[R] Suppress output from getGEO

[Duncan Murdoch]

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