R devel - Oct 2011 - suppressing stderr output from system() calls

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
-----------------------------------------------------


	[[alternative HTML version deleted]]

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 ?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 at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

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
> -----------------------------------------------------
>
>
> 	[[alternative HTML version deleted]]
>
>
-- 
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

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 at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

-- 
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