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

Simon Urbanek simon.urbanek at r-project.org
Mon May 3 22:48:35 CEST 2010 

On May 3, 2010, at 4:04 PM, David Winsemius wrote:

> 
> 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.
> 

Hmm.. now the real question is why some Leopard systems have libpng12 version 36 and some have version 42. As I said the build machine has a pristine Leopard install, I did not install any custom X11 updates - it just has all security updates.

pkginfo reveals that the file has been last updated by the 2010 Leopard security update 02:

hagal:~$ pkgutil -v --file-info /usr/X11/lib/libpng12.0.dylib
     volume: /
       path: usr/X11/lib/libpng12.0.dylib

[...]
       pkgid: com.apple.pkg.update.security.2010.002.leopard
 pkg-version: 1.0.1.1191932192
install-time: Tue Apr 13 14:18:52 2010
         uid: 0 (root)
         gid: 0 (wheel)
        mode: 100755 (-rwxr-xr-x )

I would suggest installing the latest Leopard security upgrade by hand (if your Software Update really shows up-to-date system otherwise use System Update) - it also includes the 02 update which in turn includes the updated libpng:

http://support.apple.com/kb/DL1027

(This is for Mac OS X 10.5.8 client [=not server] *ONLY*)


> 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?
> 

No, it doesn't matter.

Cheers,
Simon


> 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
>>>>>> 
>>>>> 
>>>>>    [[alternative HTML version deleted]]
>>>>> 
>>>>> _______________________________________________
>>>>> R-SIG-Mac mailing list
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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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>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>> 
>>>> 
>>> 
>>> 
>> 
>> 	[[alternative HTML version deleted]]
>> 
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> 
> David Winsemius, MD
> West Hartford, CT
> 
>

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