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 specify the path to the script or make sure it is in the same directory as I am currently in prompt> C:\my\path\to\R\bin\R CMD BATCH --no-save "--args 1 3" -- myscript.R myresults.txt In my "myresults.txt" file, 1 and 3 are elements 8 & 9 in the vector "toprint". It seems like I recall reading that some of this is platform dependent. Best regards, Josh On Fri, Oct 1, 2010 at 10:23 PM, Thomas Stewart <tgstew...@gmail.com> wrote: > 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, please let me know. > > Thanks, > -tgs > > On Fri, Oct 1, 2010 at 3:01 PM, Thomas Stewart <tgstew...@gmail.com> wrote: > >> 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 you can help me >> submit a job to an LSF cluster that allows me to pass arguments to R. >> >> Thank you, >> -tgs >> > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > -- Joshua Wiley Ph.D. Student, Health Psychology University of California, Los Angeles http://www.joshuawiley.com/ [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
