Re: getGEO error

On Thu, Jan 24, 2013 at 11:59 PM, Alyaa Mahmoud
<alyamahmoud@...> wrote:
> Dear Group
>
> I am trying to download some datasets from GEO using package GEOquery. It
> worked fine for most of the datasets except for a couple of them, I get the
> following error:
> *
> *
> Error in read.table(file = file, header = header, sep = sep, quote = quote,
>  :
>   no lines available in input
> *
> *
> This is the script line I use:
> GSE3783 <-getGEO("GSE37830", GSEMatrix = TRUE)[[1]]
>
> I also tried to download the soft files and read these directly;
> GSE37830 = getGEO (filename = "GSE37830_family.soft.gz")
>
> but I still get the same error.

Thanks, Alyaa, for the report.

This is, indeed, a bug.  It has been fixed in the current release and
devel branches (versions 2.24.1 and 2.25.1, respectively) and should
be available in the next couple of days for installation.  Note that
you will need to update to the current R version to get these changes.

Sean

> Please advise
> Thanks a lot
>
> Alyaa Mahmoud
>
> R version 2.9.2 (2009-08-24)
> x86_64-pc-linux-gnu
>
> locale:
> LC_CTYPE=C;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] GEOquery_2.8.0 RCurl_1.95-3   bitops_1.0-5   Biobase_2.4.1
>
> loaded via a namespace (and not attached):
> [1] tools_2.9.2
>
> --
> Alyaa Mahmoud
>
> "Love all, trust a few, do wrong to none"- Shakespeare
>
>         [[alternative HTML version deleted]]
>
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