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.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
>
>
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