Running R script via shell script. syntax error near unexpected token `('

Question

I am currently trying to run an R script via a shell script.

Here the R script:

test = rnorm(1:100, 1000)
write.csv(test, 'test.csv')

And here the bash script which calls the R one:

#!/bin/bash -l
#SBATCH --partition=compute
#SBATCH --job-name=test
#SBATCH --mail-type=ALL
#SBATCH [email protected]
#SBATCH --time=00:10:00
#SBATCH --nodes=1
#SBATCH --tasks-per-node=12
#SBATCH --account=myaccount
module purge
module load R
${HOME}/test.R

I think I did everything correctly, but the output returns the following error:

/mydirectory/test.R: line 3: syntax error near unexpected token `('
/mydirectory/test.R: line 3: `test = rnorm(1:100, 1000)'

Why I did I get this error?

Solution

The problem is the shell is trying to the run your ${HOME}/test.R with a bash interpreter for which it is not trying to understand the syntax from the line number 3. Use the R interpreter explicitly from which you want the test.R to run from.

Set the interpreter for your Rscript in test.R as

#!/usr/bin/env Rscript

module purge
module load R 
test = rnorm(1:100, 1000)
write.csv(test, 'test.csv')

This way with the interpreter set, you can now run it from the shell script as

Rscript ${HOME}/test.R

---

Remember, logging into R shell and running the commands on it, and trying it out in the shell script are not the same, R shell is different from the bash shell. You need to use the way to run the commands without logging into R from the command line directly and use that same approach in the shell script.

Comments

[Hauke Laging]

What is the output of ls -l ${HOME}/test.R?

[aaaaa]

p.s. if I run test.R without the shell script it works fine.

[Inian]

@aaaaa: Can you show the complete command, on how you tested the R script to be working?

[aaaaa]

it is a 2 lines R script just to see if the shell script works. I just ran it by logging into R and using 'source('test.R')' and it works.

[Inian]

@aaaaa: Remember, logging into R and running the commands, and trying it out in the shell script is not the same, R shell is different from the bash shell. Figure out a way to run the commands without logging into R from the command line directly and use that same approach in the shell script

[aaaaa]

yes, just realised that...let's see...

[aaaaa]

right..the command is Rscript and it works!

[yieldsfalsehood]

I'm quite sure the module entries are actually bash functions: modules.sourceforge.net

[Ferrybig]

After adding the shebang, you can just call the script as ${HOME}/test.R, you don't need to prepend it with the interpreter anymore