See ?system2 to answer your subject line.
But you seem confused about external programs and R's own stdout()
connection. Have you read the R News article on connections?
On Wed, 5 Oct 2011, Mark Cowley wrote:
Dear list,
I'm trying to suppress/redirect/squash the output from commands like install.packages, or
download.file. The problem is that none of: sink(..., type="message"), sink(...,
type="output"), capture.output, suppressMessages are quite doing the trick. Output gets
written to the stderr stream, despite any combination of the above suppression commands.
According to ?sink:
Messages sent to ?stderr()? (including those from ?message?, ?warning? and ?stop?) can be
diverted by ?sink(type = "message")? (see below).
I'm pretty sure it's the system(), or .Internal() calls which are the culprit,
which currently write the majority (all?) of their output to the stderr stream.
Simple example:
con <- file("stderr.txt", "w")
sink(con, type="message")
system("ls")
sink(NULL, type="message")
close(con)
# instead of the output going to stderr.txt, it gets printed to the console.
# no good either
capture.output(system("ls"))
character(0)
This is an issue, since i'm writing GenePattern modules to run R code, and if
anything is written to stderr, then the job gets hit with a 'job failed'
status, when all that might have happened is an R package got installed, or a
file got downloaded via FTP.
Any ideas? Can system() and .Internal() output be redirected to stdout?
cheers,
Mark
sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] en_AU.UTF-8/en_AU.UTF-8/C/C/en_AU.UTF-8/en_AU.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
-----------------------------------------------------
Mark Cowley, PhD
Pancreatic Cancer Program | Peter Wills Bioinformatics Centre
Garvan Institute of Medical Research, Sydney, Australia
-----------------------------------------------------
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--
Brian D. Ripley, rip...@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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