See ?system, in particular ignore.stdout, ignore.stderr and intern.
Cheers,
Simon
On Oct 5, 2011, at 5:36 AM, 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 Œstderr()‚ (including those from Œmessage‚, Œwarning‚ and
> Œstop‚) can be diverted by Œsink(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
> -----------------------------------------------------
>
>
> [[alternative HTML version deleted]]
>
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