[R] Why S4 method is not visible from another package?

[Gábor Csárdi]

Dear All,

maybe this is something obvious, I seem to be incapable of
understanding how S4 works.

So, in package 'A' I defined a "summary" method for my class:

setMethod("summary", signature(object="ListHyperGResult"),
          function(object, pvalue=pvalueCutoff(object), categorySize=NULL) {
             "whatever"
          })

"ListHyperGResult" has a subclass, "GOListHyperGResult":

setClass("GOListHyperGResult",
         representation=representation(conditional="logical"),
         contains="ListHyperGResult",
         prototype=prototype(testname="GO"))

The summary method is exported in the NAMESPACE:

exportMethods("summary")

Package 'B' depends on package 'A', this is stated in the
'DESCRIPTION' file. If I call 'summary' on a 'GOListHyperGResult' in
package B, then the default summary method is called instead of the
correct one, despite that I have

Browse[1]> showMethods("summary")
Function: summary (package base)
object="AnnDbBimap"
object="ANY"
object="Bimap"
object="DBIObject"
object="HyperGResultBase"
object="KEGGHyperGResult"
object="LinearMResultBase"
object="ListHyperGResult"
object="PFAMHyperGResult"
object="SQLiteConnection"
object="SQLiteDriver"
object="SQLiteResult"

Browse[1]> class(gos[[1]])
[1] "GOListHyperGResult"

But I still get:

Browse[1]> is(gos[[1]], "ListHyperGResult")
[1] TRUE
Browse[1]> summary(gos[[1]])
            Length              Class               Mode
                 1 GOListHyperGResult                 S4

What am I doing wrong?

> sessionInfo()
R version 2.9.0 (2009-04-17)
x86_64-redhat-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

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

other attached packages:
 [1] hgu95av2.db_2.2.12  ALL_1.4.4           ExpressionView_0.1
 [4] caTools_1.9         bitops_1.0-4.1      KEGG.db_2.2.5
 [7] GO.db_2.2.5         RSQLite_0.7-1       DBI_0.2-4
[10] eisa_0.1            genefilter_1.24.2   Category_2.10.0
[13] AnnotationDbi_1.6.0 Biobase_2.4.1       isa2_0.1

loaded via a namespace (and not attached):
[1] annotate_1.22.0 graph_1.22.2    GSEABase_1.6.0  RBGL_1.20.0
[5] splines_2.9.0   survival_2.35-4 tools_2.9.0     XML_2.6-0
[9] xtable_1.5-5
>

Thanks,
Gabor

-- 
Gabor Csardi <Gabor.Csardi at unil.ch>     UNIL DGM