Actually, try downloading the same thing from the Table Browser and see if
there isn't something like the following at the tail of the file:

843 chr11 33910774 33910775 rs4756078 0 + CC C/G/T genomic single
by-cluster,by-frequency,by-2hit-2allele,by-hapmap,by-1000genomes 0.361204
0.223906 intron exact 1
SingleClassTriA---------------------------------------------------------------------------
procedures have exceeded timeout: 1200 seconds, function has ended.

---------------------------------------------------------------------------

(this is from my attempted download of the snp135common track, but it
appears to be happening to you as well)

It would appear that we're being throttled.



On Sun, May 6, 2012 at 10:00 PM, Dario Strbenac <D.Strbenac@garvan.org.au>wrote:

> Hi,
>
> It seems some data has been added to the EST data table in UCSC that
> GenomicFeatures cannot parse.
>
> > ESTs <- makeFeatureDbFromUCSC(genome = "hg19", track = "est", tablename
> = "all_est")
> Download the all_est table ... Error in scan(file, what, nmax, sep, dec,
> quote, skip, nlines, na.strings,  :
>  line 4587019 did not have 22 elements
>
> The relevant lines of the session information are :
>
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> other attached packages:
> [1] GenomicFeatures_1.8.1
>
> - Dario.
>
> _______________________________________________
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>



-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

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