[R] R seems to "stall" after several hours on a long series of analyses... where to start?

[Duncan Murdoch]

David L. Van Brunt, Ph.D. wrote:
> Not sure where to even start on this.... I'm hoping there's some debugging I
> can do...
> 
> I have a loop that cycles through several different data sets (same
> structure, different info), performing randomForest growth and
> predictions... saving out the predictions for later study...
> 
> I get about 5 hours in (9%... of the planned iterations.. yikes!) and R just
> freezes.
> 
> This happens in interactive and batch mode execution (I can see from the
> ".Rout" file that it gets about 9% through in Batch mode, and about 6% if in
> interactive mode... does that suggest memory problems?)
> 
> I'm thinking of re-executing this same code on a different platform to see
> if that's the issue (currently using OS X)... any other suggestions on where
> to look, or what to try to get more information?
> 
> Sorry so vague... it's a LOT of code, runs fine without error for many
> iterations, so I didn't think the problem was syntax...

You could try running an external debugger to see whether it appears R 
is stuck in a loop.  I don't know what OS X debuggers are like, but on 
Windows, you can see routine names even without debugging information. 
Recompiling R with debugging info will make the results a lot easier to 
interpret.

Duncan Murdoch