[Bioc-devel] class name collision in cache: igvR and Gviz

[Michael Lawrence]

I pushed a fix into R devel.

On Wed, May 9, 2018 at 8:56 AM, Paul Shannon <
paul.thurmond.shannon at gmail.com> wrote:

> 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.michael at 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.shannon at gmail.com> wrote:
> > Hi Michael,
> >
> > > On May 4, 2018, at 1:36 PM, Michael Lawrence <
> lawrence.michael at 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.shannon at 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 at r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > >
> > >
> >
> >
> >
>
>

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