[Bioc-devel] error in stable AnnotationHub

-----Original Message-----
From: Bioc-devel [mailto:bioc-devel-bounces at r-project.org] On Behalf Of
Kasper Daniel Hansen
Sent: Saturday, October 10, 2015 11:04 PM
To: bioc-devel at r-project.org
Subject: [Bioc-devel] error in stable AnnotationHub

Using Bioconductor 3.1 and the following code

library(AnnotationHub)
ah <- AnnotationHub()
ah[["AH28868"]]

I get an error like

It seems like the record is expecting additional columns in the bed file, but it contains only ranges and score; spot checking on the hotspot.broad.bed files suggests that they all have this format. Will address, but in the mean time a workaround is

  rtracklayer::import(cache(ah["AH28868"]), format="bed", genome="hg19")

Martin

retrieving 1 resources

|=========================================================
=============|
100%
Error in value[[3L]](cond) :
  failed to load hub resource ?E003-DNase.hotspot.broad.bed.gz? of class
    EpigenomeRoadmapFile; reason: length of 'chrom' greater than length
    of 'ranges'
In addition: There were 50 or more warnings (use warnings() to see the first
50)

Best,
Kasper

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