[BioC] Problem using getGEO

[Dan Tenenbaum]

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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