[R] Capturing stderr from system()
Prof Brian Ripley
ripley at stats.ox.ac.uk
Mon Aug 7 21:28:31 CEST 2006
On Mon, 7 Aug 2006, McGehee, Robert wrote:
> I have a system command that occasionally fails and writes output to
> standard error, which R will print to the screen when ignore.stderr =
No, R does not print to the screen, your shell does. You can capture shell
and command errors by
system("command 2>&1", intern=TRUE)
or whatever the appropriate syntax for your shell is. E.g.
> system("BadCommand 2>&1", intern=TRUE)
 "sh: BadCommand: command not found"
> For example:
> > system("BadCommand")
> sh: line 1: BadCommand: command not found
(My shell does not give `line 1' here.)
> I would like to know if the above command fails, and can presumably do
> this by parsing the stderr message that R prints to the screen. My
> (hopefully simple) problem is that I can't figure out how to capture
> this output.
You are starting from a false assertion ....
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
PLEASE do note what it says about where to send programming questions.
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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