Running R batch script in a bash script

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?

Vincent Zoonekynd · Accepted Answer · 2012-03-07 08:02:11Z

4

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.)

answered Mar 7, 2012 at 8:02

Vincent Zoonekynd

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3 Comments

Homunculus Reticulli Over a year ago

Hmmm, thats interesting, I am running the bash script from a cron task.; I tested the statements on the command line whilst writing the (bash) script and WHICH R does return the bath to the R binary. As a matter of fact, R is on my path but when running as a cron task, I noticed R was not being found, and thats why I explicitly stated where to find R - and that still appears not to be working - what to do?!

Vincent Zoonekynd Over a year ago

The PATH used by crontab is defined in the crontab file itself and is usually very conservative (i.e., almost empty). You can either add the directory containing R to this PATH, or change the PATH at the begining of your script (preferred), or hardcode the path to the R executable in your script (e.g., by explicitly setting the value of your RBIN variable).

Homunculus Reticulli Over a year ago

Yup, the explicit path fixed it. Thanks!

Shawn Zhang · Accepted Answer · 2012-03-07 15:18:56Z

1

You don't put the right R call function in Bash.

Running R in command line following below command format (R CMD BATCH file output.file)

#!/bin/bash

R CMD BATCH your_file.R my.stats.output.txt

will get you 99% what you want(Make sure you have execute permission of this bash file)

The reason you didn't get it right is because when execute which R ,the control was transfer from bash file to R program , then the bash script pause the execution .

edited Mar 7, 2012 at 15:18

answered Mar 7, 2012 at 14:52

Shawn Zhang

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Comments

Dirk is no longer here · Accepted Answer · 2012-03-07 16:30:51Z

1

Nobody mentioned Rscript (comes with R) or littler which predates it:

#!/usr/bin/Rscript

z <- rnorm(5)
# ... other R commands ...

or

#!/usr/bin/r  

z <- rnorm(5)
# ... other R commands ...

both of which you can run directly once you do the usual chmod 755 filename.

answered Mar 7, 2012 at 16:30

Dirk is no longer here

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