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.
