[R-SIG-Mac] Unable to load Rcmdr with R 3.0.1 on a Mac OS X 10.8.3

[Simon Urbanek]

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 ŒRcmdr‚
> >
> > 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]]
> >
> > _______________________________________________
> > R-SIG-Mac mailing list
> > R-SIG-Mac at r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> 
> 
> 
> 
> -- 
> 
> 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
>