[Bioc-devel] Recent issue with plot method dispatch

[Martin Morgan]

On 03/14/2013 07:16 AM, Joern Toedling wrote:
> 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.

Hi Joern --

I did follow up with this on R-devel

   https://stat.ethz.ch/pipermail/r-devel/2013-March/066111.html

A change in 'intervals' triggered this problem (exporting an S4 method and hence 
generic for plot), not a change in R.

The problem was that setMethod finds the S4 generic 'plot' on the search path, 
rather than the S3 plot imported in your  name space (I personally think this is 
not correct behaviour); your namespace then exports the unmodified S3 generic, 
masking the S4 generic on the search path that your method was added to.

A better work-around is to importFrom(intervals, plot); this avoids creating 
another S4 generic 'plot'. Experience has shown that having multiple generics of 
the same function creates problems as additional packages enter the picture; 
this is what motivates the BiocGenerics package.

An additional enhancement, not under your control, would be for intervals to 
reuse the S4 plot generic from stats4 -- importFrom (stats4, plot) -- and for 
your package too to importFrom(stats4, plot); the packages would then be adding 
methods to the same generic, and could do so independently of what packages 
(other than stats4) were doing.

Martin

>
> 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")
>


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