R help - Sep 2009 - Why S4 method is not visible from another package?

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

G?bor Cs?rdi 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
>