[Swift-user] doesn't create output file

[Michael Wilde]

Erin,

Looking at your R script, it seems like it ran OK (from e1.in.Rout) but 
there is no R statement in the R input that writes the output object xz 
to the data file xy.out where your swift scriptis expecting to find it.

Also, in future email questions, send the name of the directory that you 
ran from - I had to hunt around a bit in /home/erin to find it.

- Mike

R output was:

more e1.in.Rout

R version 2.5.1 (2007-06-27)
Copyright (C) 2007 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

   Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

 > allinputs <- Sys.getenv("R_SWIFT_ARGS")
 > print(allinputs)
  R_SWIFT_ARGS
"xx.dat 25 4"
 > inputfilename <- noquote(strsplit(allinputs," ")[[1]][1])
 > start_num <- as.numeric(noquote(strsplit(allinputs," ")[[1]][2]))
 > n1 <- as.numeric(noquote(strsplit(allinputs," ")[[1]][3]))
 > print(n1)
[1] 4
 > xy <- matrix(scan(inputfilename),byrow=TRUE,ncol=5)
Read 50 items
 > xz <- apply(xy,2,mean)
 > xz
[1]  0.2526954 -0.7243118  0.2969102 -0.2283567 -0.2468762
 >
 > proc.time()
    user  system elapsed
   0.775   0.033   0.797


^^^^ No statement to write xy into xy.out (or to write out any other 
result, like xz).



On 6/3/09 10:03 PM, Hodgess, Erin wrote:
> Hi again!
> 
> I'm looking at some of Sarah's really cool stuff and trying to reproduce 
> test versions.
> 
> Here is the swift file:
> [erin at tp-login2 bin]$ cat test1.swift
> type file{}
>         #--- trying to learn from Sarah's cool stuff
> 
> 
> [erin at tp-login2 bin]$ cat test1.swift
> type file{}
>         #--- trying to learn from Sarah's cool stuff
> 
> 
>        
>         app (file simResult) simScript (file scriptFile, file inputFile, 
> int iter,int tval){
>             RInvoke  @filename(scriptFile) @filename(inputFile) iter tval;
>         }
>        
>        
>             file script<"e1.in">;
>             file inputData<"xx.dat">;
>             file simResult<"xy.out">;
>         int iter = 25;
>         int tval = 4;
>             simResult=simScript(script,inputData,iter,tval);   
> 
> [erin at tp-login2 bin]$
> 
> 
> And here is the result:
> [erin at tp-login2 bin]$ swift -tc.file tc.data test1.swift
> Swift svn swift-r2950 cog-r2406
> 
> RunID: 20090603-2200-krmao849
> Progress:
> Progress:  Checking status:1
> Progress:  Checking status:1
> Progress:  Checking status:1
> Execution failed:
>         Exception in RInvoke:
> Arguments: [e1.in, xx.dat, 25, 4]
> Host: localhost
> Directory: test1-20090603-2200-krmao849/jobs/k/RInvoke-k4l6zqbj
> stderr.txt:
> stdout.txt:
> ----
> 
> Caused by:
>         The following output files were not created by the application: 
> xy.out
> [erin at tp-login2 bin]$
> 
> 
> The tc.data is here:
> [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
> 
> Any suggestions most appreciated.
> 
> Erin
> 
> 
> 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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