Issues with R.app, Rcmdr, and saved workspaces

Dan,

Specifically, if you save a workspace during a session in which you  
have worked with Rcmdr, quit that session, start a new R session  
using that same workspace

Yes, that is a known issue with the X11 tcltk package if you try to  
save tcltk objects in the image. Basically what happens is that when  
you save a workspace containing tcltk objects, R will automatically  
load tcltk on the next start while restoring the image. This very  
often breaks things (including R crash), because R may have been  
started in a different way before (cmd line/X11/R.app...). The short  
answer is don't save tcltk objects.

The hot-fix for the Rcmdr is to run
rm(.commander.done)
before you quit R and save the image. I have no idea why this  
variable is stored in the global environment instead of a private one  
in Rcmdr, but you'll have to ask John about this.

Cheers,
Simon