[BioC] GEOquery not working, NCBI changes?

[Gad Abraham]

On Wed, Mar 3, 2010 at 8:04 PM, Sean Davis <seandavi at gmail.com> wrote:
> On Wed, Mar 3, 2010 at 6:32 AM, Gad Abraham
> <gabraham at csse.unimelb.edu.au> wrote:
>> Hi,
>>
>> I'm having trouble getting GEOquery to work recently.
>>
>> On Ubuntu 9.10/R-2.10.1/BioC 2.6.1, GEOquery 2.11.3, download.file
>> stops with "cannot open URL",
>> On Ubuntu 8.04.1/R-2.9.2/BioC 2.4.1, GEOquery 2.8.0, curlPerform stops
>> with "Server denied you to change to the given directory"
>>
>> wget downloads the file fine, but requires PASV which download.file()
>> doesn't support
>> (http://tolstoy.newcastle.edu.au/R/e6/help/09/01/0969.html)
>>
>> I suspect that NCBI has changes some server settings, is this a known issue?
>
> Hi, Gad.  I'll follow up with the GEO folks, but it appears that the
> issue was temporary.  I was able to reproduce your findings for until
> 7am EST and then the problem was gone.  Currently, GEOquery appears to
> work fine for me.  Let me know if you are still having problems.
>

Thanks Sean, it's working for me now.

Cheers,
Gad


-- 
Gad Abraham
PhD Student, Dept. CSSE and NICTA
The University of Melbourne
Parkville 3010, Victoria, Australia
email: gabraham at csse.unimelb.edu.au
web: http://www.csse.unimelb.edu.au/~gabraham