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batch file output

7 messages · David Winsemius, Gabor Grothendieck, Mikkel Grum +1 more

Mikkel Grum
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I run a batch file with the following command in Windows XP:

C:\R\R-2.12.1\bin\Rterm.exe --no-save --no-restore <C:\users\me\file.R> C:\users\me\file.out 2>&1

Is there any way to get only the output of R in file.out, without getting all the code from file.R too?

Any help greatly appreciated,
Mikkel
David Winsemius
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On Dec 28, 2010, at 8:09 AM, Mikkel Grum wrote:

            

      
      
      
    

        
Put a sink(file="C:\users\me\file2.out") in the file.R would be one  
way but your general strategy looks a bit strange. One does not  
generally use the interactive version of R for batch execution. See:

http://stat.ethz.ch/R-manual/R-patched/library/utils/html/BATCH.html

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      David Winsemius
    

    

      
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On Dec 28, 2010, at 8:27 AM, David Winsemius wrote:

        

            

      
      
      
    

        
Would probably work better to use forward slashes.

            

      
      
      
    

        
David Winsemius, MD
West Hartford, CT

  
  


  


      

    

    

      
      

        


  

        

      Gabor Grothendieck
    

    

      
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On Tue, Dec 28, 2010 at 8:09 AM, Mikkel Grum <mi2kelgrum at yahoo.com> wrote:

            

      
      
      
    

        
Try Rscript.exe in your R distribution.

Also in the batchfiles distribution, http://batchfiles.googlecode.com,
there is a file #Rscript.bat, that can be used to turn an R script
into a Windows batch file.   #Rscript without arguments gives
instructions.

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Mikkel Grum
    

    

      
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Thanks. The way I run it, I can determine what version of R to run with which script. Don't know how to do that with R CMD BATCH.

Placing options(echo = FALSE) in the infile solves my problem. I got that from the page you linked to.

Mikkel

        
--- On Tue, 12/28/10, David Winsemius <dwinsemius at comcast.net> wrote:

        

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      David Winsemius
    

    

      
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On Dec 28, 2010, at 10:38 AM, Mikkel Grum wrote:

        

            

      
      
      
    

        
Seems as though something like this (using absolute path to the  
instance of R.exe)  should work:

C:\R\R-2.12.1\bin\R CMD BATCH [options] infile [outfile]

At least if I remember my command line Windows conventions  ... it's  
been a few years.

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Joshua Wiley
    

    

      
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On Tue, Dec 28, 2010 at 5:09 AM, Mikkel Grum <mi2kelgrum at yahoo.com> wrote:

            

      
      
      
    

        
I'm a bit surprised this worked for you...did you customize your build
so that Rterm.exe is in \bin\ rather than a subfolder for its specific
architecture?

            

      
      
      
    

        
I did not see anyone else mention this, so I wanted to add that with R
CMD BATCH you can add the --slave argument to avoid needing to add
options(echo = FALSE) to all your scripts.  The --no-timing option
stops proc.time() from running at the end.

For example from the command prompt I can run 'sample.R' using 32 bit R:

C:\R\R-2.12.1\bin\i386\R CMD BATCH --slave --no-timing "sample.R"
"sampleout.txt"

HTH,

Josh