problems with X11 in R 2.11.0
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.
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?
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 I don't know why Seth has an outdated libpng in the X11 installation.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
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