I just ran the code successfully with sessionInfo below.  Could be transient
network issue?

> sessionInfo()
R version 2.12.0 Patched (2010-11-28 r53696)
Platform: x86_64-apple-darwin10.4.0/x86_64 (64-bit)

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices datasets  tools     utils     methods
[8] base

other attached packages:
[1] GenomicFeatures_1.2.3 GenomicRanges_1.2.2   IRanges_1.8.7
[4] weaver_1.16.0         codetools_0.2-6       digest_0.4.2

loaded via a namespace (and not attached):
[1] BSgenome_1.18.2    Biobase_2.10.0     Biostrings_2.18.2
DBI_0.2-5
[5] RCurl_1.5-0        RSQLite_0.9-4      XML_3.2-0
biomaRt_2.6.0
[9] rtracklayer_1.10.6


On Thu, Dec 23, 2010 at 8:52 PM, Burak Kutlu <bkutlu@systemsbiology.org>wrote:

> D'oh!
>
> Here it is
>
> > hg19KnownGene <- makeTranscriptDbFromUCSC(genome = "hg19", tablename =
> "knownGene")
> Download the knownGene table ... Error in curlPerform(url = url,
> headerfunction = header$update, curl = curl,  :
>  transfer closed with outstanding read data remaining
>
> I also failed to mention this is about GenomicFeatures package.
> Thanks Steve!
> -burak
>
> On Thu, Dec 23, 2010 at 4:46 PM, Steve Lianoglou
> <mailinglist.honeypot@gmail.com> wrote:
> > Hi,
> >
> > On Thu, Dec 23, 2010 at 7:38 PM, Burak Kutlu <bkutlu@systemsbiology.org>
> wrote:
> >> Hi
> >>
> >> For some reason I started getting error for the following call
> >> hg19KnownGene <- makeTranscriptDbFromUCSC(genome = "hg19", tablename =
> >> "knownGene")
> >
> > I'm not sure how we can shed some light on this without you providing
> > the error that you're getting ;-)
> >
> > Can you paste that into a follow up email?
> >
> > Thanks,
> >
> > -steve
> >
> > --
> > Steve Lianoglou
> > Graduate Student: Computational Systems Biology
> >  | Memorial Sloan-Kettering Cancer Center
> >  | Weill Medical College of Cornell University
> > Contact Info: http://cbio.mskcc.org/~lianos/contact<http://cbio.mskcc.org/%7Elianos/contact>
> >
>
>
>
> --
> Burak Kutlu, PhD.
> Research Scientist
> Hood Lab
> Institute for Systems Biology
>
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