This sounds like an operating system specific question, in that "submit the R script to a PBS HPC scheduler" would be the kind of action that would run R with very different environment variables and possibly different access credentials than your usual interactive terminal. A thorough reading of the "Installation and Administration Guide" and some study of your HPC documentation are in order. -- Sent from my phone. Please excuse my brevity.
On July 11, 2017 5:25:20 PM PDT, Bogdan Tanasa <[email protected]> wrote: >Dear all, > >please could you advise me on the following : I've written a R script >that >reads 3 arguments from the command line, i.e. : > >" args <- commandArgs(TRUE) >TUMOR <- args[1] >GERMLINE <- args[2] >CHR <- args[3] ". > >when I submit the R script to a PBS HPC scheduler, I do the following >(below), but ... I am getting an error message. >(I am not posting the error message, because the R script I wrote works >fine when it is run from a regular terminal ..) > >Please may I ask, how do you usually submit the R scripts with command >line >arguments to PBS HPC schedulers ? > >qsub -d $PWD -l nodes=1:ppn=4 -l vmem=10gb -m bea -M [email protected] \ >-v TUMOR="tumor.bam",GERMLINE="germline.bam",CHR="chr22" \ >-e script.efile.chr22 \ >-o script.ofile.chr22 \ >script.R > >Thank you very very much ! > >-- bogdan > > [[alternative HTML version deleted]] > >______________________________________________ >[email protected] mailing list -- To UNSUBSCRIBE and more, see >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. ______________________________________________ [email protected] mailing list -- To UNSUBSCRIBE and more, see 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.
