Re: [Rd] R | vnc | X11 fonts

From: Evan Cooch <>
Date: Sat 29 Jul 2006 - 16:05:50 GMT

> I don't think xset q is the right diagnostic tool. I suspect that it
> just reflects a default setting of vnc. Those directories could be
> empty for all that it knows. xfontsel might be more to the point if
> you need to know whether the fonts are actually available.
> However, I can't reproduce similar behaviour on FC5 with the
> straightforward vncserver/vncviewer/twm default setup (i.e., it runs
> demo(graphics)). So I suspect you need to dig deeper or tell us more
> details about what goes wrong, e.g. how exactly are you running your R
> scripts, will they work from the console, etc.

OK - here's the nitty gritty. Specifically, its fonts in some graphics outputs for a script that seem to be missing. Graphics are not particularly fancy - use defaults for fonts:


matrix.image(y,y,elas.eigen,xlab="year t",ylab="year t+1",col=topo.colors(100));
title("Elasticity from eigenvectors");
abline(h=0); abline(v=0);

  1. if I run from console, use standard FC 5 gnome desktop, then everything works just as it should.
  2. if I connect via vnc to the machine, using twm, and run the same script, then all seems fine. From within the xterm that pops up when you first fire up twm, xset gives the font paths I specified in /usr/bin/vncserver. Looking at the .log file in .vnc shows everything seems to be working OK, except for one error message:

X Error of failed request: BadLength (poly request too large or internal Xlib length error)

But otherwise, ok.

3. But, if I modify xstartup in .vnc, to use something other than twm, then...problems. In xstartup in .vnc we see the default


# Uncomment the following two lines for normal desktop:
# exec /etc/X11/xinit/xinitrc

[ -x /etc/vnc/xstartup ] && exec /etc/vnc/xstartup [ -r $HOME/.Xresources ] && xrdb $HOME/.Xresources xsetroot -solid grey
vncconfig -iconic &
xterm -geometry 80x24+10+10 -ls -title "$VNCDESKTOP Desktop" & twm &

I'd like to run the standard FC 5 gnome desktop, so I try the following:

  1. uncomment the first two lines, then comment out everything else:

# Uncomment the following two lines for normal desktop: unset SESSION_MANAGER
 exec /etc/X11/xinit/xinitrc

#[ -x /etc/vnc/xstartup ] && exec /etc/vnc/xstartup
#[ -r $HOME/.Xresources ] && xrdb $HOME/.Xresources
#xsetroot -solid grey
#vncconfig -iconic &
#xterm -geometry 80x24+10+10 -ls -title "$VNCDESKTOP Desktop" &
#twm &

Restart vncserver, then try to vnc to desktop. Looks good - there it is, my background image (cute picture of new baby boy), tarted up icons etc. Bring up a term window - first clue something is wrong - the fonts in the term window are 'very jagged' (i.e., look 'wrong'). xset q shows font path(s) are set correctly. Fire up xfontsel (which I know little about) - tells me 3579 name match. But, when I execute the xfontsel command, it tells me

Warning: Missing charsets in String to FontSet conversion Warning: Unable to load any usable font

The last warning is clearly worrisome - and consistent with the 'wrong font' appearence in the term window, and the fact that when I now X11() from within R, I get an error message, and when I try the R script, needless to say it bombs - can't find the basic fonts it needs to label axes in the graphs.

Summary: so, using twm, R seems to work fine - fonts there, graphics generated. But, when I try to bring it up on the gnome desktop, all sorts of problems. I know I could use a different window manager - better than twm, not as whizzy as the gnome desktop (e.g., fluxbox), but that is somewhat beside the point. I'm trying to figure out why xterm is not picking up the fonts through vnc. I'm going to "guess" (literally) that its some interaction of vncserver (which is just a script - I've explicity FontPath statements there for the X11 fonts), xorg.conf (ditto), and gnome.

What puzzles me is why I see this on my Fedora Core 5 box (xorg based), but not my RHEL 3 machine (XFree based). Perhaps in said difference there is a clue.

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