[Bioc-devel] Recent issue with plot method dispatch

[Dan Tenenbaum]

On Wed, Mar 13, 2013 at 4:02 AM, Joern Toedling <j.toedling at 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
>
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