On Fri, Jan 29, 2010 at 10:04 AM, Craig P. Pyrame <crap...@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 ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.