Gábor Csárdi wrote:
> 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
Hi Gabor
It is not S4 alone, but S4 + name spaces that are giving you problems.
You probably want to Import: A rather than depends, and importFrom(A,
summary).
As it stands, inside the B name space, you find base::summary, whereas
you've defined a method on summary that has been promoted to a generic
in one of the packages that A imports (probably AnnotationDbi).
This is a little bit of a guess; at some level it might seem more
appropriate to Import: AnnotationDbi and importFrom(AnnotationDbi,
summary) (or wherever the generic for summary that you are trying to use
is created).
Martin
> 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
>
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