[BioC] GEOquery getGEO error in read.table

[Sean Davis]

On Tue, Jan 8, 2013 at 12:40 AM, Dave Tang <davetingpongtang at gmail.com> 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

Hi, Dave.

I have not been able to reproduce your error on linux or mac, but that
doesn't mean there is not a problem.  There have been intermittent
problems in the past associated with NCBI servers that might cause
truncated downloads, but that is hard to sort out.  In any case, could
you try this again when you get a chance to see if the problem has
resolved itself?

Thanks,
Sean


> 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
>
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