[BioC] GEOquery not working, NCBI changes?

Gad Abraham gabraham at csse.unimelb.edu.au
Thu Mar 4 05:39:33 CET 2010

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.


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

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