[R] R script from Python

Prof Brian Ripley ripley at stats.ox.ac.uk
Sat Oct 18 06:33:06 CEST 2008

This is a python not an R problem.

Use of redirection is handled by a shell, not by the executable (usually: 
it could depend on the compiler).  The Windows system and popen commands 
(and hence R's system()) does not use a shell: POSIX OSes do.

It will be cleaner to use Rscript to run scripts.

Please ask Python questions on a Python help list.

On Sat, 18 Oct 2008, Tomislav Puđa wrote:

> Hi,
> I'm trying to execute R-script from Python. I'm using R 2.7.2, Python 2.5
> and WinXP.
> I don't won't to use Python/R interface because of nature of project.

You'll need to explain the arbtirary restrictions you are imposing here.

> Python code :
> import subprocess
> command  = 'c:\\Program Files\\R\\R-2.7.2\\bin\\Rterm.exe --vanilla -q
> <d:\\test\\run\\geneBank.r> d:\\output.out'
> subprocess.Popen(command).wait()
> After that, I get error messages on Rterm.exe terminal :
> ARGUMENT 'd<:\lloydMax.r>' __ignored__
> ARGUMENT 'd:\output.txt' __ignored__
> Why ?
> 	[[alternative HTML version deleted]]
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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

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