In the mail archives I found a solution that sets environment parameters. http://www.r-project.org/nocvs/mail/r-help/2001/5411.html However I would rather not create the temp files. ----------------------------------------------------- I am using the following method... :: File: Rba #!/bin/sh ## ## ARG 1 is the R program to RUN ## rest of line are arguments if [ $# -eq 0 ] ; then echo echo "usage: Rba RPROGRAM.r ARG1 ARG2 ...." echo exit fi program=$1 shift cmdargs=$* gtime R --quiet \ --no-save \ $cmdargs < $program ----------------------------------------------------- When I acquire the variables in the R program: userargs<-commandArgs() # set parameters from commandline inputfile<-userargs[4] outputfile<-userargs[5] I get the following error/warnings ARGUMENT 'filename1' __ignored__ ARGUMENT 'filename2' __ignored__ Does anyone know what this means?, the parameters appear to make into my program correctly. ----------------------------------------------------- Ideally there would get a PERL GetOpt::Long or Shell getopt capability/module.