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:
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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
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
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