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<TITLE>RE: [Swift-user] upgraded to error one</TITLE>
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<P><FONT SIZE=2>It never finishes.<BR>
<BR>
<BR>
<BR>
Erin M. Hodgess, PhD<BR>
Associate Professor<BR>
Department of Computer and Mathematical Sciences<BR>
University of Houston - Downtown<BR>
mailto: hodgesse@uhd.edu<BR>
<BR>
<BR>
<BR>
-----Original Message-----<BR>
From: Ben Clifford [<A HREF="mailto:benc@hawaga.org.uk">mailto:benc@hawaga.org.uk</A>]<BR>
Sent: Fri 6/12/2009 5:54 PM<BR>
To: Hodgess, Erin<BR>
Cc: swift-user@ci.uchicago.edu<BR>
Subject: Re: [Swift-user] upgraded to error one<BR>
<BR>
<BR>
if you run RPermInvoke.sh with appropriate commandline parameters and then<BR>
on the immediately following command line, type: echo $? what number do<BR>
you get?<BR>
<BR>
On Fri, 12 Jun 2009, Hodgess, Erin wrote:<BR>
<BR>
> I found some problems with RPermInvoke.sh, but still am having problems as you can see:<BR>
><BR>
><BR>
><BR>
><BR>
> [erin@tp-login2 bin]$ swift -tc.file tc.data perm1.swift<BR>
> Swift svn swift-r2950 cog-r2406<BR>
><BR>
> RunID: 20090612-1714-qye382u3<BR>
> Progress:<BR>
> Progress: Checking status:1<BR>
> Progress: Checking status:1<BR>
> Progress: Checking status:1<BR>
> Execution failed:<BR>
> Exception in RPermInvoke:<BR>
> Arguments: [permutations.R, 4, 1]<BR>
> Host: localhost<BR>
> Directory: perm1-20090612-1714-qye382u3/jobs/7/RPermInvoke-7q5yf6cj<BR>
> stderr.txt:<BR>
> stdout.txt:<BR>
> ----<BR>
><BR>
> Caused by:<BR>
> Exit code 1<BR>
> [erin@tp-login2 bin]$ cat tc.data<BR>
> #NOTE WELL: fields in this file must be separated by tabs, not spaces<BR>
> # and there must be no trailing whitespace at the end of each line.<BR>
> #<BR>
> # sitename app pathname (ignored) (ignored) profiles<BR>
> localhost echo /bin/echo INSTALLED INTEL32::LINUX null<BR>
> teraport echo /bin/echo INSTALLED INTEL32::LINUX null<BR>
> localhost translate /usr/bin/tr INSTALLED INTEL32::LINUX null<BR>
> localhost R /home/erin/R-2.9.0/bin/R INSTALLED INTEL32::LINUX null<BR>
> localhost wc /usr/bin/wc INSTALLED INTEL32::LINUX null<BR>
> localhost convert /usr/bin/convert INSTALLED INTEL32::LINUX null<BR>
> localhost RInvoke /home/erin/R-2.9.0/bin/RInvoke.sh INSTALLED INTEL32::LINUX null<BR>
> teraport RInvoke /home/erin/R-2.9.0/bin/RInvoke.sh INSTALLED INTEL32::LINUX null<BR>
> localhost RPermInvoke /home/erin/R-2.9.0/bin/RPermInvoke.sh INSTALLED INTEL32::LINUX null<BR>
> [erin@tp-login2 bin]$ cat perm1.swift<BR>
> # for running the script permutations.R<BR>
> # swift will give R the permutation number<BR>
> # and the matrices for running the t-test<BR>
> # and will produce a file results/<permnumber><study>.out<BR>
><BR>
> type file{}<BR>
><BR>
> (file rout) perm_r (file scriptname, int pnum, int pstart)<BR>
> {<BR>
> app<BR>
> {<BR>
> RPermInvoke @filename(scriptname) pnum pstart ;<BR>
> }<BR>
> }<BR>
><BR>
><BR>
> file r_script<single_file_mapper; file="permutations.R">;<BR>
><BR>
> #file perm_matrix<single_file_mapper; file="kiddata_NG-S.txt">;<BR>
><BR>
> foreach i in [1:1]<BR>
> {<BR>
> file r_out <single_file_mapper; file=@strcat("results/",i,".NG-S.out")>;<BR>
> (r_out) = perm_r(r_script,4,i);<BR>
> }<BR>
><BR>
> [erin@tp-login2 bin]$ cat RPermInvoke.sh<BR>
> #!/bin/bash<BR>
><BR>
><BR>
> export R_SCRIPT=$1<BR>
> shift<BR>
> export R_SWIFT_ARGS="$*"<BR>
><BR>
><BR>
> /home/erin/R-2.9.0/bin/R CMD BATCH --vanilla $R_SCRIPT<BR>
> [erin@tp-login2 bin]$<BR>
><BR>
><BR>
> Erin M. Hodgess, PhD<BR>
> Associate Professor<BR>
> Department of Computer and Mathematical Sciences<BR>
> University of Houston - Downtown<BR>
> mailto: hodgesse@uhd.edu<BR>
><BR>
><BR>
<BR>
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