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<TITLE>upgraded to error one</TITLE>
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<P><FONT SIZE=2>I found some problems with RPermInvoke.sh, but still am having problems as you can see:<BR>
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<BR>
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[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>
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