[R] [newbie] modules.sourceforge.net and system(...) calls
Tom Roche
Tom_Roche at pobox.com
Wed Feb 8 22:56:28 CET 2012
summary: how to write an R script that requires certain 'modules'
(in the modules.sourceforge.net sense, not the generic sense)?
details:
I'm writing an R script (beginning
#!/usr/bin/env Rscript
) that uses a system call to one of the fine NCO tools
http://nco.sourceforge.net/
to run on a linux cluster that uses the fine Environment Modules
package
http://modules.sourceforge.net/
My script works if I remember to do
$ module add nco
before I run the script; if not, I get
sh: <name of tool/>: command not found
since the Environment Modules setup paths, etc. So I'm wondering,
1 How best to write a script that both sets up the module and runs my R?
Is there an R package that provides modules.sf.net compatibility,
so that I can run the whole thing via Rscript? Or should I do a
shell script that does something like
module add nco
R CMD BATCH myscript.r
Or something completely different?
2 How to catch failure of system(...) calls, so as to fail fast?
(E.g., in case I try to run the R script without setting up the
modules first.)
TIA, Tom Roche <Tom_Roche at pobox.com>
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