[Bioc-devel] Recent issue with plot method dispatch

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")