[R] R/Splus--Perl Interface && ssh

From: XIAO LIU <xiaoliu_at_jhmi.edu>
Date: Thu 28 Apr 2005 - 02:02:42 EST


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'

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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Received on Thu Apr 28 02:07:53 2005

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