Hi Michael, This is now fixed in 1.13.22. Sorry it took so long - fell off the radar. Val On 05/18/2013 04:38 PM, Michael Lawrence wrote: > Entering this code: > > library(TxDb.Hsapiens.UCSC.hg19.knownGene) > library(LungCancerLines) > exons <- exons(TxDb.Hsapiens.UCSC.hg19.knownGene, vals = list(gene_id = > "7157")) > counts <- summarizeOverlaps(exons, LungCancerBamFiles()) > > Yields: > > Note: method with signature 'GAlignments#Vector' chosen for function > 'countOverlaps', > target signature 'GAlignments#GRanges'. > "Vector#GenomicRanges" would also be valid > Note: method with signature 'GAlignments#Vector' chosen for function > 'countOverlaps', > target signature 'GAlignments#GRanges'. > "Vector#GenomicRanges" would also be valid > > While this is apparently harmless, a couple of questions: > > - What is the rationale for defining countOverlaps methods on 'Vector'? If > this is a simple wrapper, why not go all the way to ANY? > > - Would it be feasible to avoid these Notes (which probably unnecessarily > worry the user), for example by defining specific methods for GenomicRanges > and GRangesList? I realize that dual dispatch is inherently prone to > ambiguities, but some brute-forcing might be worth the effort. > > Michael > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >