[Bioc-devel] error in stable AnnotationHub

[Morgan, Martin]

> -----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
> 
> 	[[alternative HTML version deleted]]
> 
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