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 <dtene...@fhcrc.org> wrote: > On Wed, Mar 13, 2013 at 4:02 AM, Joern Toedling <j.toedl...@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 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
