Rcmdr package downloads not permanent
On Ubuntu the default installation of R will not allow you to update packages properly. You can connect to CRAN and download packages and then use them for the session, but after you 'quit()' and then restart Rcmdr it will ask you to download the packages again. I was finally able to get the Rcmdr libraries to update permanently. This is a manual work-around process. If you ever have to update a packages again then find the /tmp directory where R is putting the downloaded packages. In this example it is Rtmp3PTJXf. For you it will be different.
cd /usr/local/lib/R/site-library gunzip -c "/tmp/Rtmp3PTJXf/downloaded_packages/multcomp_1.0-2.tar.gz" | tar xf - chown -R root:staff .
Note that you can start Rcmdr as root if you use 'ssh -Y' option before connecting the R server and you use `sudo sux -` to become root instead of using `sudo su -`. The `sux` command is a wrapper around `su` that handles all the X11 authentication forwarding. This may help you if you think it helps to start Rcmdr as root.