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

Wed Mar 19 16:31:09 CET 2008

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
>>>
>>> _______________________________________________
>>> 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
> ========================================
>
>
>
>
>
> 	[[alternative HTML version deleted]]
>
> _______________________________________________
> R-SIG-Mac mailing list
> R-SIG-Mac at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac