[Bioc-devel] GenomicFeatures FeatureDB EST Table Error

Dario Strbenac D.Strbenac at garvan.org.au
Mon May 7 07:00:05 CEST 2012


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.

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