R help - Jul 2006 - R as shell script

Hi,

I am considering if I should invest in learning R. Based on the
language definition and introductory documents, it seems nice. But now
I am faced with a problem: I want to be able to run R programs easily
from the unix shell, and write scripts that can automatically select R
as the interpreter:

#!/usr/bin/R
cat("Hello world.\n")

This of course doesn't work, because /usr/bin/R is a shell script.

I have been able to create a binary wrapper that calls R with the
correct arguments, which is documented here:

http://kavaro.fi/mediawiki/index.php/Using_R_from_the_shell

This still lacks eg. standard input (but I have no idea how I can
implement it in R) and full command line argument passing (can be
done), but am I on the right track, or is there already something that
does what I need?

juha

[Juha Vierinen]
>Hi,
Hello, Juha.  Your request, quoted below, is likely more appropriate for
R help than for R devel, so I'm redirecting this reply there.
>I am considering if I should invest in learning R. Based on the
>language definition and introductory documents, it seems nice. But now
>I am faced with a problem: I want to be able to run R programs easily
>from the unix shell, and write scripts that can automatically select R
>as the interpreter:
>#!/usr/bin/R
>cat("Hello world.\n")
>This of course doesn't work, because /usr/bin/R is a shell script.
>I have been able to create a binary wrapper that calls R with the
>correct arguments, which is documented here:
>http://kavaro.fi/mediawiki/index.php/Using_R_from_the_shell
>This still lacks eg. standard input (but I have no idea how I can
>implement it in R) and full command line argument passing (can be
>done), but am I on the right track, or is there already something that
>does what I need?
I'm often using something like:

   #!/bin/sh
   R --slave --vanilla <<EOF

   # Your R source code goes here!

   EOF

Within your script, shell substitution for $1, etc., will occur.  So 
with a bit of imagination, you can do about anything :-).  Simple 
enough!  Make sure you `cat' or `print' explicitly whatever has to be 
written on standard output: for one, I usually prefer full control in 
scripts over automatic printing of given expressions.

-- 
Fran?ois Pinard   http://pinard.progiciels-bpi.ca

Juha Vierinen wrote:
> Hi,
> 
> I am considering if I should invest in learning R. Based on the
> language definition and introductory documents, it seems nice. But now
> I am faced with a problem: I want to be able to run R programs easily
> from the unix shell, and write scripts that can automatically select R
> as the interpreter:
> 
> #!/usr/bin/R
> cat("Hello world.\n")
> 
> This of course doesn't work, because /usr/bin/R is a shell script.
> 
> I have been able to create a binary wrapper that calls R with the
> correct arguments, which is documented here:
> 
> http://kavaro.fi/mediawiki/index.php/Using_R_from_the_shell
> 
> This still lacks eg. standard input (but I have no idea how I can
> implement it in R) and full command line argument passing (can be
> done), but am I on the right track, or is there already something that
> does what I need?
If you search the mailing list archives:

http://tolstoy.newcastle.edu.au/R/

you can find entries like the following (searching on "bang"):

http://tolstoy.newcastle.edu.au/R/devel/05/01/1910.html

which implements similar functionality. But I thought this would be a 
fun little (distracting) project, so I created an R wiki page:

http://wiki.r-project.org/rwiki/doku.php?id=developers:rinterp

with source code describing how to solve this problem by embedding R 
within your C program. Here's the main function:

/* rinterp: shebang support for R
  *
  * Usage:
  *
  * From the command line:
  * $ rinterp filename
  *
  * In a file:
  * --------------------
  * #!/path/to/rinterp
  * cat("hello world\n");
  * --------------------
  */
int main(int argc, char **argv){

     /* R embedded arguments */
     char *R_argv[] = {"RINTERP", "--gui=none",
"--slave", "--silent",
"--vanilla","--no-readline"};
     int R_argc = sizeof(R_argv)/sizeof(R_argv[0]);

     struct stat sbuf;

     /* Setenv R_HOME: insert or replace into environment.
      * The RHOME macro is defined during configure
      */
     if (setenv("R_HOME",RHOME,1) != 0){
         perror("ERROR: couldn't set/replace R_HOME");
         exit(1);
     }

     /* Assume last argument is the file we want to source.
      * Ignore other args for now.
      */
     if (argc > 1) {/* don't try and source rinterp binary */
         if (stat(argv[argc-1],&sbuf) != 0){
             perror(argv[argc-1]);
             exit(1);
         }
     } else {
         fprintf(stderr,"Usage: rinterp filename\n");
         exit(1);
     }

     /* Initialize R interpreter */
     Rf_initEmbeddedR(R_argc, R_argv);

     /* Now call R function source(filename) */
     call_fun1str("source",argv[argc-1]);

     exit(0);
}

Feel free to logon to the R wiki and contribute to the page. I think it 
would be interesting to solve this once and for all.

Cheers!
-- 
Jeffrey Horner       Computer Systems Analyst         School of Medicine
615-322-8606         Department of Biostatistics   Vanderbilt University