[R-SIG-Mac] X11 problem after migration to Leopard

Wed Mar 19 16:20:10 CET 2008

A suggestion that one sees fairly frequently on other mailing lists 
for this class of problem is to create a new user, login as that new 
user, and try from there. If things work, then the hypothesis of 
lurking config files  (or in some cases, broken preference files), is 
considered to be confirmed.

-Don

At 8:35 AM +0100 3/19/08, 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?
>
>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
>>>
>>>  _______________________________________________
>>>  R-SIG-Mac mailing list
>>>  R-SIG-Mac at stat.math.ethz.ch
>>>  https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>
>>>
>>
>
>========================================
>Martin Eklund
>PhD Student
>Department of Pharmaceutical Biosciences
>Uppsala University, Sweden
>Ph: +46-18-4714281
>========================================
>
>
>
>
>
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>
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-- 
--------------------------------------
Don MacQueen
Environmental Protection Department
Lawrence Livermore National Laboratory
Livermore, CA, USA
925-423-1062