Re: [R] Pass Arguments to R with an LSF submit

2010-10-01 Thread Joshua Wiley
Hi, I have no idea about LSF managed clusters, but on Windows at least I use (and maybe you can try it): Create a script file (.R) with: # toprint <- commandArgs() length(toprint) print(toprint) # Now moving to the command prompt, either

Re: [R] Pass Arguments to R with an LSF submit

2010-10-01 Thread Thomas Stewart
On further review, it appears that & has nothing to do with the problems I'm experiencing. For some reason, the computer gods don't like --args 1 3. A solution I've found is outlined in the R-help archives: http://tolstoy.newcastle.edu.au/R/help/05/02/13163.html . If you know of another solution

[R] Pass Arguments to R with an LSF submit

2010-10-01 Thread Thomas Stewart
I'm trying to run R in batch mode on an LSF managed cluster. In simple settings, I can do it just fine. The trouble I'm having is when I try to pass arguments to the batch job. For example, bsub R CMD BATCH --args 1 3 commandfile.R & LSF doesn't like the &, and it doesn't run. I'm hoping one