Date: Sun, 6 May 2012 22:36:53 -0700
From: "Tim Triche, Jr." <tim.triche at gmail.com>
Subject: Re: [Bioc-devel] GenomicFeatures FeatureDB EST Table Error
To: D.Strbenac at garvan.org.au
Cc: bioc-devel at r-project.org
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 at 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.