stubs \
 -               readline tiff xcb xcb-render xcb-shm z \
 +               pangocairo-1.0 pangoft2-1.0 pcre pixman-1 png pthread \
 +               pthread-stubs readline tiff xcb xcb-render xcb-shm z \
                ${MODFORTRAN_WANTLIB} ${MODTK_WANTLIB}

  MASTER_SITES=  http://cran.r-project.org/src/base/R-2/ \
 Index: patches/patch-configure
 ===
 RCS file: /cvs/ports/math/R/patches/patch-configure,v
 retrieving revision 1.10
 diff -u -p -r1.10 patch-configure
 --- patches/patch-configure     11 Mar 2009 08:21:33 -      1.10
 +++ patches/patch-configure     19 Jan 2012 16:10:45 -
 @@ -1,6 +1,69 @@
  $OpenBSD: patch-configure,v 1.10 2009/03/11 08:21:33 sthen Exp $
  configure.orig     Thu Dec 18 14:03:48 2008
 -+++ configure  Wed Mar 11 00:21:36 2009
 +--- configure.orig     Thu Dec 18 15:03:48 2008
  configure  Thu Jan 19 14:38:44 2012
 +@@ -31142,7 +31142,7 @@ echo $as_me: WARNING: Use of flat namespace is 
 reques
 +   openbsd*)
 +     ## looks like ${wl} is not defined here.  Perhaps in libtool code?
 +     if test -z `echo __ELF__ | $CC -E - | grep __ELF__`; then
 +-      main_ldflags=${wl}-export-dynamic
 ++      main_ldflags=${wl}--export-dynamic
 +       shlib_ldflags=-shared -fPIC
 +     fi
 +     ;;
 +@@ -52736,13 +52736,13 @@ rm -f core conftest.err conftest.$ac_objext 
 conftest_i
 +         if test -n $gl_have_pthread; then
 +           # The program links fine without libpthread. But it may actually
 +           # need to link with libpthread in order to create multiple 
 threads.
 +-          { echo $as_me:$LINENO: checking for pthread_kill in -lpthread 
 5
 +-echo $ECHO_N checking for pthread_kill in -lpthread... $ECHO_C 6; }
 ++          { echo $as_me:$LINENO: checking for pthread_kill in -pthread 5
 ++echo $ECHO_N checking for pthread_kill in -pthread... $ECHO_C 6; }
 + if test ${ac_cv_lib_pthread_pthread_kill+set} = set; then
 +   echo $ECHO_N (cached) $ECHO_C 6
 + else
 +   ac_check_lib_save_LIBS=$LIBS
 +-LIBS=-lpthread  $LIBS
 ++LIBS=-pthread  $LIBS
 + cat conftest.$ac_ext _ACEOF
 + /* confdefs.h.  */
 + _ACEOF
 +@@ -52806,7 +52806,7 @@ fi
 + { echo $as_me:$LINENO: result: $ac_cv_lib_pthread_pthread_kill 5
 + echo ${ECHO_T}$ac_cv_lib_pthread_pthread_kill 6; }
 + if test $ac_cv_lib_pthread_pthread_kill = yes; then
 +-  LIBMULTITHREAD=-lpthread LTLIBMULTITHREAD=-lpthread
 ++  LIBMULTITHREAD=-pthread LTLIBMULTITHREAD=-pthread
 +              # On Solaris and HP-UX, most pthread functions exist also in 
 libc.
 +              # Therefore pthread_in_use() needs to actually try to create a
 +              # thread: pthread_create from libc will fail, whereas
 +@@ -52824,13 +52824,13 @@ fi
 +
 +         else
 +           # Some library is needed. Try libpthread and libc_r.
 +-          { echo $as_me:$LINENO: checking for pthread_kill in -lpthread 
 5
 +-echo $ECHO_N checking for pthread_kill in -lpthread... $ECHO_C 6; }
 ++          { echo $as_me:$LINENO: checking for pthread_kill in -pthread 5
 ++echo $ECHO_N checking for pthread_kill in -pthread... $ECHO_C 6; }
 + if test ${ac_cv_lib_pthread_pthread_kill+set} = set; then
 +   echo $ECHO_N (cached) $ECHO_C 6
 + else
 +   ac_check_lib_save_LIBS=$LIBS
 +-LIBS=-lpthread  $LIBS
 ++LIBS=-pthread  $LIBS
 + cat conftest.$ac_ext _ACEOF
 + /* confdefs.h.  */
 + _ACEOF
 +@@ -52895,8 +52895,8 @@ fi
 + echo ${ECHO_T}$ac_cv_lib_pthread_pthread_kill 6; }
 + if test $ac_cv_lib_pthread_pthread_kill = yes; then
 +   gl_have_pthread=yes
 +-             LIBTHREAD=-lpthread LTLIBTHREAD=-lpthread
 +-             LIBMULTITHREAD=-lpthread LTLIBMULTITHREAD=-lpthread
 ++  

Fix math/R

2012-01-19 Thread David Coppa 
Hi,

This diff fixes R's problem with pthread undefined symbols, as
reported here:

http://marc.info/?l=openbsd-portsm=132196919327917

and here:

http://marc.info/?l=openbsd-portsm=132187529729922

It also fixes libpthread linkage (-lpthread - -pthread) and
an incorrect usage of the --export-dynamic linker flag (it's
'-Wl,--export-dynamic', not '-Wl,-export-dynamic'.

Tested on sparc64 and amd64.
Ok?

ciao,
David

Index: Makefile
===
RCS file: /cvs/ports/math/R/Makefile,v
retrieving revision 1.44
diff -u -p -r1.44 Makefile
--- Makefile3 Nov 2011 20:28:09 -   1.44
+++ Makefile19 Jan 2012 16:10:45 -
@@ -4,7 +4,7 @@ SHARED_ONLY=Yes
 
 COMMENT=   clone of S, a powerful math/statistics/graphics language
 DISTNAME=  R-2.8.1
-REVISION=  6
+REVISION=  7
 SHARED_LIBS=   Rlapack 29.0 \
Rblas   29.0
 
@@ -20,8 +20,8 @@ PERMIT_DISTFILES_FTP= Yes
 WANTLIB=   GL ICE SM X11 Xext Xmu Xrender Xss Xt \
bz2 c cairo expat fontconfig freetype glib-2.0 \
gmodule-2.0 gobject-2.0 gthread-2.0 jpeg m ncurses pango-1.0 \
-   pangocairo-1.0 pangoft2-1.0 pcre pixman-1 png  pthread-stubs \
-   readline tiff xcb xcb-render xcb-shm z \
+   pangocairo-1.0 pangoft2-1.0 pcre pixman-1 png pthread \
+   pthread-stubs readline tiff xcb xcb-render xcb-shm z \
${MODFORTRAN_WANTLIB} ${MODTK_WANTLIB}
 
 MASTER_SITES=  http://cran.r-project.org/src/base/R-2/ \
Index: patches/patch-configure
===
RCS file: /cvs/ports/math/R/patches/patch-configure,v
retrieving revision 1.10
diff -u -p -r1.10 patch-configure
--- patches/patch-configure 11 Mar 2009 08:21:33 -  1.10
+++ patches/patch-configure 19 Jan 2012 16:10:45 -
@@ -1,6 +1,69 @@
 $OpenBSD: patch-configure,v 1.10 2009/03/11 08:21:33 sthen Exp $
 configure.orig Thu Dec 18 14:03:48 2008
-+++ configure  Wed Mar 11 00:21:36 2009
+--- configure.orig Thu Dec 18 15:03:48 2008
 configure  Thu Jan 19 14:38:44 2012
+@@ -31142,7 +31142,7 @@ echo $as_me: WARNING: Use of flat namespace is reques
+   openbsd*)
+ ## looks like ${wl} is not defined here.  Perhaps in libtool code?
+ if test -z `echo __ELF__ | $CC -E - | grep __ELF__`; then
+-  main_ldflags=${wl}-export-dynamic
++  main_ldflags=${wl}--export-dynamic
+   shlib_ldflags=-shared -fPIC
+ fi
+ ;;
+@@ -52736,13 +52736,13 @@ rm -f core conftest.err conftest.$ac_objext 
conftest_i
+ if test -n $gl_have_pthread; then
+   # The program links fine without libpthread. But it may actually
+   # need to link with libpthread in order to create multiple threads.
+-  { echo $as_me:$LINENO: checking for pthread_kill in -lpthread 5
+-echo $ECHO_N checking for pthread_kill in -lpthread... $ECHO_C 6; }
++  { echo $as_me:$LINENO: checking for pthread_kill in -pthread 5
++echo $ECHO_N checking for pthread_kill in -pthread... $ECHO_C 6; }
+ if test ${ac_cv_lib_pthread_pthread_kill+set} = set; then
+   echo $ECHO_N (cached) $ECHO_C 6
+ else
+   ac_check_lib_save_LIBS=$LIBS
+-LIBS=-lpthread  $LIBS
++LIBS=-pthread  $LIBS
+ cat conftest.$ac_ext _ACEOF
+ /* confdefs.h.  */
+ _ACEOF
+@@ -52806,7 +52806,7 @@ fi
+ { echo $as_me:$LINENO: result: $ac_cv_lib_pthread_pthread_kill 5
+ echo ${ECHO_T}$ac_cv_lib_pthread_pthread_kill 6; }
+ if test $ac_cv_lib_pthread_pthread_kill = yes; then
+-  LIBMULTITHREAD=-lpthread LTLIBMULTITHREAD=-lpthread
++  LIBMULTITHREAD=-pthread LTLIBMULTITHREAD=-pthread
+  # On Solaris and HP-UX, most pthread functions exist also in 
libc.
+  # Therefore pthread_in_use() needs to actually try to create a
+  # thread: pthread_create from libc will fail, whereas
+@@ -52824,13 +52824,13 @@ fi
+ 
+ else
+   # Some library is needed. Try libpthread and libc_r.
+-  { echo $as_me:$LINENO: checking for pthread_kill in -lpthread 5
+-echo $ECHO_N checking for pthread_kill in -lpthread... $ECHO_C 6; }
++  { echo $as_me:$LINENO: checking for pthread_kill in -pthread 5
++echo $ECHO_N checking for pthread_kill in -pthread... $ECHO_C 6; }
+ if test ${ac_cv_lib_pthread_pthread_kill+set} = set; then
+   echo $ECHO_N (cached) $ECHO_C 6
+ else
+   ac_check_lib_save_LIBS=$LIBS
+-LIBS=-lpthread  $LIBS
++LIBS=-pthread  $LIBS
+ cat conftest.$ac_ext _ACEOF
+ /* confdefs.h.  */
+ _ACEOF
+@@ -52895,8 +52895,8 @@ fi
+ echo ${ECHO_T}$ac_cv_lib_pthread_pthread_kill 6; }
+ if test $ac_cv_lib_pthread_pthread_kill = yes; then
+   gl_have_pthread=yes
+- LIBTHREAD=-lpthread LTLIBTHREAD=-lpthread
+- LIBMULTITHREAD=-lpthread LTLIBMULTITHREAD=-lpthread
++ LIBTHREAD=-pthread LTLIBTHREAD=-pthread
++ LIBMULTITHREAD=-pthread LTLIBMULTITHREAD=-pthread
+ fi
+ 
+   if test -z $gl_have_pthread; then
 @@