[R-SIG-Mac] problems with X11 in R 2.11.0

David Winsemius dwinsemius at comcast.net
Mon May 3 22:04:45 CEST 2010


On May 3, 2010, at 3:37 PM, steven mosher wrote:

> I have 10.5.8.  I posted on this a while back.
>
> I also had version 36.. I believe for lippng.
>
(Calling X11() did not really "crash" my machine. but it reported a  
serious error and asked me to save and restart.

otools reports my version in that directory is 36.0.0.

	/usr/X11/lib/libpng12.0.dylib (compatibility version 36.0.0, current  
version 36.0.0)

(Of course, it also lists about 10 other locations as well. Should I  
have posted the entire output? )

I install all updates when they are pushed. I just did a Software  
Update of my 10.5.8 machine and it says I am up-to-date.

Does it matter that I set a fairly long Sys.env path in my .Rprofile  
and that "/usr/X11/lib" is not in that path?

Sys.setenv(PATH="/opt/local/bin:/opt/local/sbin:/sw/bin:/sw/sbin:/usr/ 
bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/texbin:/usr/X11/bin:/usr/ 
X11R6/bin")

For the record, I am not having problems with R or RGL which I believe  
requires X11 for some of its display. And capabilities() thinks I have  
X11:

 > capabilities()
     jpeg      png     tiff    tcltk      X11     aqua http/ftp   
sockets   libxml
     TRUE     TRUE     TRUE     TRUE     TRUE     TRUE     TRUE      
TRUE     TRUE
     fifo   cledit    iconv      NLS  profmem    cairo
     TRUE     TRUE     TRUE     TRUE     TRUE     TRUE


sessionInfo()
R version 2.10.1 RC (2009-12-09 r50695)

### I don't really want to update to 2.11.0 because of the Hmisc  
incompatibility. I use Harrell's packages extensively.

x86_64-apple-darwin9.8.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] lattice_0.18-3

loaded via a namespace (and not attached):
[1] grid_2.10.1  tools_2.10.1

>
>
> On Mon, May 3, 2010 at 12:01 PM, Simon Urbanek
> <simon.urbanek at r-project.org>wrote:
>
>> I can only second Brian's response. The build machine is a  
>> completely clean
>> Mac OS X 10.5.8 (up to date with all recent security updates) - I  
>> have not
>> installed any custom X11 updates. I don't know why Seth has an  
>> outdated
>> libpng in the X11 installation. Seth, please make sure your system  
>> is up to
>> date. Given the date of the last update I would suspect that   
>> Software
>> Update should resolve this issue (if that is the case it's  
>> nonetheless a
>> little annoying that Apple's security update would break backward
>> compatibility).
>>
>> Cheers,
>> Simon
>>
>>
>> On May 3, 2010, at 1:19 AM, Prof Brian Ripley wrote:
>>
>>> Something is wrong with your system software.  On my Leopard box:
>>>
>>> tystie% otool -L
>> /Library/Frameworks/R.framework/Resources/modules/i386/R_X11.so
>>> ...
>>>      /usr/X11/lib/libpng12.0.dylib (compatibility version 42.0.0,
>> current version 42.0.0)
>>>
>>> So your /usr/X11/lib/libpng12.0.dylib is different from mine (and  
>>> from
>> the CRAN build machine's).
>>>
>>> Your choices are
>>>
>>> - to resolve this (and it is not an R issue). I'd start by running  
>>> the
>> software updater ....
>>>
>>> - to build R from the sources against the software on your machine.
>>>
>>> On Sun, 2 May 2010, steven mosher wrote:
>>>
>>>> I had the same Issue with 2.10.1. never got it resolved. I was  
>>>> hoping
>> that
>>>> 2.11 would fix it...alas
>>>>
>>>> On Thu, Apr 29, 2010 at 2:59 PM, Seth Schommer <scschommer at gmail.com 
>>>> >
>> wrote:
>>>>
>>>>> I installed R 2.11.0 today and immediately came across an issue  
>>>>> I did
>>>>> not experience using version 2.10.1.  For some reason, I can not  
>>>>> use
>>>>> X11 in R.  Here's a simple example:
>>>>>
>>>>>
>>>>>> X11()
>>>>> Error in X11() : X11 module cannot be loaded
>>>>> In addition: Warning message:
>>>>> In X11() :
>>>>> unable to load shared library
>>>>> '/Library/Frameworks/R.framework/Resources/modules/i386/R_X11.so':
>>>>> dlopen(/Library/Frameworks/R.framework/Resources/modules/i386/ 
>>>>> R_X11.so,
>>>>> 6): Library not loaded: /usr/X11/lib/libpng12.0.dylib
>>>>> Referenced from:
>>>>> /Library/Frameworks/R.framework/Resources/modules/i386/R_X11.so
>>>>> Reason: Incompatible library version: R_X11.so requires version
>>>>> 42.0.0 or later, but libpng12.0.dylib provides version 36.0.0
>>>>>> sessionInfo()
>>>>> R version 2.11.0 (2010-04-22)
>>>>> i386-apple-darwin9.8.0
>>>>>
>>>>> locale:
>>>>> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>>>>>
>>>>> attached base packages:
>>>>> [1] stats     graphics  grDevices utils     datasets  methods    
>>>>> base
>>>>>
>>>>>
>>>>> I'm running Mac OS X 10.5.8.  This error occurs when running  
>>>>> R.app and
>>>>> while running R from the terminal.  After experience this I
>>>>> reinstalled 2.10.1 and tried the same command and had no problems.
>>>>> Just to make sure, I installed 2.11.0 again, and sure enough, I  
>>>>> got
>>>>> the same error.  Is this a bug, or have I done something wrong?
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Seth
>>>>>
>>>>> _______________________________________________
>>>>> R-SIG-Mac mailing list
>>>>> R-SIG-Mac at stat.math.ethz.ch
>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>>
>>>>
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>>>>
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>>>
>>> --
>>> 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
>>>
>>> _______________________________________________
>>> R-SIG-Mac mailing list
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>>>
>>>
>>
>>
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David Winsemius, MD
West Hartford, CT



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