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export variable from bash to R

2 messages · sophie, Krzysztof Mitko

sophie
# 
Dear R experts

This probably seems very easy to you guys, but I'm a beginner and would be
really glad if someone helped me with this:
I am trying to automate the execution of an R script (let's call it
"myscript.R") by passing a variable from a bash script to myscript.R. 
I know I can use the command Rscript, but I don't know how to declare in
bash which variable will be accessed by the "commandArgs" command in
myscript.R.

So my bash script looks about like this:

#!/bin/bash

VARIABLES=( a b c d )

for i in ${VARIABLES[@]}; do
	VARIABLENAME=$i
	Rscript -e 'source("myscript.R")' 
done

In myscript.R, I would like to use the current VARIABLENAME when executing
the program, i.e.,
myscript <- function()	{

args <- commandArgs(TRUE)     # args should now be set to either a,b,c, or d
load(paste("/home/user/../../", args, ".RData", sep=""))    #  this defines
the path to the data file that will be used in this run
                                                                                                   
...further commands...
}

At the moment, myscript.R doesn't seem to be executed at all when I execute
the bash script.
Any help will be greatly appreciated!

Thanks,
sophie







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Krzysztof Mitko
# 
W dniu 29.10.2012 11:43, sophie pisze:
VARIABLES=(a b c d)
for i in ${VARIABLES[@]}
do
	Rscript myscript.R $i
done
When loading the script with "source", the output won't show up unless
you explicitely print it (see ?source). Maybe it's executed but you just
don't see the output?