Suppress output from getGEO
On 29/01/2010 10:04 AM, Craig P. Pyrame wrote:
Dear R-ers, I am using getGEO to download expression data from the Gene Expression Omnibus. With default settings, when a file is downloaded and parsed, lots of dotted lines are printed in the terminal, like this: .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... .......... downloaded 50.2 Mb but many more! I tried to suppress this rather unhelpful behavior with capture.output and sink, as below, but to no effect:
> capture.output(getGEO(GEO=GEO)) # GEO is some GEO id
> sink('/dev/null'); getGEO(GEO=GEO); sink()
Is this an issue with getGEO, or some underlying function? How can I avoid having the terminal spammed? Could the function responsible for this annoying output be modified to put an end to this?
getGEO is a Bioconductor package. Feel free to insult the helpful people there if you want to alienate them, but please don't crosspost here. Duncan Murdoch