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

Martin Eklund martin.eklund at farmbio.uu.se
Thu Mar 20 10:42:33 CET 2008 

On Mar 20, 2008, at 10:02 , Prof Brian Ripley wrote:

> On Thu, 20 Mar 2008, Martin Eklund wrote:
>
>> [snip]
>
> Including snipping the vital data!  (Please don't do that.)

Sorry - won't do it again!


>>> 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.
>>>
>>
>> As you say, I did indeed have a locale problem. I've never had any
>> reasons to worry about locale settings before and therefore know
>> hardly anything about them, but if I change the locale according to
>> Sys.setlocale("LC_CTYPE", "C") plotting works like a charm.  
>> However, I
>> have to change the locale every time I start a new session. Is  
>> there a
>> way to permanently change this setting?
>
> Setting LC_ALL=C in the environment does that.
>
> However, it seems pretty unlikely that you really want to do that in  
> Sweden. The issue seems to be that you have the encoding set to an  
> invalid value
>
>> locale:
>> C/UTF-8/C/C/C/C
>
> is wrong.  So try setting LC_ALL=sv_SE.UTF-8, or if you only want  
> the character set to be UTF-8, LC_CTYPE=en_US.UTF-8
>
> I just tested
>
> blacklark% env LC_CTYPE=sv_SE.UTF-8 R
>> Sys.getlocale()
> [1] "C/sv_SE.UTF-8/C/C/C/C"
>
> and it is displaying correctly on X11 plots.
>
> I suggest you track down the incorrect setting of LC_CTYPE.


Thank you - that did the trick. I simply added

LC_ALL=sv_SE.ISO8859-1
export LC_ALL

to my .bash_profile, and it now works perfectly.

Cheers,

Martin.



>
>
>>
>> Thank you all for your help!
>>
>> Best regards,
>>
>> Martin.
>>
>>
>>
>>>>> 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
>>>
>>
>> ========================================
>> 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
>>
>
> -- 
> Brian D. Ripley,                  ripley at stats.ox.ac.uk
> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
> University of Oxford,             Tel:  +44 1865 272861 (self)
> 1 South Parks Road,                     +44 1865 272866 (PA)
> Oxford OX1 3TG, UK                Fax:  +44 1865 272595

========================================
Martin Eklund
PhD Student
Department of Pharmaceutical Biosciences
Uppsala University, Sweden
Ph: +46-18-4714281

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