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