Unable to load Rcmdr with R 3.0.1 on a Mac OS X 10.8.3
Sarah,
On Aug 21, 2013, at 9:32 PM, Sarah Hardy wrote:
Dear Simon,
Did you try "Repair Disk Permissions" in "Disk Utility"?
Not previously, but I just did and some things were repaired. Then I installed Rcmdr again (but didn't reinstall R 3.0.1), but got the same results. Here is the output you asked for:
system("ls -ld /usr/local /usr/local/lib /usr/local/lib/libtcl*")
ls: /usr/local/lib/libtcl*: Permission denied drwxr-xr-x 7 root wheel 238 Aug 19 16:44 /usr/local drwx------ 31 macports wheel 1054 Aug 21 16:08 /usr/local/lib
Ah, I see, MacPorts has messed up your system (why am I not surprised ;)). If you don't use MacPorts yourself (it causes more headaches than good IMHO) I would suggest blowing away /usr/local and re-installing R. If you don't want to resort to such drastic measures, you can try changing the permissions with something like (in Terminal, not R): sudo chmod a+rx /usr/local/* That will fix your immediate problem, but MacPorts may have messed with other places as well. Cheers, Simon
I also went back to the Disk Utility and selected "Verify Disk Permissions". It said:
Permissions differ on "usr/sbin/pppd"; should be -r-xr-xr-x ; they are -r-sr-xr-x .
Warning: SUID file "usr/sbin/pppd" has been modified and will not be repaired.
This Mac is from our loaner pool and was used for one year by professor who just retired. He did teach a technology education course so I'm not sure what kind of things he might have played around with.
Thank you for your assistance,
Sarah
On Wed, Aug 21, 2013 at 8:28 PM, Simon Urbanek <simon.urbanek at r-project.org> wrote:
Sarah,
errno=13 is "permission denied" so it seems like your system's access control is somewhat misconfigured. Did you try "Repair Disk Permissions" in "Disk Utility"?
If that doesn't help please send us the output of the following R command:
system("ls -ld /usr/local /usr/local/lib /usr/local/lib/libtcl*")
Thanks,
Simon
On Aug 21, 2013, at 7:51 PM, Sarah Hardy wrote:
Using R 3.0.1 on a Mac OS X 10.8.3 I have been unable to load the package Rcmdr. I am not a regular Mac user, but I need to be able to help my students who have Macs install R and Rcmdr to use it in my Intro Stats class. To that end, this week I have been working on a Mac from our loaner pool. I have been able to successfully install Rcmdr on Macs of all OS X types with previous versions of R, so this is a new problem for me. Note that before attempting to install or load Rcmdr I installed XQuartz and I can plot to a graphics window without any problems so I assume it is working properly. Following the directions on http://socserv.mcmaster.ca/jfox/Misc/Rcmdr/installation-notes.html I have been able to install the Rcmdr package without apparent problems. But when I attempt to load the Rcmdr package, either with the Package Manager or by typing
library(Rcmdr)
I get the following error messages: Loading required package: car Loading required package: MASS Loading required package: nnet Error : .onLoad failed in loadNamespace() for 'tcltk', details: call: dyn.load(file, DLLpath = DLLpath, ...) error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/tcltk/libs/tcltk.so': dlopen(/Library/Frameworks/R.framework/Versions/3.0/Resources/library/tcltk/libs/tcltk.so, 10): Library not loaded: /usr/local/lib/libtcl8.6.dylib Referenced from: /Library/Frameworks/R.framework/Versions/3.0/Resources/library/tcltk/libs/tcltk.so Reason: no suitable image found. Did find: /usr/local/lib/libtcl8.6.dylib: stat() failed with errno=13 /usr/local/lib/libtcl8.6.dylib: stat() failed with errno=13 Error: package or namespace load failed for ?Rcmdr? It looks to me like Rcmdr is attempting to load a tcltk CRAN package which no longer exists with R 3.0.1 (which is now bundled with Tck/Tk 8.6.0). One of the many things I have tried is installing tcltk-8.5.5-x11.pkg<http://cran.cnr.berkeley.edu/bin/macosx/tools/tcltk-8.5.5-x11.pkg>, but, as warned, that did not work. I have contacted the Rcmdr package author who suggested that I uninstall R (which was an adventure in and of itself) and reinstall it, but I had the same exact problems. He also suggested that I seek help on the R Mac OS X help list and so here I am. I am hoping someone can point me toward a solution as the start of the semester is nearly upon us. Thank you, Sarah Hardy -- Sarah Hardy, PhD Associate Professor of Mathematics University of Maine Farmington 207-778-7124 Office: Brinkman 100 [[alternative HTML version deleted]]
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-- Sarah Hardy, PhD Associate Professor of Mathematics University of Maine Farmington 207-778-7124 Office: Brinkman 100 Link to Schedule: http://faculty.umf.maine.edu/~hardys/SHardyCalendar.html sarah.hardy at maine.edu