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

Simon Urbanek simon.urbanek at r-project.org
Mon May 3 23:30:23 CEST 2010 

On May 3, 2010, at 5:04 PM, David Winsemius wrote:

> 
> On May 3, 2010, at 4:48 PM, Simon Urbanek wrote:
> 
>> 
>> 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
> 
> 
> Thanks, Simon;
> 
> Just a note before I hit the restart button ... the package that is current is Security Update 2010-003 and my log files show that I already installed it on 4/16/2010. The log files do not have an entry for Security Update 2010-002.
> 
> (But 2010-003 does say it incorporates all previous updates.)
> 

With the 2010-02 update installed you should see:

hagal:~$ ls -l /usr/X11/lib/libpng12.0.dylib 
-rwxr-xr-x  1 root  wheel  684448 Dec  7 23:33 /usr/X11/lib/libpng12.0.dylib

That matches the content of the update package:

ginaz:su$ lsbom SecUpd2010-003.pkg/Bom |grep /libpng12.0.d
./usr/X11/lib/libpng12.0.dylib	100755	0/0	684448	3378515879

So the update should really solve the issue.
FWIW the full output on the build machine:

hagal:~$ ls -l /usr/X11/lib/libpng12*dylib
lrwxr-xr-x  1 root  wheel      16 Apr 13 13:40 /usr/X11/lib/libpng12.0.24.0.dylib -> libpng12.0.dylib
lrwxr-xr-x  1 root  wheel      16 Apr 13 13:58 /usr/X11/lib/libpng12.0.35.0.dylib -> libpng12.0.dylib
lrwxr-xr-x  1 root  wheel      16 Apr 13 14:18 /usr/X11/lib/libpng12.0.41.0.dylib -> libpng12.0.dylib
-rwxr-xr-x  1 root  wheel  684448 Dec  7 23:33 /usr/X11/lib/libpng12.0.dylib
lrwxr-xr-x  1 root  wheel      16 Apr 13 13:40 /usr/X11/lib/libpng12.dylib -> libpng12.0.dylib

hagal:~$ otool -L /usr/X11/lib/libpng12.0.dylib
/usr/X11/lib/libpng12.0.dylib:
	/usr/X11/lib/libpng12.0.dylib (compatibility version 42.0.0, current version 42.0.0)
	/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.3)
	/usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 111.1.4)

Cheers,
Simon



> -- 
> David.
> 
>> 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
>>>>>>> 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
>>>>>> 
>>>>>> _______________________________________________
>>>>>> 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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>>> 
>>> David Winsemius, MD
>>> West Hartford, CT
>>> 
>>> 
>> 
> 
> David Winsemius, MD
> West Hartford, CT
> 
>

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