Cryptic error message from subsetByOverlaps, maybe related to recent update to extractROWS? #88
Description
My CAGEfightR package has recently produced a cryptic error message on the Bioconductor servers, that I cannot myself reproduce:
Running examples in ‘CAGEfightR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: trackCTSS
> ### Title: Create Genome Browser track of CTSSs.
> ### Aliases: trackCTSS trackCTSS,GRanges-method
> ### trackCTSS,RangedSummarizedExperiment-method trackCTSS,GPos-method
>
> ### ** Examples
>
> library(Gviz)
Loading required package: grid
> data(exampleCTSSs)
> data(exampleUnidirectional)
> data(exampleBidirectional)
>
> # Example uni- and bidirectional clusters
> TC <- rowRanges(subset(exampleUnidirectional, width>=100)[3,])
> BC <- rowRanges(exampleBidirectional[3,])
>
> # Create pooled trakc
> subsetOfCTSSs <- subsetByOverlaps(exampleCTSSs, c(BC, TC, ignore.mcols=TRUE))
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'extractROWS': no slot of name "NAMES" for this object of class "IPos"
Calls: subsetByOverlaps ... FUN -> extractROWS -> slot -> .handleSimpleError -> h
Execution halted
I haven't changed any code in CAGEfightR, so I assume it must be some upstream changes to the core Bioconductor packages. After looking around, there was recent change to the the extractROWS generic in this commit: 16f29b6, which is the same function throwing the error.
I am unable to determine what is going on with that commit, but it seems to remove a call to updateObject. The StitchedGPos I'm trying to subset should be up to date (GenomicRanges:::.get_GPos_version returns "current").