[Swift-user] upgraded to error one

[Hodgess, Erin]

It never finishes.



Erin M. Hodgess, PhD
Associate Professor
Department of Computer and Mathematical Sciences
University of Houston - Downtown
mailto: hodgesse at uhd.edu



-----Original Message-----
From: Ben Clifford [mailto:benc at hawaga.org.uk]
Sent: Fri 6/12/2009 5:54 PM
To: Hodgess, Erin
Cc: swift-user at ci.uchicago.edu
Subject: Re: [Swift-user] upgraded to error one
 

if you run RPermInvoke.sh with appropriate commandline parameters and then 
on the immediately following command line, type: echo $?  what number do 
you get?

On Fri, 12 Jun 2009, Hodgess, Erin wrote:

> I found some problems with RPermInvoke.sh, but still am having problems as you can see:
> 
> 
> 
> 
> [erin at tp-login2 bin]$ swift -tc.file tc.data perm1.swift
> Swift svn swift-r2950 cog-r2406
> 
> RunID: 20090612-1714-qye382u3
> Progress:
> Progress:  Checking status:1
> Progress:  Checking status:1
> Progress:  Checking status:1
> Execution failed:
> 	Exception in RPermInvoke:
> Arguments: [permutations.R, 4, 1]
> Host: localhost
> Directory: perm1-20090612-1714-qye382u3/jobs/7/RPermInvoke-7q5yf6cj
> stderr.txt: 
> stdout.txt: 
> ----
> 
> Caused by:
> 	Exit code 1
> [erin at tp-login2 bin]$ cat tc.data
> #NOTE WELL: fields in this file must be separated by tabs, not spaces
> #           and there must be no trailing whitespace at the end of each line.
> #
> # sitename      app     pathname        (ignored)       (ignored)       profiles
> localhost       echo    /bin/echo       INSTALLED       INTEL32::LINUX  null
> teraport        echo    /bin/echo       INSTALLED       INTEL32::LINUX  null
> localhost	translate	/usr/bin/tr	INSTALLED	INTEL32::LINUX	null
> localhost	R	/home/erin/R-2.9.0/bin/R	INSTALLED	INTEL32::LINUX	null
> localhost       wc	/usr/bin/wc     INSTALLED       INTEL32::LINUX	null
> localhost       convert	/usr/bin/convert	INSTALLED	INTEL32::LINUX	null
> localhost	RInvoke	/home/erin/R-2.9.0/bin/RInvoke.sh	INSTALLED	INTEL32::LINUX	null
> teraport	RInvoke /home/erin/R-2.9.0/bin/RInvoke.sh       INSTALLED	INTEL32::LINUX  null
> localhost	RPermInvoke	/home/erin/R-2.9.0/bin/RPermInvoke.sh	INSTALLED	INTEL32::LINUX	null
> [erin at tp-login2 bin]$ cat perm1.swift
> # for running the script permutations.R
> # swift will give R the permutation number
> # and the matrices for running the t-test
> # and will produce a file results/<permnumber><study>.out
> 
> type file{}
> 
> (file rout) perm_r (file scriptname, int pnum, int pstart)
>         {
>         app
>                 {
>                 RPermInvoke @filename(scriptname) pnum pstart ;
>                 }
>         }
> 
> 
> file r_script<single_file_mapper; file="permutations.R">;
> 
> #file perm_matrix<single_file_mapper; file="kiddata_NG-S.txt">;
> 
> foreach i in [1:1]
>         {
>         file r_out <single_file_mapper; file=@strcat("results/",i,".NG-S.out")>;
>         (r_out) = perm_r(r_script,4,i);
>         }
> 
> [erin at tp-login2 bin]$ cat RPermInvoke.sh
> #!/bin/bash
> 
> 
> export R_SCRIPT=$1
> shift
> export R_SWIFT_ARGS="$*"
> 
> 
> /home/erin/R-2.9.0/bin/R CMD BATCH --vanilla $R_SCRIPT
> [erin at tp-login2 bin]$ 
> 
> 
> Erin M. Hodgess, PhD
> Associate Professor
> Department of Computer and Mathematical Sciences
> University of Houston - Downtown
> mailto: hodgesse at uhd.edu
> 
> 

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