[Rd] S4 Method Collisions with "[" (PR#4075)

[colin at colinsmith.org]

Full_Name: Colin A. Smith
Version: 1.8.0
OS: Mac OS X 10.2.6
Submission from: (NULL) (216.102.90.18)


Both Biobase and my package annaffy use S4 classes to define methods for "[".
Both packages use the save image method of installation. (See annaffy 1.0.3 in
BioC CVS.)

Depending on how both packages are loaded, the Biobase definitions seem to be
getting masked out:

> library(Biobase)
> library(annaffy)
> showMethods("[")

Function "[":
x = "ANY"
x = "container"
x = "phenoData"
x = "exprSet"
x = "aafList"
x = "aafTable"

> library(annaffy)
(annaffy loads Biobase in .First.lib)
> showMethods("[")

Function "[":
x = "ANY"
x = "aafList"
x = "aafTable"