Ista,
Thanks for this method, it works! Unfortunately 'R' still spits
everything out to std out, but the variable as you describe below grabs only
the final output variable, similar to how functions or scripts work
internally within 'R'. Thanks!
Kjetil,
Thanks also for your input, but when I tried your method it captured all
of the output, the output is simply redirected from std out to the file, so
that all the undesirable stuff is also captured. Since Ista's method was
working for me, the problem is solved, but I just thought I'd pass on my
results.
Regards,
Mike
"Telescopes and bathyscaphes and sonar probes of Scottish lakes,
Tacoma Narrows bridge collapse explained with abstract phase-space maps,
Some x-ray slides, a music score, Minard's Napoleanic war:
The most exciting frontier is charting what's already here."
-- xkcd
--
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On Fri, Dec 3, 2010 at 12:11 PM, Ista Zahn <iz...@psych.rochester.edu>wrote:
> Hi Mike,
> Is this what you want?
>
> #!/bin/bash
> myTest=$(Rscript testing.R.r)
> echo "myTest contains"
> echo $myTest
>
> Note that testing.R.r will have to cat() or print() myResult (e.g, my
> testing.R.r contains
>
> myResult <- paste("Hello World")
> cat(myResult)
>
> Best,
> Ista
>
> On Fri, Dec 3, 2010 at 1:23 PM, Mike Williamson <this.is....@gmail.com>
> wrote:
> > Hey everyone,
> >
> > I know that I can call 'R' from other scripts, and that I can make
> > command calls from 'R' (e.g., using system() ). But how can I get 'R' to
> > RETURN values to the script that called it. E.g., I would like to be
> able
> > to do something like the following (as a simpler example) from a bash
> > script:
> >
> > #!/bin/bash
> >
> > myTest=echo /usr/local/bin/R --no-restore --no-save -f testing.R.r
> >
> > echo "myTest contains"
> > echo $myTest
> >
> >
> > And ideally this should write out the results of the
> > "testing.R.rscript". So that if the testing.
> > R.r script said something simple like:
> >
> > myResult <- paste("Hello World")
> >
> > Then in the output of the bash script, it should say "myTest
> > contains\nHello World" or something quite similar. But instead it says
> > myTest contains
> > R version 2.11.1 (2010-05-31) Copyright (C) 2010 The R Foundation for
> > Statistical Computing ISBN 3-900051-07-0 R is free software and comes
> with
> > ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain
> > conditions. Type 'license()' or 'licence()' for distribution details.
> > Natural language support but running in an English locale R is a
> > collaborative project with many contributors. Type 'contributors()' for
> more
> > information and 'citation()' on how to cite R or R packages in
> publications.
> > Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()'
> > for an HTML browser interface to help. Type 'q()' to quit R. > > >
> myResult
> > <- paste("Hello World") [1]
> >
> > As you can see, the return from the bash call is really just capturing
> > everything in the ST OUT once 'R' is called, which is not what I want. I
> > have tried several variations, using a function - return combination,
> etc.
> > I have also looked through help pages & documentation. As far as I can
> > tell, it seems no one ever bothers to get information OUT of 'R' and into
> > other scripts. I could write to a csv file & read that file, but that
> seems
> > a REALLY clunky way to handle variable passing.
> >
> > Thanks for any help!
> > Regards,
> > Mike
> >
> >
> >
> >
> > "Telescopes and bathyscaphes and sonar probes of Scottish lakes,
> > Tacoma Narrows bridge collapse explained with abstract phase-space maps,
> > Some x-ray slides, a music score, Minard's Napoleanic war:
> > The most exciting frontier is charting what's already here."
> > -- xkcd
> >
> > --
> > Help protect Wikipedia. Donate now:
> > http://wikimediafoundation.org/wiki/Support_Wikipedia/en
> >
> > [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
>
>
>
> --
> Ista Zahn
> Graduate student
> University of Rochester
> Department of Clinical and Social Psychology
> http://yourpsyche.org
>
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