[BioC] getGEO error

[Sean Davis]

On Sat, Jan 26, 2013 at 4:35 AM, Alyaa Mahmoud <alyamahmoud at gmail.com> wrote:
> Thanks a lot for the replies.
>
> I updated to "R version 2.15.0 (2012-03-30" to but I still get the same
> error msg;
>
>  test = getGEO ("GSE17221")
> Found 1 file(s)
> GSE17221_series_matrix.txt.gz
> Using locally cached version: /tmp/RtmpBQOrpt/GSE17221_series_matrix.txt.gz
> Using locally cached version of GPL8891 found here:
> /tmp/RtmpBQOrpt/GPL8891.soft
> Error in read.table(file = file, header = header, sep = sep, quote = quote,
>  :
>   no lines available in input

Hi, Alyaa.

The version of GEOquery with the bug fixed (I hope) is not quite
available.  It should probably be available in about 12 hours--the
build system takes a while to do its magic.  You'll want to re-install
GEOquery using biocLite('GEOquery') and then make sure that the
version of GEOquery that gets installed is 2.24.1.  If you still have
problems after that, definitely let us know and be sure to include the
output of sessionInfo() in your email.

Thanks for your patience,
Sean


>
>
> On Fri, Jan 25, 2013 at 4:35 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>
>> On Thu, Jan 24, 2013 at 11:59 PM, Alyaa Mahmoud <alyamahmoud at gmail.com>
>> 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]]
>> >
>> > _______________________________________________
>> > Bioconductor mailing list
>> > Bioconductor at r-project.org
>> > https://stat.ethz.ch/mailman/listinfo/bioconductor
>> > Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>
>
>
> --
> Alyaa Mahmoud
>
> "Love all, trust a few, do wrong to none"- Shakespeare
>
>         [[alternative HTML version deleted]]
>
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