R help - Apr 2005 - R/Splus--Perl Interface && ssh

Hi:

I'm using RSPerl_0.6-3 calling R from Perl under UNIX system. My perl
programs with the RSPerl work well in my computer.  If submitting these programs
to a UNIX system by 'ssh' or to GNQS system by 'qsub', these
programs do not work even though both systems can run R.  Details are following.
Any suggestion will be highly appreciated.

Xiao

My perl program 'tt.pl'
   #!/usr/bin/perl -w
   use R;
   use RReferences;
   &R::initR("--silent");
   &R::setDebug(0);
   &R::library("RSPerl");
   @t = &R::call("min", (1,2));

I have a script 'doRSPerltt' for the perl program
   #!/bin/csh
   setenv LD_LIBRARY_PATH /usr/lib/R/lib
   setenv R_HOME /usr/lib/R
   perl -I/usr/lib/R/site-library/RSPerl/examples/../share/blib/arch
-I/usr/lib/R/site-library/RSPerl/examples/../share/blib/lib
-I/usr/lib/R/site-library/RSPerl/scripts t
t.pl

I used ssh to submit my job to machine 'queen'
   ssh queen 'cd /nfs/fs/clarke/xiaoliu && ./doRSPerltt'
An error message returns
   Fatal error: you must specify `--save', `--no-save' or
`--vanilla'

If using 'qsub' to submit my job to a GNQS system
   qsub
   doRSPerltt
An error message returns
   Warning: no access to tty (Bad file descriptor).
   Thus no job control in this shell.
   Fatal error: you must specify `--save', `--no-save' or
`--vanilla'


-------------- next part --------------
XIAO LIU wrote:
> Hi:
> 
> I'm using RSPerl_0.6-3 calling R from Perl under UNIX system.  My perl
programs with the RSPerl work well in my computer.  However, if submitting to
GNQS system, these programs do not work.  It requires defining
'--vanilla'.  Can anyone tell me what I should do?
> 
Are you certain this has something to do with RSPerl.
Specifically, have you tried running an R program on a GNQS system
and ensuring that works without --vanilla (as part of the command line
arguments)?

If it is only for RSPerl, perhaps you would do well to post the
error message that is generated.

> Thank in advance
> 
> Xiao
> 
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Duncan Temple Lang                duncan at wald.ucdavis.edu
Department of Statistics          work:  (530) 752-4782
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Davis, CA 95616, USA

On Wed, 27 Apr 2005, XIAO LIU wrote:
> I'm using RSPerl_0.6-3 calling R from Perl under UNIX system. My perl 
> programs with the RSPerl work well in my computer.  If submitting these 
> programs to a UNIX system by 'ssh' or to GNQS system by
'qsub', these
> programs do not work even though both systems can run R.  Details are 
> following.  Any suggestion will be highly appreciated.
>
> My perl program 'tt.pl'
>   #!/usr/bin/perl -w
>   use R;
>   use RReferences;
>   &R::initR("--silent");
Hint: that is not correct for batch use.  Please do read `An Introduction 
to R' for how to invoke R appropriately.

[...]

Please do read the posting guide and choose an less inappropriate list.

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595