S4 Method Collisions with "[" (PR#4075)
colin@colinsmith.org wrote:
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)
I'm not sure exactly what's happening, but with (or without) saved images you should put a require(Biobase) _in the main source_ for the library (in order to guarantee that it's there when setMethod(), etc. calls are evaluated). There is then no need to load it separately in .First.lib. I'm a little surprised this worked at all. (We're trying to arrange that the source code for the package looks the same as it would if source'd directly into the global environment.)
showMethods("[")
Function "[": x = "ANY" x = "aafList" x = "aafTable"
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