Message-ID: <4B62F906.90402@gmail.com>
Date: 2010-01-29T15:04:38Z
From: Craig P. Pyrame
Subject: Suppress output from getGEO
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