[R] [BioC] Suppress output from getGEO

[Sean Davis]

On Fri, Jan 29, 2010 at 10:04 AM, Craig P. Pyrame <crappyr at gmail.com> 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?

Hi, Craig.  These dots are from the output from download.file().
GEOquery was modified to use "quiet=TRUE" on December 8, 2009.  If you
would like to take advantage of this change, you can use the
development version of GEOquery.

Sean