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R as shell script

3 messages · Juha Vierinen, Jeffrey Horner

Original
Juha Vierinen
# 
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
Jeffrey Horner
#
Juha Vierinen wrote:
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!
3 days later
Juha Vierinen
# 
Hi Jeffrey!

Great work with rinterp! I had barely read into the R embedded API and
somebody implements exactly what I need. Thank you! I played around
with it a bit and I was able to access stdin() without any
modifications, I have added a stdin example to the wiki. I hope this
can be considered for inclusion to the R distribution.

I took a quick stab at adding making a copy of argc and argv to the R
script, but those macros look quite scary, so I might be doing many
more mistakes than I am aware of (hint: malloc). Now command line
arguments are also passed, and the following also works:

--------args.r:
#!/usr/bin/rinterp

cat("n args: ")
cat(argc)
cat("\n")
for (i in 1:argc)
{
  cat(sprintf("arg %d = %s\n",i,argv[i]))
}
-------------
n args: 4
arg 1 = ./args.r
arg 2 = a
arg 3 = b
arg 4 = c

The attachment contains the new rinterp.c

juha
On 7/14/06, Jeffrey Horner <jeff.horner at vanderbilt.edu> wrote: