[R] export variable from bash to R

Barry Rowlingson b.rowlingson at lancaster.ac.uk
Tue Oct 30 17:02:31 CET 2012

On Tue, Oct 30, 2012 at 2:03 PM, sophie <melanie.bieli at bluewin.ch> wrote:
> Hi Barry
> Thank you very much for your reply. I changed my scripts according to your
> suggestions - this is how they look now:
> #!/bin/bash
> VARIABLES=( a b c d )
> for i in ${VARIABLES[@]}; do
>       export VARIABLENAME=$i
>       Rscript -e 'source("myscript.R")'
> done
> and in the R program, I used
> args <- Sys.getenv("VARIABLENAME")  instead of args <- commandArgs(TRUE)
> But when I add the "R --slave", the program hangs, so I left it out (you
> said it was just to cut out the startup messages, so I assumed it shouldn't
> really matter).

 It didn't hang, it was probably sitting there waiting for you to say
q() - I was just using it interactively.

> It's still not working, though. There is no error message,
> but the R program still doesn't seem to be executed (@Krzysztof: The R
> program makes plots - since these plots are not produced,  I figured that
> something with the call of myscript.R is not working)
> Any ideas or suggestions?

 Does it produce any printed output? Can you add some print statements
to see where it gets to?

$ cat myscript.R
print("Hello world")
$ Rscript -e 'source("myscript.R")'
[1] "Hello world"

 - here at least I know its finding the right script.


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