[BioC] GEOquery getGEO error in read.table

[Textoris Julien]

Hi Dave,

I could not reproduce your error with R2.15.2 and GEOQuery 2.23.1

I updated to GEOQuery 2.24 as you and i also worked without error ?

Are you sure you have Curl and XML libs (outside R) installed properly ?

Julien



On 08/01/2013 06:40, Dave Tang wrote:
> 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,
>
>