R help - Jan 2007 - Capturing output from external executables, in windows

Hi,

Any help on the following would be much appreciated

I wish to capture the output (currently going to console) from an 
external executable.

The executable is successfully run using

     system("program -switch ")

and the output printed to the DOS console.

How do I capture this output? I have tried redirecting the output to a 
text file, and then reading this in
    
     system("program -switch > textfile.txt")
     data<-scan("textfile.txt")

But this does not seem to work (the textfile.txt is not written). It 
does however work if I invoke the console to be permanent 

     system("cmd /K program -switch > textfile.txt")
     data<-scan("textfile.txt")

Unfortunately, this leaves me with an open console window I have to 
close manually.

Is there a way of doing this (under windows) using system( ) or some 
other command? It appears that pipe( ) may do it, but I cannot 
understand the documentation.

An example of the appropriate syntax would be an enormous help.

Thanks in advance,

Darren

Darren.Obbard at ed.ac.uk

-- 

Darren Obbard
Institute of Evolutionary Biology
Ashworth Labs
Kings Buildings
University of Edinburgh, UK

You can try:

system("command", show.output.on.console=TRUE)



On 24/01/07, Darren Obbard <darren.obbard@ed.ac.uk>
wrote:
>
> Hi,
>
> Any help on the following would be much appreciated
>
> I wish to capture the output (currently going to console) from an
> external executable.
>
> The executable is successfully run using
>
>      system("program -switch ")
>
> and the output printed to the DOS console.
>
> How do I capture this output? I have tried redirecting the output to a
> text file, and then reading this in
>
>      system("program -switch > textfile.txt")
>      data<-scan("textfile.txt")
>
> But this does not seem to work (the textfile.txt is not written). It
> does however work if I invoke the console to be permanent
>
>      system("cmd /K program -switch > textfile.txt")
>      data<-scan("textfile.txt")
>
> Unfortunately, this leaves me with an open console window I have to
> close manually.
>
> Is there a way of doing this (under windows) using system( ) or some
> other command? It appears that pipe( ) may do it, but I cannot
> understand the documentation.
>
> An example of the appropriate syntax would be an enormous help.
>
> Thanks in advance,
>
> Darren
>
> Darren.Obbard@ed.ac.uk
>
> --
>
> Darren Obbard
> Institute of Evolutionary Biology
> Ashworth Labs
> Kings Buildings
> University of Edinburgh, UK
>
> ______________________________________________
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>


-- 
Henrique Dallazuanna

	[[alternative HTML version deleted]]

On 1/24/2007 8:22 AM, Darren Obbard wrote:
> Hi,
> 
> Any help on the following would be much appreciated
> 
> I wish to capture the output (currently going to console) from an 
> external executable.
> 
> The executable is successfully run using
> 
>      system("program -switch ")
> 
> and the output printed to the DOS console.
> 
> How do I capture this output? I have tried redirecting the output to a 
> text file, and then reading this in
>     
>      system("program -switch > textfile.txt")
>      data<-scan("textfile.txt")
> 
> But this does not seem to work (the textfile.txt is not written). 
The redirection character ">" is normally handled by the shell. 
The
system() function is low level, so it will pass it directly to your program.
 >
It
> does however work if I invoke the console to be permanent 
> 
>      system("cmd /K program -switch > textfile.txt")
>      data<-scan("textfile.txt")
> 
> Unfortunately, this leaves me with an open console window I have to 
> close manually.
Use the /C option instead of /K; it executes and then terminates.  Or 
use the "intern" or "show.output.on.console" arg to
system().

Duncan Murdoch
> 
> Is there a way of doing this (under windows) using system( ) or some 
> other command? It appears that pipe( ) may do it, but I cannot 
> understand the documentation.
> 
> An example of the appropriate syntax would be an enormous help.
> 
> Thanks in advance,
> 
> Darren
> 
> Darren.Obbard at ed.ac.uk
>

Is this for RGui under Windows?  I will assume so (but 'in windows' is
not
unambiguous, and there are alternative front-ends like Rterm).

Have you consulted the help page for system()?: this is precisely what 
'show.output.on.console' is for.

You cannot redirect in system (it does say so on the current help page): 
you need to use shell().

On Wed, 24 Jan 2007, Darren Obbard wrote:
> Hi,
>
> Any help on the following would be much appreciated
>
> I wish to capture the output (currently going to console) from an
> external executable.
>
> The executable is successfully run using
>
>     system("program -switch ")
>
> and the output printed to the DOS console.
>
> How do I capture this output? I have tried redirecting the output to a
> text file, and then reading this in
>
>     system("program -switch > textfile.txt")
>     data<-scan("textfile.txt")
>
> But this does not seem to work (the textfile.txt is not written). It
> does however work if I invoke the console to be permanent
>
>     system("cmd /K program -switch > textfile.txt")
>     data<-scan("textfile.txt")
>
> Unfortunately, this leaves me with an open console window I have to
> close manually.
>
> Is there a way of doing this (under windows) using system( ) or some
> other command? It appears that pipe( ) may do it, but I cannot
> understand the documentation.
>
> An example of the appropriate syntax would be an enormous help.
system("program -switch ", show.output.on.console=TRUE)

could it be any easier?  (Well, in the next version of R that will be 
default, so a little.)
> Thanks in advance,
>
> Darren
>
> Darren.Obbard at ed.ac.uk
>
>
-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595