[BioC] makeTranscriptDbFromBiomart error

[Steve Lianoglou]

Hi Stefanie,

On Thu, Jun 7, 2012 at 5:16 AM, Stefanie Tauber
<stefanie.tauber at univie.ac.at> wrote:
> Hi
>
> I just tried it with R 2.15, I get the same error.
>
> If I follow your suggestion:
>
> txdb <- makeTranscriptDbFromUCSC(genome="hg19", tablename="ensGene")
>
>
> I get:
>
> Download the ensGene table ... OK
> Extract the 'transcripts' data frame ... OK
> Extract the 'splicings' data frame ... OK
> Download and preprocess the 'chrominfo' data frame ... Error in
> download.file(url, destfile, quiet = TRUE) :
>   cannot open URL
> 'http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz'
> In addition: There were 50 or more warnings (use warnings() to see the first
> 50)
[snip]

Strange ... I also get the same warnings you get (the "cds cumulative
length is not a multiple of 3") for some transcripts, but I think this
is something beyond our control. I don't get any error(s) when
downloading and building the TxDB, so it completes fine for me.

I'm actually running the *-devel versions of the bioc packages w/
R-2.15.x so it's not very easy for me to check the current released
GenomicFeatures package, but I'd be a bit surprised if the error is
there.

Could you paste the output of `sessionInfo()` after you call
`library(GenomicFeatures)` when running your new R-2.15.x install?

-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