Thanks Martin, Simon and Brian,
They're all good suggestions for code that I write, however how can I suppress
stderr from pre-existing code. For instance, install.packages has 3 system
calls.
Perhaps a better worded question would be: how can I redirect the output of
this command:
install.packages("MASS", lib="/tmp", type="source")
As I mentioned before, sink doesn't do the trick
con <- file("stderr.txt", "w")
sink(con, type="message")
install.packages("MASS", lib="/tmp", type="source")
sink(NULL, type="message")
close(con)
Martin will be familiar with the Bioconductor package oligo, which likes to
download pd info package on the fly and install them - the embedded call to
download.file is noisy, as is the resulting installation of said package.
Short of rewriting install.package & all code which has embedded
install.packages calls, are there any other ways?
@Brian, thanks for the pointer to the news article on connections - I did learn
something there
cheers,
Mark
On 06/10/2011, at 3:59 AM, Martin Morgan wrote:
> On 10/05/2011 02:36 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.
>
> Hi Mark --
>
> For download.file, the argument quiet=TRUE suppresses output messages; this
> option can be used in ... for install.packages, too (according to the
> documentation). This is good enough to quieten the regular chatter on a
> successful operation. To catch errors and suppress warnings also, maybe a
> construct like
>
> url = "http://r-project.org/doesnotexist";
> tryCatch(suppressWarnings(
> capture.output(download.file(url, tempfile(), quiet=TRUE))),
> error=function(...) {})
>
> Martin
>
>> 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
>> -----------------------------------------------------
>>
>>
>> [[alternative HTML version deleted]]
>>
>>
>>
>>
>> ______________________________________________
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
> --
> Computational Biology
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>
> Location: M1-B861
> Telephone: 206 667-2793
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