Question: runCommandline error - bash: module: command not found
0
gravatar for rj.innet
12 months ago by
rj.innet0
rj.innet0 wrote:

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!!

ADD COMMENTlink written 12 months ago by rj.innet0

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 REPLYlink written 12 months ago by Thomas Girke1.7k

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 REPLYlink written 12 months ago by rj.innet0
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