[BioC] Problem using getGEO

[Dan Tenenbaum]

On Tue, Jul 23, 2013 at 3:49 PM, Goelz, Nicholas
<nicholas_goelz at brown.edu> wrote:
> Shoot, that's just a typo by me.  I used GDS10 and still got the error.

Could be a firewall or proxy setting at your institution.

Are you able to download the file by pasting this url into your web browser?

ftp://ftp.ncbi.nlm.nih.gov/geo/datasets/GDSnnn/GDS10/soft/GDS10.soft.gz

Dan


> Thanks for your quick response though
>
>
> On Tue, Jul 23, 2013 at 3:48 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
>>
>> On Tue, Jul 23, 2013 at 3:40 PM, Nick Goelz <nickgoelz at gmail.com> wrote:
>> > Hi all
>> >
>> > I'm having a problem with the getGEO(...) function of the package
>> > GEOquery.
>> >  I've looked through the previous responses to this problem but the
>> > fixes
>> > aren't working for me.  I'm working on a mac and have R 3.0.1. and I
>> > have a
>> > good internet connection.  When I open R, I enter
>> >
>> >>library(GEOquery)
>> >>options('download.file.method.GEOquery' = 'curl')
>> >>getGEO("GDS1")
>> >
>> > and get this
>> >
>> > curl: (7) Failed to connect to 2607:f220:41e:250::11: No route to host
>> > File stored at:
>> >
>> > /var/folders/00/162s57712tngn2shq_1mxg5c0000gn/T//Rtmp3xusrK/GDS10.soft.gz
>> > Error in gzfile(fname, open = "rt") : cannot open the connection
>> > In addition: Warning messages:
>> > 1: In download.file(myurl, destfile, mode = mode, quiet = TRUE, method =
>> > getOption("download.file.method.GEOquery")) :
>> >   download had nonzero exit status
>> > 2: In gzfile(fname, open = "rt") :
>> >   cannot open compressed file
>> >
>> > '/var/folders/00/162s57712tngn2shq_1mxg5c0000gn/T//Rtmp3xusrK/GDS10.soft.gz',
>> > probable reason 'No such file or directory'
>> > ------------------------------
>> > Leaving out the 'options' method gives me this:
>> >
>> > Error in download.file(myurl, destfile, mode = mode, quiet = TRUE,
>> > method =
>> > getOption("download.file.method.GEOquery")) :
>> >   cannot open URL '
>> > ftp://ftp.ncbi.nlm.nih.gov/geo/datasets/GDSnnn/GDS10/soft/GDS10.soft.gz'
>> > --------------------------------
>> > I have had issues downloading from GEO files from the internet before,
>> > so
>> > this may be an issue with my security settings.  However my firewall is
>> > not
>> > turned on and I am not sure what else could cause problems like this.
>> >
>> > Any input would be really helpful, thanks for you time
>> >
>>
>> It may be that there is no GDS1 dataset.
>>
>> It doesn't work for me either, but I am able to do this:
>>
>> getGEO("GDS10")
>>
>> Dan
>>
>>
>> > Nick
>> >
>> >         [[alternative HTML version deleted]]
>> >
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>