R help - Jan 2003 - Exception Handling

R Users:

How can I catch R errors and depend on this error call other R
functions in Perl? 

The foolowing is the error message when I use perl call R. 

Error in nls(modout ~ exp(-b1 * modin)/(b2 + b3 * modin), trace = F,
start = c(b1 = 0.005,  : 
        singular gradient
Segmentation fault



Thanks,

Zhongming

Zhongming,
> R Users:
> 
> How can I catch R errors and depend on this error call other R
> functions in Perl? 
I am working on similar issues, perhaps. The simple CGI-type approach I am
exploring just involves having Perl check for such a string, such as
"Execution Halted" or the one you saw. Then you can decide what to do
with
Perl for reporting the error.  For a more general solution, it may be that
you add a simple cat() string that says your R function/program succeeded
and then have Perl check for that. (I presume you are using Perl's system()
to make the call from Perl to R.)

To get more information from R about the exception/error in your program,
see various related functions, such as options("show.error.messages"),
geterrmessage(), try(), traceback(), etc.  There is a lot of flexibility in
both R and Perl to customize things as specific-to-general as you want them.

Hope this helps.

Best,
Bill

----------------------------------------
Bill Pikounis, Ph.D.
http://biometrics.merck.com/

Biometrics Research Department
Merck Research Laboratories
PO Box 2000, MailDrop RY84-16  
126 E. Lincoln Avenue
Rahway, New Jersey 07065-0900
USA

v_bill_pikounis at merck.com

Phone: 732 594 3913
Fax: 732 594 1565

> -----Original Message-----
> From: Zhongming Yang [mailto:Zhongming.Yang at cchmc.org]
> Sent: Wednesday, January 15, 2003 10:35 AM
> To: r-help at stat.math.ethz.ch
> Subject: [R] Exception Handling
> 
> 
> R Users:
> 
> How can I catch R errors and depend on this error call other R
> functions in Perl? 
> 
> The foolowing is the error message when I use perl call R. 
> 
> Error in nls(modout ~ exp(-b1 * modin)/(b2 + b3 * modin), trace = F,
> start = c(b1 = 0.005,  : 
>         singular gradient
> Segmentation fault
> 
> 
> 
> Thanks,
> 
> Zhongming
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> http://www.stat.math.ethz.ch/mailman/listinfo/r-help
> 
------------------------------------------------------------------------------

Zhongming Yang <Zhongming.Yang at cchmc.org>
wrote:
> How can I catch R errors and depend on this error call other R
> functions in Perl? 
Here's a little Perl script that invokes R.  If it is called with a positive
numerical argument, then R exits with that status, and Perl catches it via $?.
Note the script file in /tmp is saved (intentionally) if R exits abnormally.
See also the help pages for q(), stop(), and options("error").


#!/usr/local/bin/perl
(($arg1) = @ARGV) || die "Must pass a numerical argument.\n";
$script = "/tmp/rwrap$$.R";
open(SCRIPT, ">$script");
print SCRIPT <<EOF;
  arg1 <- $arg1
  options(error=expression(q(status=arg1)))
  if (arg1 > 0) log("a")
  q()
EOF
close(SCRIPT);
system("R --vanilla --slave < $script");
($Rstat = $?/256) && die "Aborted in R with status $Rstat.\n";
unlink $script;


-- 
                              -- David Brahm (brahm at alum.mit.edu)