[BioC] GEOquery not working, NCBI changes?

Gad Abraham gabraham at csse.unimelb.edu.au
Fri Mar 5 15:25:17 CET 2010

On Thu, Mar 4, 2010 at 12:39 PM, Gad Abraham
<gabraham at csse.unimelb.edu.au> wrote:
> 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.

FWIW, getting the same problem now:

$ Rscript -e 'library(GEOquery); g <- getGEO("GSE3414.RData"); save(g,
Loading required package: methods
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: RCurl
Loading required package: bitops
Error in curlPerform(curl = curl, .opts = opts, .encoding = .encoding) :
  Server denied you to change to the given directory
Calls: getGEO ... getAndParseGSEMatrices -> getURL -> curlPerform -> .Call

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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