runCommandline error - bash: module: command not found

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rj.innet • 0

@rjinnet-17036

Last seen 6.2 years ago

I was running the runCommandline command in Rstudio and encountering the error as given below

> bampaths <- runCommandline(args=args)
bash: module: command not found
bash: module: command not found
Error in system2(command, args = commandargs, stdout = TRUE, stderr = TRUE) :
error in running command

Any insight and answers to solve this error will be highly appreciated.

Thanks!!

runCommandline systemPipeR bash • 1.4k views

ADD COMMENT • link 6.2 years ago rj.innet • 0

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Could you please provide the command(s) that you use to generate the args object that is used by runCommandline. In addition, please provide the output of sessionInfo() executed in an R session right after the error occurred.

Thomas

ADD REPLY • link 6.2 years ago Thomas Girke ★ 1.7k

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As my system does not have a module system, I edited the *.param files, by deleting the modules option line, which was used to generate the args object given to runCommandline. But the error still persists.

ADD REPLY • link 6.2 years ago rj.innet • 0

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