Question

I am trying to run a batch script (set of R commands saved in a file), from a bash script. For some reason, the statement in the bash script that runs the R script works when I type it manually on the command line, however when the statement is executed in the batch script it fails with the error:

munge_data.sh: line 17: –file=stats.R: command not found

Here is a snippet of the bash script:

#!/bin/bash
SCRIPTDIR=/path/to/some/directory
RBIN=`which R`

cd $SCRIPTDIR

$RBIN --file=stats.R > my.stats.output.txt # <- this is line 17 in my script

Can anyone spot what is causing this problem?

Answer 1

Apprently, which R returned nothing, probably because R is not in your PATH, so that $RBIN is empty, and the shell tries to run an inexistent command --file=stats.R.

(If R is supposed to be in the PATH, you can just call it R, without using a variable.)