Dear Sean

It worked perfectly fine. Thank you very much for all your efforts.

Kindest regards,
Alyaa


On Sat, Jan 26, 2013 at 3:45 PM, Sean Davis <sdavis2@mail.nih.gov> wrote:

> On Sat, Jan 26, 2013 at 4:35 AM, Alyaa Mahmoud <alyamahmoud@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@mail.nih.gov>
> wrote:
> >
> >> On Thu, Jan 24, 2013 at 11:59 PM, Alyaa Mahmoud <alyamahmoud@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@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]]
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@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]]

