[Bioc-devel] ExpressionSet and LumiBatch: inheritance problem in S4 methods for union class

Hi,

I am getting an error when calling an S4 method, which is defined for a
union class that includes ExpressionSet, on a LumiBatch object:

The error prototype is as follows:

- 'A' is Union of 'B' and 'C'
- 'D' extends 'C'
- a method myfun() exists for class 'A'
=> myfun('C') works but not myfun('D')

Error is like:
Error in (function (classes, fdef, mtable)  :
   unable to find an inherited method for function ?myfun? for signature
?"D"?

This works well on a toy example, but breaks when ExpressionSet are
involved.
So, I don't know if this is an R problem or something related to class
ExpressionSet, or possibly LumiBatch (I Cc Pan Du for this reason). I
remember that a while ago I was getting such errors even when defining the
method for ExpressionSet and calling it on LumiBatch objects.

Thank you for any help.

Bests,
Renaud

##############################
# Toy example:
##############################

R --vanilla --quiet <<EOF

setClass('B', contains = 'character')
setClass('C', contains = 'character')
setClass('D', contains = 'C')
setClassUnion('A', c('B', 'C'))

setGeneric('myfun', function(x, ...) standardGeneric('myfun'))
setMethod('myfun', 'A', function(x) print(class(x)) )

# works on C
myfun(new('C'))

# works on D
try( myfun(new('D')) )

# seems that inherits does not catch the inheritance
d <- new('D')
is(d, 'A')
inherits(d, 'A')
extends(class(d), 'A')
EOF

## OUTPUT FOR TOY EXAMPLE

setClass('B', contains = 'character')
setClass('C', contains = 'character')
setClass('D', contains = 'C')
setClassUnion('A', c('B', 'C'))

setGeneric('myfun', function(x, ...) standardGeneric('myfun'))

[1] "myfun"

setMethod('myfun', 'A', function(x) print(class(x)) )

[1] "myfun"

# works on C
myfun(new('C'))

[1] "C"
attr(,"package")
[1] ".GlobalEnv"

# works on D
try( myfun(new('D')) )

[1] "D"
attr(,"package")
[1] ".GlobalEnv"

# seems that inherits does not catch the inheritance
d <- new('D')
is(d, 'A')

[1] TRUE

inherits(d, 'A')

[1] TRUE

extends(class(d), 'A')

[1] TRUE

#####################################################
# Concrete example with ExpressionSet and LumiBatch objects:
#####################################################

### RUN

R --vanilla <<EOF
library(Biobase)
setGeneric('myfun', function(x, ...) standardGeneric('myfun'))
setClassUnion('A', c('matrix', 'ExpressionSet'))
setMethod('myfun', 'A', function(x){
     print(class(x))
})

# works on ExpressionSet
data(sample.ExpressionSet)
myfun(sample.ExpressionSet)

# not working on LumiBatch
library(lumi)
data(example.lumi)
try( myfun(example.lumi) )

# seems that inherits does not catch the inheritance
is(example.lumi, 'A')
inherits(example.lumi, 'A')
extends(class(example.lumi), 'A')

# define method for ExpressionSet ?
setMethod('myfun', 'ExpressionSet', function(x){
     message('ExpressionSet method')
     print(class(x))
})

# works well
myfun(sample.ExpressionSet)
myfun(example.lumi)

# Session info
sessionInfo()
EOF


##################
#### OUTPUT FOR EXPRESSIONSET
##################

R version 3.0.0 (2013-04-03) -- "Masked Marvel"
Copyright (C) 2013 The R Foundation for Statistical Computing
Platform: i686-pc-linux-gnu (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

   Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

library(Biobase)

Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ?BiocGenerics?

The following objects are masked from ?package:parallel?:

     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
     clusterExport, clusterMap, parApply, parCapply, parLapply,
     parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from ?package:stats?:

     xtabs

The following objects are masked from ?package:base?:

     anyDuplicated, as.data.frame, cbind, colnames, duplicated, eval,
     Filter, Find, get, intersect, lapply, Map, mapply, match, mget,
     order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
     rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table,
     tapply, union, unique, unlist

Welcome to Bioconductor

     Vignettes contain introductory material; view with
     'browseVignettes()'. To cite Bioconductor, see
     'citation("Biobase")', and for packages 'citation("pkgname")'.

setGeneric('myfun', function(x, ...) standardGeneric('myfun'))

[1] "myfun"

setClassUnion('A', c('matrix', 'ExpressionSet'))
setMethod('myfun', 'A', function(x){

+     print(class(x))
+ })
[1] "myfun"

# works on ExpressionSet
data(sample.ExpressionSet)
myfun(sample.ExpressionSet)

[1] "ExpressionSet"
attr(,"package")
[1] "Biobase"

# not working on LumiBatch
library(lumi)

KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Warning messages:
1: replacing previous import ?image? when loading ?graphics?
2: replacing previous import ?nleqslv? when loading ?nleqslv?

data(example.lumi)
try( myfun(example.lumi) )

Error in (function (classes, fdef, mtable)  :
   unable to find an inherited method for function ?myfun? for signature
?"LumiBatch"?

# seems that inherits does not catch the inheritance
is(example.lumi, 'A')

[1] TRUE

inherits(example.lumi, 'A')

[1] FALSE

extends(class(example.lumi), 'A')

[1] TRUE

# define method for ExpressionSet ?
setMethod('myfun', 'ExpressionSet', function(x){

+     message('ExpressionSet method')
+     print(class(x))
+ })
[1] "myfun"

# works well
myfun(sample.ExpressionSet)

ExpressionSet method
[1] "ExpressionSet"
attr(,"package")
[1] "Biobase"

myfun(example.lumi)

ExpressionSet method
[1] "LumiBatch"
attr(,"package")
[1] "lumi"

# Session info
sessionInfo()

R version 3.0.0 (2013-04-03)
Platform: i686-pc-linux-gnu (32-bit)

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=C                 LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] lumi_2.12.0        Biobase_2.20.0     BiocGenerics_0.6.0

loaded via a namespace (and not attached):
  [1] affy_1.38.1           affyio_1.28.0         annotate_1.38.0
  [4] AnnotationDbi_1.22.5  beanplot_1.1          BiocInstaller_1.10.1
  [7] Biostrings_2.28.0     colorspace_1.2-2      DBI_0.2-6
[10] GenomicRanges_1.12.2  grid_3.0.0            illuminaio_0.2.0
[13] IRanges_1.18.0        KernSmooth_2.23-10    lattice_0.20-15
[16] limma_3.16.3          MASS_7.3-26           Matrix_1.0-12
[19] matrixStats_0.8.1     mclust_4.1            methylumi_2.6.1
[22] mgcv_1.7-22           minfi_1.6.0           multtest_2.16.0
[25] nleqslv_2.0           nlme_3.1-109          nor1mix_1.1-4
[28] preprocessCore_1.22.0 RColorBrewer_1.0-5    reshape_0.8.4
[31] R.methodsS3_1.4.2     RSQLite_0.11.3        siggenes_1.34.0
[34] splines_3.0.0         stats4_3.0.0          survival_2.37-4
[37] tools_3.0.0           XML_3.96-1.1          xtable_1.7-1
[40] zlibbioc_1.6.0

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