[Bioc-devel] IRanges::endoapply looks for FUN in the wrong places?

[Martin Morgan]

After this

     library(RNAseqData.HNRNPC.bam.chr14)
     library(TxDb.Hsapiens.UCSC.hg19.knownGene)
     fls <- RNAseqData.HNRNPC.bam.chr14_BAMFILES
     exByGn <- exonsBy(TxDb.Hsapiens.UCSC.hg19.knownGene, "gene")

Rsamtools is loaded but not attached; it's 
summarizeOverlaps,GRanges,character-method is available (maybe it shouldn't be, 
but that's a different question). Invoking

     summarizeOverlaps(exByGn, fls)

results in

 > summarizeOverlaps(exByGn, fls)
Error in get(as.character(FUN), mode = "function", envir = envir) :
   object 'obeyQname<-' of mode 'function' was not found

with

 > traceback()
14: get(as.character(FUN), mode = "function", envir = envir)
13: match.fun(FUN)
12: lapply(as.list(X), FUN = FUN, ...)
11: lapply(as.list(X), FUN = FUN, ...)
10: lapply(X, FUN = FUN, ...)
9: lapply(X, FUN = FUN, ...)
8: endoapply(object, "obeyQname<-", value = value)
7: endoapply(object, "obeyQname<-", value = value)
6: `obeyQname<-`(`*tmp*`, value = FALSE)
5: `obeyQname<-`(`*tmp*`, value = FALSE)
4: BamFileList(reads, yieldSize = yieldSize, obeyQname = FALSE,
        asMates = !singleEnd)
3: .local(features, reads, mode, ignore.strand, ...)
2: summarizeOverlaps(exByGn, fls)
1: summarizeOverlaps(exByGn, fls)

and the parent.frame() of the environment (where the search at line 14 starts) 
is IRanges, but should be Rsamtools (where endoapply was invoked).

Martin
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