[BioC] GEOquery getGEO error in read.table

[Dave Tang]

Dear mailing list,

I've been trying to use GEOquery to fetch microarray data from GEO but to  
no avail. I've searched online and found several discussions about a  
similar problem but the bug was solved for an older version.

Here I've just tried to run the first couple of steps of the vignette:

library(GEOquery)
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following object(s) are masked from 'package:stats':

     xtabs

The following object(s) are masked from 'package:base':

     Filter, Find, Map, Position, Reduce, anyDuplicated, cbind,
     colnames, duplicated, eval, get, intersect, lapply, mapply, mget,
     order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int,
     rownames, sapply, setdiff, table, tapply, union, unique

Welcome to Bioconductor

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

Setting options('download.file.method.GEOquery'='curl')
#no issue here
gds <- getGEO("GDS507")
File stored at:
/tmp/RtmpqHbIvi/GDS507.soft.gz
#error here
gds <- getGEO("GSM11805")
File stored at:
/tmp/RtmpqHbIvi/GSM11805.soft
Error in read.table(file = file, header = header, sep = sep, quote =  
quote,  :
   no lines available in input

I've tried this for several other microarray datasets and I get the same  
error message.

Here's my sessionInfo():

sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] C

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

other attached packages:
[1] GEOquery_2.24.0    Biobase_2.18.0     BiocGenerics_0.4.0

loaded via a namespace (and not attached):
[1] RCurl_1.95-3 XML_3.95-0.1

Cheers,


-- 
Dave