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












1














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 --mail-user=myemail@blabla.com

#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?






bash shell-script error-handling r syntax







share|improve this question
























  • What is the output of ls -l ${HOME}/test.R?
    – Hauke Laging
    Dec 2 '17 at 13:20










  • here's the output: -rwxr--r-- 1 username Dec 2 11:37 /mydirectory/test.R
    – aaaaa
    Dec 2 '17 at 13:32










  • p.s. if I run test.R without the shell script it works fine.
    – aaaaa
    Dec 2 '17 at 13:37






  • 1




    @aaaaa: Can you show the complete command, on how you tested the R script to be working?
    – Inian
    Dec 2 '17 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
    – Inian
    Dec 2 '17 at 13:56
















1














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 --mail-user=myemail@blabla.com

#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?






bash shell-script error-handling r syntax







share|improve this question
























  • What is the output of ls -l ${HOME}/test.R?
    – Hauke Laging
    Dec 2 '17 at 13:20










  • here's the output: -rwxr--r-- 1 username Dec 2 11:37 /mydirectory/test.R
    – aaaaa
    Dec 2 '17 at 13:32










  • p.s. if I run test.R without the shell script it works fine.
    – aaaaa
    Dec 2 '17 at 13:37






  • 1




    @aaaaa: Can you show the complete command, on how you tested the R script to be working?
    – Inian
    Dec 2 '17 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
    – Inian
    Dec 2 '17 at 13:56














1












1








1







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 --mail-user=myemail@blabla.com

#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?






bash shell-script error-handling r syntax







share|improve this 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 --mail-user=myemail@blabla.com

#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?






bash shell-script error-handling r syntax




bash shell-script error-handling r syntax






share|improve this question















share|improve this question













share|improve this question




share|improve this question








edited 1 hour ago









Rui F Ribeiro

39.2k1479130




39.2k1479130










asked Dec 2 '17 at 10:47









aaaaa

11016




11016












  • What is the output of ls -l ${HOME}/test.R?
    – Hauke Laging
    Dec 2 '17 at 13:20










  • here's the output: -rwxr--r-- 1 username Dec 2 11:37 /mydirectory/test.R
    – aaaaa
    Dec 2 '17 at 13:32










  • p.s. if I run test.R without the shell script it works fine.
    – aaaaa
    Dec 2 '17 at 13:37






  • 1




    @aaaaa: Can you show the complete command, on how you tested the R script to be working?
    – Inian
    Dec 2 '17 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
    – Inian
    Dec 2 '17 at 13:56


















  • What is the output of ls -l ${HOME}/test.R?
    – Hauke Laging
    Dec 2 '17 at 13:20










  • here's the output: -rwxr--r-- 1 username Dec 2 11:37 /mydirectory/test.R
    – aaaaa
    Dec 2 '17 at 13:32










  • p.s. if I run test.R without the shell script it works fine.
    – aaaaa
    Dec 2 '17 at 13:37






  • 1




    @aaaaa: Can you show the complete command, on how you tested the R script to be working?
    – Inian
    Dec 2 '17 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
    – Inian
    Dec 2 '17 at 13:56
















What is the output of ls -l ${HOME}/test.R?
– Hauke Laging
Dec 2 '17 at 13:20




What is the output of ls -l ${HOME}/test.R?
– Hauke Laging
Dec 2 '17 at 13:20












here's the output: -rwxr--r-- 1 username Dec 2 11:37 /mydirectory/test.R
– aaaaa
Dec 2 '17 at 13:32




here's the output: -rwxr--r-- 1 username Dec 2 11:37 /mydirectory/test.R
– aaaaa
Dec 2 '17 at 13:32












p.s. if I run test.R without the shell script it works fine.
– aaaaa
Dec 2 '17 at 13:37




p.s. if I run test.R without the shell script it works fine.
– aaaaa
Dec 2 '17 at 13:37




1




1




@aaaaa: Can you show the complete command, on how you tested the R script to be working?
– Inian
Dec 2 '17 at 13:39




@aaaaa: Can you show the complete command, on how you tested the R script to be working?
– Inian
Dec 2 '17 at 13:39




2




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
– Inian
Dec 2 '17 at 13:56




@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
– Inian
Dec 2 '17 at 13:56










1 Answer
1






active

oldest

votes


















5














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.






share|improve this answer























  • I'm quite sure the module entries are actually bash functions: modules.sourceforge.net
    – liori
    Dec 2 '17 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
    – Ferrybig
    Dec 2 '17 at 20:11











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1 Answer
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active

oldest

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1 Answer
1






active

oldest

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active

oldest

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active

oldest

votes









5














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.






share|improve this answer























  • I'm quite sure the module entries are actually bash functions: modules.sourceforge.net
    – liori
    Dec 2 '17 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
    – Ferrybig
    Dec 2 '17 at 20:11
















5














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.






share|improve this answer























  • I'm quite sure the module entries are actually bash functions: modules.sourceforge.net
    – liori
    Dec 2 '17 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
    – Ferrybig
    Dec 2 '17 at 20:11














5












5








5






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.






share|improve this answer














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.







share|improve this answer














share|improve this answer



share|improve this answer








edited Dec 2 '17 at 14:27

























answered Dec 2 '17 at 10:55









Inian

3,860824




3,860824












  • I'm quite sure the module entries are actually bash functions: modules.sourceforge.net
    – liori
    Dec 2 '17 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
    – Ferrybig
    Dec 2 '17 at 20:11


















  • I'm quite sure the module entries are actually bash functions: modules.sourceforge.net
    – liori
    Dec 2 '17 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
    – Ferrybig
    Dec 2 '17 at 20:11
















I'm quite sure the module entries are actually bash functions: modules.sourceforge.net
– liori
Dec 2 '17 at 14:53






I'm quite sure the module entries are actually bash functions: modules.sourceforge.net
– liori
Dec 2 '17 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
– Ferrybig
Dec 2 '17 at 20:11




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
– Ferrybig
Dec 2 '17 at 20:11


















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