[BioC] failure in GDS2eSet() in package GEOquery

[Wittner, Ben, Ph.D.]

Hello,

If I execute the following three lines:

library('GEOquery')
gds <- getGEO('GSE2034')
eset <- GDS2eSet(gds)

I get the following error message after the call to GDS2eSet():

Error in function (classes, fdef, mtable)  :
  unable to find an inherited method for function "Table", for signature "GSE"

I'm using R version 2.6.0 and GEOquery version 2.2.0 (see details below), but it
also happens with R version 2.5.2 and GEOquery version 2.0.6.

Any help would be appreciated.

Thanks.

-Ben

---------------------------------------------------------------------------

> eset <- GDS2eSet(gds)
trying URL
'http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL96&form=text&vie
w=full'
Content type 'geo/text' length unknown
opened URL
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
(many such lines deleted)
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
...
downloaded 23.4 Mb

File stored at:
/tmp/Rtmpf1P0of/GPL96.soft
Error in function (classes, fdef, mtable)  :
  unable to find an inherited method for function "Table", for signature "GSE"

> version
               _
platform       x86_64-unknown-linux-gnu
arch           x86_64
os             linux-gnu
system         x86_64, linux-gnu
status
major          2
minor          6.0
year           2007
month          10
day            03
svn rev        43063
language       R
version.string R version 2.6.0 (2007-10-03)
> packageDescription('GEOquery')
Package: GEOquery
Type: Package
Title: Get data from NCBI Gene Expression Omnibus (GEO)
Version: 2.2.0
Date: 2007-09-24
Author: Sean Davis <sdavis2 at mail.nih.gov>
Maintainer: Sean Davis <sdavis2 at mail.nih.gov>
Depends: methods,Biobase,RCurl
Suggests: limma
biocViews: Microarray, DataImport, OneChannel, TwoChannel, SAGE
Description: The NCBI Gene Expression Omnibus (GEO) is a public
        repository of microarray data (>150,000 experiments).  Given
        the rich and varied nature of these data, it is only natural to
        want to apply BioConductor tools to these data.  GEOquery is
        the bridge between GEO and BioConductor.
License: GPL version 2
Packaged: Wed Oct 3 14:31:57 2007; biocbuild
Built: R 2.6.0; ; 2007-11-05 16:42:50; unix

-- File: /home/bwittner/R-2.6.0/library/GEOquery/DESCRIPTION
>


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