Passing command line arguments to R CMD BATCH

Question

I have been using R CMD BATCH my_script.R from a terminal to execute an R script. I am now at the point where I would like to pass an argument to

Answer 1

You need to put arguments before my_script.R and use - on the arguments, e.g.

R CMD BATCH -blabla my_script.R

commandArgs() will receive -blabla as a character string in this case. See the help for details:

$ R CMD BATCH --help
Usage: R CMD BATCH [options] infile [outfile]

Run R non-interactively with input from infile and place output (stdout
and stderr) to another file.  If not given, the name of the output file
is the one of the input file, with a possible '.R' extension stripped,
and '.Rout' appended.

Options:
  -h, --help        print short help message and exit
  -v, --version     print version info and exit
  --no-timing           do not report the timings
  --            end processing of options

Further arguments starting with a '-' are considered as options as long
as '--' was not encountered, and are passed on to the R process, which
by default is started with '--restore --save --no-readline'.
See also help('BATCH') inside R.