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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.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
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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
Suppress output from getGEO
4 messages · Craig P. Pyrame, Duncan Murdoch, Sean Davis
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
Duncan Murdoch wrote:
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
Duncan, Do you consider this sort of output from a function helpful in any way? I don't, and I can't see how anyone could, this must be some sort of mistake, bug, whatever you call it. While it's possibly getGEO to create this output, it's also not unlikely that the output is actually generated by some underlying function that has nothing to do with Bioconductor. I can imagine a function that has this 'convenient' feature of printing dots while loading data, but the files loaded by getGEO are so large (for example, 50MB) that the 'convenience' is turned into annoyance. I included r-help precisely because I suspect it's not Bioconductor's fault in this case. Besides, I think you might want to make efforts to be less aggressive. I don't think my use of words in my previous message was inappropriate, but yours seems to be. I apologize if my post hurt your feelings, and now expect you do the same, 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