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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?

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8
  • What is the output of ls -l ${HOME}/test.R? Commented Dec 2, 2017 at 13:20
  • here's the output: -rwxr--r-- 1 username Dec 2 11:37 /mydirectory/test.R Commented Dec 2, 2017 at 13:32
  • p.s. if I run test.R without the shell script it works fine. Commented Dec 2, 2017 at 13:37
  • 1
    @aaaaa: Can you show the complete command, on how you tested the R script to be working? Commented Dec 2, 2017 at 13:39
  • 2
    @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 Commented Dec 2, 2017 at 13:56

2 Answers 2

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6

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.

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2
  • I'm quite sure the module entries are actually bash functions: modules.sourceforge.net Commented Dec 2, 2017 at 14:53
  • 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 Commented Dec 2, 2017 at 20:11
0

I faced a same issue while running script on Ubuntu container, after replacing the \r\n with \n it works. Open it the script using a text editor and replace all the \r\n with \n

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