R help - Dec 2010 - How to get 'R' to talk BACK to other languages / scripts??

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]]

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.mvw at 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 at 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

see below.

On Fri, Dec 3, 2010 at 3:23 PM, Mike Williamson <this.is.mvw at 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.
>
Look at this example:

kjetil at kjetil:~$ R --vanilla < test.R > outtest.txt
kjetil at kjetil:~$ cat outtest.txt

R version 2.13.0 Under development (unstable) (2010-11-26 r53672)
Copyright (C) 2010 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)

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.
>  test <- 1:10
>  test <- sample(test)
>  cat(file=stdout(), test, "\n")
3 10 9 7 2 4 6 5 1 8
> q("no")
kjetil at kjetil:~$ cat test.R
 test <- 1:10
 test <- sample(test)
 cat(file=stdout(), test, "\n")
q("no")

kjetil at kjetil:~$





> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?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 at 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.
>