Have a look at showMethods(), see if your method shows up in the registry.

See "Access to the Registry" section of this presentation for more
information:

http://www.r-project.org/conferences/useR-2004/Keynotes/Leisch.pdf


On 13 March 2013 16:59, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:

> On Wed, Mar 13, 2013 at 4:02 AM, Joern Toedling <j.toedling@imb-mainz.de>
> wrote:
> > Hello,
> >
> > I have encountered a strange issue with the plotting function in my
> package
> > "girafe" that I need some help with. I haven't changed anything in the
> plot
> > methods or the NAMESPACE of the package recently, and it worked before,
> yet
> > I observe the following error now.
> >
> > When calling the "plot" method for objects of the class
> > "AlignedGenomeIntervals", rather than using the appropriate S4 method and
> > calling another function (plotAligned), R falls back to the S3 method
> > "plot.Intervals_full" (Intervals_full is the class that
> > AlignedGenomeIntervals indirectly inherits from). Please see below for
> the
> > sessionInfo() output.
> >
> > Has anybody encountered the same behaviour or any insights what might be
> > going on? I'm grateful for any suggestions what I could fix in the method
> > definition and/or the NAMESPACE. I guess as a workaround I could add an
> S3
> > plot method for the "AlignedGenomeIntervals" calls but that would be
> rather
> > ugly.
>
> I don't have an answer but I can supply some more information. The
> package started to break (with the same error) in release as well as
> in devel, so the problem is not (merely) a change in R-devel.
>
> However, I cannot reproduce the problem on my own laptop with the
> identical sessionInfo() as on petty (mac devel build machine) where it
> breaks.
> Actually, not totally identical, my laptop's running r62117 and petty
> is running r62077, but the other devel build machines are running
> newer R and the release machines are running R 2.15.3.
>
> Dan
>
> >
> > Thanks in advance,
> > Joern
> >
> >
> >> sessionInfo()
> > R Under development (unstable) (2013-03-12 r62224)
> > Platform: x86_64-unknown-linux-gnu (64-bit)
> > ...
> > other attached packages:
> >  [1] org.Mm.eg.db_2.9.0     RSQLite_0.11.2 DBI_0.2-5
> >  [4] AnnotationDbi_1.21.13  Biobase_2.19.3 girafe_1.11.2
> >  [7] genomeIntervals_1.15.1 intervals_0.14.0 ShortRead_1.17.10
> > [10] latticeExtra_0.6-24    RColorBrewer_1.0-5 lattice_0.20-13
> > [13] Rsamtools_1.11.21      Biostrings_2.27.11 GenomicRanges_1.11.36
> > [16] IRanges_1.17.37        BiocGenerics_0.5.6 BiocInstaller_1.9.7
> >
> > loaded via a namespace (and not attached):
> > [1] bitops_1.0-5    BSgenome_1.27.1 hwriter_1.3     stats4_3.1.0
> > [5] tcltk_3.1.0     tools_3.1.0     zlibbioc_1.5.0
> >
> >
> > Example producing the error:
> >
> > library("girafe")
> > example("plotAligned")
> >
> >
> >
> >
> > --
> > Joern Toedling, PhD
> > Core Facility Bioinformatics
> > Institute of Molecular Biology gGmbH (IMB)
> > http://www.imb-mainz.de
> > Tel.: +49 6131 39 21528
> >
> > _______________________________________________
> > 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
>

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