suppressing stderr output from system() calls
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]]
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