[Bioc-devel] Recent issue with plot method dispatch

Joern Toedling j.toedling at imb-mainz.de
Wed Mar 13 12:02:27 CET 2013


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.

Thanks in advance,

 > 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:


Joern Toedling, PhD
Core Facility Bioinformatics
Institute of Molecular Biology gGmbH (IMB)
Tel.: +49 6131 39 21528

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