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:
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
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.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... ..........
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
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