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