[R-SIG-Mac] problems with X11 in R 2.11.0
David Winsemius
dwinsemius at comcast.net
Mon May 3 23:04:56 CEST 2010
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.)
--
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
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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
>>>>> 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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>>
>> David Winsemius, MD
>> West Hartford, CT
>>
>>
>
David Winsemius, MD
West Hartford, CT
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