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

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