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