[Bioc-devel] Recent issue with plot method dispatch

[Joern Toedling]

Hello,

thanks for following up on this, Martin. Indeed the problem was the 
missing S4 generic for "plot" was the problem. For some reason, the most 
recent version of R requires to declare this explicitly or to import the 
generic "plot" from another package. While before, I think that such a 
generic was created automatically when one defined a "plot" method for a 
S4 class.

The previous example:
library("girafe")
example(plotAligned)

actually works if you add a 'setGeneric("plot")' before calling 
'example(plotAligned)'.

I have added this to the development version of 'girafe'. It's 
unfortunate that such changes to R can also break the release version 
but since the release package is there from previous build versions and 
the next release will be soon, it's probably not worth to make any major 
efforts there.

Cheers,
Joern

On 03/13/2013 08:32 PM, Martin Morgan wrote:
> On 03/13/2013 04:02 AM, Joern Toedling 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 think this is a bug in S4, triggered by complex relations between 
> the intervals and girafe package. I'll pursue this on R-devel.
>
> I can reproduce this with a PkgA that has DESCRIPTION with
>
> Depends: intervals
> Imports: graphics
>
> NAMESPACE:
>
> importFrom(graphics, "plot")
> export("plot")
> exportMethods("plot")
>
> R/tmp.R
>
> setClass("A")
> setMethod("plot", "A", function(x, y, ...) {})
>
>
> and then
>
> > library(PkgA)
> Loading required package: intervals
> > plot
> function (x, y, ...)
> UseMethod("plot")
> <environment: namespace:graphics>
>
> notice that 'plot' is reported as an S3 generic, but should be an S4 
> generic.
>
> Removing Depends: intervals or changing to importsFrom(intervals, 
> "plot") recovers S4 export
>
> > library(PkgA)
> Loading required package: intervals
> > plot
> standardGeneric for "plot" defined from package "graphics"
>
> function (x, y, ...)
> standardGeneric("plot")
> <environment: 0x60aea90>
> Methods may be defined for arguments: x, y
> Use  showMethods("plot")  for currently available ones.
>
>
> The 'intervals' package Depends: on methods but nothing else. It 
> defines S3 and S4 methods on plot, creating an implicit S4 generic in 
> the process. It's NAMESPACE has
>
> S3method( "plot", "Intervals" )
> S3method( "plot", "Intervals_full" )
> exportMethods("plot")
>
> and we have
>
> > library(intervals)
> > plot
> standardGeneric for "plot" defined from package "graphics"
>
> function (x, y, ...)
> standardGeneric("plot")
> <environment: 0x68cdc78>
> Methods may be defined for arguments: x, y
> Use  showMethods("plot")  for currently available ones.
>
>
>


>
> 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")