Running R script via shell script. syntax error near unexpected token `('
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
edited 1 hour ago
Rui F Ribeiro
39.2k1479130
asked Dec 2 '17 at 10:47
aaaaa
11016
|
show 3 more comments
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
edited 1 hour ago
Rui F Ribeiro
39.2k1479130
asked Dec 2 '17 at 10:47
aaaaa
11016
What is the output ofls -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 withoutlogging into Rfrom the command line directly and use that same approach in the shell script
– Inian
Dec 2 '17 at 13:56
|
show 3 more comments
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
edited 1 hour ago
Rui F Ribeiro
39.2k1479130
asked Dec 2 '17 at 10:47
aaaaa
11016
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
edited 1 hour ago
Rui F Ribeiro
39.2k1479130
asked Dec 2 '17 at 10:47
aaaaa
11016
edited 1 hour ago
Rui F Ribeiro
39.2k1479130
asked Dec 2 '17 at 10:47
aaaaa
11016
edited 1 hour ago
Rui F Ribeiro
39.2k1479130
edited 1 hour ago
Rui F Ribeiro
39.2k1479130
edited 1 hour ago
Rui F Ribeiro
39.2k1479130
39.2k1479130
asked Dec 2 '17 at 10:47
aaaaa
11016
asked Dec 2 '17 at 10:47
aaaaa
11016
asked Dec 2 '17 at 10:47
aaaaa
11016
11016
What is the output ofls -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 withoutlogging into Rfrom the command line directly and use that same approach in the shell script
– Inian
Dec 2 '17 at 13:56
|
show 3 more comments
What is the output ofls -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 withoutlogging into Rfrom 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
|
show 3 more comments
1 Answer
1
active
oldest
votes
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 ${HOME}/test.R
Remember, logging into R shell and running the commands on it, and trying it out in the shell script are not the same, R shell is different from the bash shell. You need to use the way to run the commands without logging into R from the command line directly and use that same approach in the shell script.
answered Dec 2 '17 at 10:55
Inian
3,860824
I'm quite sure themoduleentries are actually bash functions: modules.sourceforge.net
– liori
Dec 2 '17 at 14:53
After adding the shebang, you can just call the script as${HOME}/test.R, you don't need to prepend it with the interpreter anymore
– Ferrybig
Dec 2 '17 at 20:11
add a comment |
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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 ${HOME}/test.R
Remember, logging into R shell and running the commands on it, and trying it out in the shell script are not the same, R shell is different from the bash shell. You need to use the way to run the commands without logging into R from the command line directly and use that same approach in the shell script.
answered Dec 2 '17 at 10:55
Inian
3,860824
I'm quite sure themoduleentries are actually bash functions: modules.sourceforge.net
– liori
Dec 2 '17 at 14:53
After adding the shebang, you can just call the script as${HOME}/test.R, you don't need to prepend it with the interpreter anymore
– Ferrybig
Dec 2 '17 at 20:11
add a comment |
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 ${HOME}/test.R
Remember, logging into R shell and running the commands on it, and trying it out in the shell script are not the same, R shell is different from the bash shell. You need to use the way to run the commands without logging into R from the command line directly and use that same approach in the shell script.
answered Dec 2 '17 at 10:55
Inian
3,860824
I'm quite sure themoduleentries are actually bash functions: modules.sourceforge.net
– liori
Dec 2 '17 at 14:53
After adding the shebang, you can just call the script as${HOME}/test.R, you don't need to prepend it with the interpreter anymore
– Ferrybig
Dec 2 '17 at 20:11
add a comment |
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.
answered Dec 2 '17 at 10:55
Inian
3,860824
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 ${HOME}/test.R
Remember, logging into R shell and running the commands on it, and trying it out in the shell script are not the same, R shell is different from the bash shell. You need to use the way to run the commands without logging into R from the command line directly and use that same approach in the shell script.
answered Dec 2 '17 at 10:55
Inian
3,860824
edited Dec 2 '17 at 14:27
answered Dec 2 '17 at 10:55
Inian
3,860824
answered Dec 2 '17 at 10:55
Inian
3,860824
answered Dec 2 '17 at 10:55
Inian
3,860824
3,860824
I'm quite sure themoduleentries are actually bash functions: modules.sourceforge.net
– liori
Dec 2 '17 at 14:53
After adding the shebang, you can just call the script as${HOME}/test.R, you don't need to prepend it with the interpreter anymore
– Ferrybig
Dec 2 '17 at 20:11
add a comment |
I'm quite sure themoduleentries 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
add a comment |
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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 Rfrom the command line directly and use that same approach in the shell script– Inian
Dec 2 '17 at 13:56