[Swift-user] upgraded to error one

[Hodgess, Erin]

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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