[BioC] Problem with a specific GEO dataset.

[Shawn Garbett [guest]]

If I use GEOquery as follows:

gse <- getGEO("GSE21259", GSEMatrix=TRUE)

I get the following warnings after the load:

Warning messages:
1: In read.table(con, sep = "\t", header = FALSE, nrows = nseries) :
  seek on a gzfile connection returned an internal error
2: In read.table(con, sep = "\t", header = FALSE, nrows = nsamples) :
  seek on a gzfile connection returned an internal error
3: In readLines(con, 1) : seek on a gzfile connection returned an internal error
4: In read.table(file = file, header = header, sep = sep,  ... :
  seek on a gzfile connection returned an internal error
5: In read.table(file = file, header = header, sep = sep,  ... :
  seek on a gzfile connection returned an internal error
6: In read.table(con, sep = "\t", header = FALSE, nrows = nseries) :
  seek on a gzfile connection returned an internal error
7: In read.table(con, sep = "\t", header = FALSE, nrows = nsamples) :
  seek on a gzfile connection returned an internal error
8: In readLines(con, 1) : seek on a gzfile connection returned an internal error
9: In read.table(file = file, header = header, sep = sep,  ... :
  seek on a gzfile connection returned an internal error
10: In read.table(file = file, header = header, sep = sep,  ... :
  seek on a gzfile connection returned an internal error
11: In read.table(con, sep = "\t", header = FALSE, nrows = nseries) :
  seek on a gzfile connection returned an internal error
12: In read.table(con, sep = "\t", header = FALSE, nrows = nsamples) :
  seek on a gzfile connection returned an internal error
13: In readLines(con, 1) : seek on a gzfile connection returned an internal error
14: In read.table(file = file, header = header, sep = sep,  ... :
  seek on a gzfile connection returned an internal error
15: In read.table(file = file, header = header, sep = sep,  ... :
  seek on a gzfile connection returned an internal error

Then things that should work don't, i.e.:

> GPLList(gse)
Error in function (classes, fdef, mtable)  : 
  unable to find an inherited method for function "GPLList", for signature "list"
> GSMList(gse)
Error in function (classes, fdef, mtable)  : 
  unable to find an inherited method for function "GSMList", for signature "list"

(1) Am I doing something wrong?
(2) Is this data set on GEO broken in some way?
(3) Or is it a bioconductor error?

 -- output of sessionInfo(): 

R version 2.13.2 (2011-09-30)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] GEOquery_2.19.4 Biobase_2.12.2 

loaded via a namespace (and not attached):
[1] RCurl_1.6-10 XML_3.4-3   

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