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

[Valerie Obenchain]

Sorry. This was likely my error when I created the replacement methods. 
I see you've fixed it in svn, Martin, thanks.

Val

On 11/20/2013 07:00 PM, Michael Lawrence wrote:
> Right, match.fun() needs to be within the initial endoapply, not later.
> Isn't the convention though to use `obeyQname<-` in this case? Or should
> there be a convention?
>
>
> On Wed, Nov 20, 2013 at 5:18 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
>
>> 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
>> --
>> Computational Biology / Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N.
>> PO Box 19024 Seattle, WA 98109
>>
>> Location: Arnold Building M1 B861
>> Phone: (206) 667-2793
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
> 	[[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>