Hi Michael, > On May 4, 2018, at 1:36 PM, Michael Lawrence <lawrence.mich...@gene.com> > wrote: > > Do you have a reproducible example of this? It's probably a bug in the > methods package. >
Sorry I did not get to this sooner. Here are two symptoms of the cache class name collision: 1) igvR::displayTrack, if called after motifbreakR::plotMB, fails (see error message below) 2) plotMB, if called after igvR is loaded, reports the class name collision. - Paul library(SNPlocs.Hsapiens.dbSNP150.GRCh38) library(BSgenome.Hsapiens.UCSC.hg38) library(motifbreakR) snp <- "rs12050029" snps.gr <- snps.from.rsid(rsid = snp, dbSNP=SNPlocs.Hsapiens.dbSNP150.GRCh38, search.genome=BSgenome.Hsapiens.UCSC.hg38) results <- motifbreakR(snpList = snps.gr, filterp = TRUE, pwmList = query(MotifDb, "jaspar2018"), threshold = 1e-4, method = "ic", bkg = c(A=0.25, C=0.25, G=0.25, T=0.25), BPPARAM = BiocParallel::bpparam("SerialParam")) plotMB(results = results, rsid = snp, effect = c("weak", "strong")) library(igvR) igv <- igvR() setGenome(igv, "hg38") snp.track <- GRangesAnnotationTrack("snp", snps.gr, color="red") displayTrack(igv, snp.track) # this error is only seen if motifbreakR - and thus Gviz - have been loaded # otherwise, displayTrack works fine # Error in if (trackType == "variant" && source == "file" && fileFormat == : # missing value where TRUE/FALSE plotMB(results = results, rsid = snp, effect = c("weak", "strong")) # Found more than one class "AnnotationTrack" in cache; using the first, from namespace 'Gviz' # Also defined by 'igvR' # Found more than one class "AnnotationTrack" in cache; using the first, from namespace 'Gviz' # Also defined by 'igvR' # Found more than one class "AnnotationTrack" in cache; using the first, from namespace 'Gviz' # Also defined by 'igvR' # Found more than one class "AnnotationTrack" in cache; using the first, from namespace 'Gviz' # Also defined by 'igvR' # Found more than one class "AnnotationTrack" in cache; using the first, from namespace 'Gviz' # Also defined by 'igvR' # Found more than one class "AnnotationTrack" in cache; using the first, from namespace 'Gviz' # Also defined by 'igvR' > Michael > > On Fri, May 4, 2018 at 10:52 AM, Paul Shannon > <paul.thurmond.shan...@gmail.com> wrote: > I just discovered a class name collision - AnnotationTrack, in Gviz and my > new package igvR. wish to get wise counsel before proceeding with a fix. > Here’s the error message: > > Found more than one class "AnnotationTrack" in cache; > using the first, from namespace ‘igvR' Also defined by ‘Gviz’ > > AnnotationTrack is an abstract base class in my new package igvR. The > concrete derived classes at present are > > DataFrameAnnotationTrack > GRangesAnnotationTrack > UCSCBedAnnotationTrack > > It would be easy for me to rename AnnotationTrack to “GenomeAnnotationTrack” > or even “igvAnnotationTrack”, thereby avoiding the name clash. > > Reasonable? Fix in both release and devel? > > Thanks - > > - Paul > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel