[BioC] Suppress output from getGEO

Craig P. Pyrame crappyr at gmail.com
Fri Jan 29 16:04:38 CET 2010


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?

Best regards,
Craig



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