On Thu, Oct 25, 2012 at 2:27 PM, Brent Pedersen <bpederse@gmail.com> wrote:

> Hi, with a call like
> > getGEO("GSE15219", destdir="/tmp/", GSEMatrix=TRUE)
> I get:
> Found 1 file(s)
> GSE15219_series_matrix.txt.gz
>   % Total    % Received % Xferd  Average Speed   Time    Time     Time
>  Current
>                                  Dload  Upload   Total   Spent    Left
>  Speed
> 100  762k  100  762k    0     0   313k      0  0:00:02  0:00:02 --:--:--
>  330k
> 100  762k  100  762k    0     0   301k      0  0:00:02  0:00:02
> --:--:--  301kFile stored at:
> /tmp//GPL6255.soft
> Error in read.table(file = file, header = header, sep = sep, quote =
> quote,  :
>   no lines available in input
>
>
> Is there something I can do to get around this error?
>
>
Hi, Brent.

Thanks for the report.  This is due to a change in behavior of NCBI GEO
with regard to GEO platform records.  I have contacted NCBI GEO staff to
see if this is a problem on their end or a permanent change in behavior.
 I'll let you know as soon as I hear.

Sean



>
> > sessionInfo()
> R version 2.15.1 (2012-06-22)
> 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_2.23.5    Biobase_2.16.0     BiocGenerics_0.2.0
>
> loaded via a namespace (and not attached):
> [1] RCurl_1.95-1.1 XML_3.95-0.1
> >
>
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