Hi Michael,
Thank you for this work and the explanation. It’s good to know that my problem
will feed back into improvements in the methods package.
I opted for a simpler workaround, for now, renaming my abstract class to avoid
the collision.
- Paul
> On May 8, 2018, at 8:25 AM, Michael Lawrence <lawrence.mich...@gene.com>
> wrote:
>
> Thanks Paul.
>
> I've made improvements to the methods package so that there will no longer be
> any messages about AnnotationTrack being duplicated, but I'll need to work
> through some failures this is causing in tests.
>
> The first issue is interesting though. Since Gviz defines an initialize() for
> AnnotationTrack, dispatch ends up using that intsead of the default. That
> method (incorrectly in my opinion) silently drops unrecognized arguments in
> "..." so it is effectively a no-op. Ideally the method would eventually call
> callNextMethod(). Not doing so makes assumptions about how the parent object
> is initialized. It would also make this case work, just by luck. This is one
> reason why defining initialize() methods is tricky and should be avoided.
>
> Unfortunately, the methods package will dispatch to a method, regardless of
> the package of origin, unless there are methods with signatures containing
> two or more classes of the same name. This might be easy to fix but there
> could be performance regressions. This problem will happen all the time if
> there are initialize() methods around. You should be able to avoid this just
> by defining your own initialize() method that just calls the next method.
> Ideally though Gviz would just drop its one.
>
> Michael
>
> On Mon, May 7, 2018 at 11:14 AM, Paul Shannon
> <paul.thurmond.shan...@gmail.com> wrote:
> 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
