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.urba...@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 <scschom...@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
>>>>>>>>
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>>>>>>>>
>>>>>>>
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>>>>>>>
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>>>>>>>
>>>>>>
>>>>>> --
>>>>>> Brian D. Ripley, rip...@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
>>>>>>
>>>>>> _______________________________________________
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>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>
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>>>>
>>>> _______________________________________________
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>>>
>>> David Winsemius, MD
>>> West Hartford, CT
>>>
>>>
>>
>
> David Winsemius, MD
> West Hartford, CT
>
>
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