From mtmorgan at fhcrc.org  Mon Jun  9 00:04:36 2008
From: mtmorgan at fhcrc.org (Martin Morgan)
Date: Sun, 08 Jun 2008 15:04:36 -0700
Subject: [Rd] R CMD CHECK WARNING inappropriate for S4 method?
Message-ID: <6phd4mr7fd7.fsf@lamprey.fhcrc.org>

The package 'graph' defines classes graph and graphNEL (extending
graph) and a union,graph,graph-method. These are all exported and
fully documented.

The package 'GSEABase' Imports: graph and importClassesFrom(graph,
graphNEL). GSEABase defines methods on union for its own classes (not
graph / graphNEL), and has exportMethods(union).
union,graph,graph-method is not used in GSEABase.

R version 2.8.0 Under development (unstable) (2008-06-08 r45879)
reports from R CMD CHECK GSEABase

* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic 'union' and siglist 'graph,graph'

I guess union,graph,graph-method is exposed to the user indirectly by
its import along with the graph class and export along with the
newly-defined union methods.

It would seem inappropriate to document union,graph,graph-method in
GSEABase. Making GSEABase Depend: graph rather than Import: graph does
not help.

Any guidance welcome.

Thanks,

Martin
-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M2 B169
Phone: (206) 667-2793



[Rd] R CMD CHECK WARNING inappropriate for S4 method?
Martin Morgan