[R] Running Shell Script with R

[Steve Lianoglou]

One more thing I probably overlooked:

On Mon, Nov 28, 2011 at 1:24 PM, Steve Lianoglou
<mailinglist.honeypot at gmail.com> 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 <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.
>>
>> ______________________________________________
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>> 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