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
> >
> >
>
>
>
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