Message-ID: <4B62FB32.4040503@stats.uwo.ca>
Date: 2010-01-29T15:13:54Z
From: Duncan Murdoch
Subject: Suppress output from getGEO
In-Reply-To: <4B62F906.90402@gmail.com>
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