Displaying 3 results from an estimated 3 matches for "command_line_argu".
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2017 Jul 12
0
submitting R scripts with command_line_arguments to PBS HPC clusters
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
2017 Jul 12
2
submitting R scripts with command_line_arguments to PBS HPC clusters
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,
2017 Jul 12
1
submitting R scripts with command_line_arguments to PBS HPC clusters
Hi,
The problem is most likely, you need to call a R CMD BATCH with your arguments and the R-script inside of a shell script that you submit to your qsub.
Unfortunately we don't use qsub anymore so can't test it, but it should be as follows:
R-script eg. test.R:
> ##First read in the arguments listed at the command line
> args=(commandArgs(TRUE))
>
> ##args is now a list of