X11 problem after migration to Leopard
On Mar 19, 2008, at 12:35 AM, Martin Eklund wrote:
Hi everyone again, sessionInfo() gives the following output: ====================== R version 2.6.2 (2008-02-08) i386-apple-darwin8.10.1 locale: C/UTF-8/C/C/C/C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] rcompgen_0.1-17 ====================== I have upgraded to the latest X11 from http://trac.macosforge.org/projects/xquartz and I have also tried the tip about how to fix X11 at http://r.research.att.com/building.html . However, none of these actions fixes the problem. I have also tried to reinstall R (though I didn't have any hopes that it would fix the problem - but to be on the safe side...). When I migrated to Leopard I made a disc image of my old system, put it on an external hard drive, installed Leopard on my computer, then used the migration assistant to install my old user account again from the external hard drive. So, as Kasper Hansen suggests, it is quite likely that the problem is related to some old config file lurking around somewhere. Problem is that I have no idea where or what it could be (as I said before, I have disabled the DISPLAY settings that I had before to get plotting to work from the command line when running Tiger). Any suggestions what could be wrong?
Hmm, I would fire up R on the command line and do something like
Sys.getenv("DISPLAY")
Sys.getenv("PATH")
that way you can figure out what environment variables R is using. How
they are set is hard to know, but as I said, candidates are (all in
the HOME directory or perhaps in the directory where you run R)
.profile
.MacOS/.environment.plist
.bashrc
.bash_login
.Rprofile
.Rlib
Having said that, my _guess_ based on the warning messages is that you
probably have a locale problem (which may or may not be connected to
whether X11 finds the fonts). I am using the default locale (= I have
a clean install, uses english as my system language and have not
touched anything) and I get the following from sessionInfo():
locale:
en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
whereas you seem to have something different:
locale:
C/UTF-8/C/C/C/C
I know little about locales, except that they sometime cause
problems... :)
Another thing you could try to help debug is to run X11 from the Aqua
GUI.
Kasper
Thank you! Cheers, Martin. On Mar 18, 2008, at 8:14 , Simon Urbanek wrote:
Martin, as per posting guide you have forgotten all of the very important piece of information - R version and the locale. I cannot reproduce the problems you describe, so please share with us at least the output of sessionInfo(). In general, if you want to use X11 on Leopard seriously, you may want to upgrade it (see http://trac.macosforge.org/projects/ xquartz ), because the version shipped with Leopard is known to be quite broken. Cheers, Simon On Mar 18, 2008, at 3:11 PM, Martin Eklund wrote:
Hi,
After migrating to Leopard I have problems with X11 when sunning R
from the command line (which I prefer). I acknowledge that this most
likely is not an R issue, but I thought that somebody else on this
list might have had the same problem and has a nice solution to
offer...
When trying to plot something in R from the command line (it works
however from the R GUI) I get the following error message:
===========================================
Error in X11() :
could not find any X11 fonts
Check that the Font Path is correct.
In addition: Warning messages:
1: In X11() :
locale not supported by Xlib: some X ops will operate in C locale
2: In X11() : X cannot set locale modifiers
===========================================
So, it seems like R cannot find the fonts. Issuing xset -q in the
terminal generates the following output:
===========================================
Keyboard Control:
auto repeat: on key click percent: 0 LED mask: 00000000
auto repeat delay: 660 repeat rate: 25
auto repeating keys: 00ffffffffffff7f
00ffffffffffffff
ffffffffffffffff
ffffffffffffffff
bell percent: 50 bell pitch: 400 bell duration: 100
Pointer Control:
acceleration: 2/1 threshold: 4
Screen Saver:
prefer blanking: yes allow exposures: yes
timeout: 600 cycle: 600
Colors:
default colormap: 0x21 BlackPixel: 0 WhitePixel: 16777215
Font Path:
/usr/X11/lib/X11/fonts/misc/,/usr/X11/lib/X11/fonts/TTF/,/usr/X11/
lib/X11/fonts/OTF,/usr/X11/lib/X11/fonts/Type1/,/usr/X11/lib/X11/
fonts/
100dpi/,/usr/X11/lib/X11/fonts/75dpi/
Bug Mode: compatibility mode is disabled
PMS (Energy Star):
Display is not capable of DPMS
Font cache:
Server does not have the FontCache Extension
===========================================
To me the font path in this output seems correct.
I have disabled all DISPLAY settings that I previously had in
my .bash_profile and my PATH variable is set according to: export
PATH=
$PATH:/usr/local/bin:/Applications:/usr/X11/bin:/usr/X11/lib:.
Any suggestions about how to fix this problem is greatly
appreciated!
Thank you very much!
Best regards,
Martin.
========================================
Martin Eklund
PhD Student
Department of Pharmaceutical Biosciences
Uppsala University, Sweden
Ph: +46-18-4714281
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