One more thing I probably overlooked: On Mon, Nov 28, 2011 at 1:24 PM, Steve Lianoglou <[email protected]> wrote: > Hi John, > > Hard to say (for me) what's going on ... is there any errors in any > relevant logs anywhere? > > Also, note that you don't have to write a bash script to run your R > script .. you can write a script with a shebang like so:
Perhaps your bash wrapper script is necessary for your cluster submission? (I vaguely remember having to write this some time ago). Anyway, perhaps the options(error=) thing may help, but you might also have better luck posting this on the highperformance computing mailing list here: https://stat.ethz.ch/mailman/listinfo/r-sig-hpc -steve > ===================== > #!/usr/bin/env Rscript > > ## R code here. > ===================== > > And the R code will run as a command line script .. maybe that can > prove helpful in your situation. When doing so, I find it helpful to: > > (1) To set R to exit when some error happens in your code you didn't > account for. In "shell/Rscript" mode (or whatever we call it), I've > found that when an error happens, the script just goes through to the > next command. To get R to do so, I set the appropriate options() at > the top of my script like so: > > options(error=function(err) { > cat("An error happened you didn't account for\n") > cat("\n\n") > quit(save='no', status=1) > }) > > (2) I find it handy to use the optparse package from CRAN to help > parsing command line arguments and options/flags: > > http://cran.r-project.org/web/packages/optparse/index.html > > HTH, > -steve > > On Mon, Nov 28, 2011 at 11:10 AM, jp134711 <[email protected]> wrote: >> I'm having some trouble getting my shell script to work. I've checked out the >> Intro to R Manual and a host of other websites, but I still can't get the >> script to work when I submit the job to the cluster. >> >> Here is my main R code: >> >> ##Load Libraries >> ##... >> >> ## Load Time Data >> Args <- commandArgs(trailingOnly = TRUE); >> print(Args); >> timeDat <- read.flowSet(files=NULL, path=Args[1]); >> save(timeDat,file = Args[2]); >> >> Here is my shell script file >> >> >> #!/bin/bash >> #$ -cwd >> #$ -q all.q >> >> R --slave --vanilla --file="/home/jpura/Desktop/FDA_Trial_Data/testscript.R" >> --args "/home/jpura/Desktop/FDA_Trial_Data/Experiment_1/" >> "/home/jpura/Desktop/FDA_Trial_Data/testscript.RData" >> >> It runs just fine (i.e. I get the right output file, which is >> testscript.RData) when I type the lines in the shell script file directly >> into the command prompt. However, when I try to submit the file using: >> >> qsub "path/to/testscript.sh", I don't get the desired output file. >> >> Any insights to this is be greatly appreciated. >> >> Thanks, >> John >> >> >> -- >> View this message in context: >> http://r.789695.n4.nabble.com/Running-Shell-Script-with-R-tp4115734p4115734.html >> Sent from the R help mailing list archive at Nabble.com. >> >> ______________________________________________ >> [email protected] 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. >> > > > > -- > Steve Lianoglou > Graduate Student: Computational Systems Biology > | Memorial Sloan-Kettering Cancer Center > | Weill Medical College of Cornell University > Contact Info: http://cbio.mskcc.org/~lianos/contact > -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ______________________________________________ [email protected] 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.
