R help - Nov 2011 - Running Shell Script with R

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


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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:

====================#!/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 <johnandrewpura at gmail.com>
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.
>
> ______________________________________________
> R-help at 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.
>


-- 
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