[BioC] makeTranscriptDbFromUCSC() fails to download table

[Ann Loraine]

Hello,

I have a quick question about how this is working behind the scenes.

Does the code access the Table Browser web interface at UCSC?

I'm very interested in this .. it seems like a very convenient way to
access a lot of data in various useful formats without having to
manually download anything.

Is there an easy way I can browse the source code on-line or check out
just a portion of the Bioconductor repository so that I can see how
this feature is working?

Where does this code reside in the repository?

(I'm looking at http://www.bioconductor.org/developers/source-control/)

Sincerely,

Ann Loraine



On Thu, Dec 23, 2010 at 11:18 PM, Vincent Carey
<stvjc at channing.harvard.edu> wrote:
> 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 at 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 at gmail.com> wrote:
>> > Hi,
>> >
>> > On Thu, Dec 23, 2010 at 7:38 PM, Burak Kutlu <bkutlu at 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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