From jmc at research.bell-labs.com  Sat Sep  6 10:40:45 2003
From: jmc at research.bell-labs.com (John Chambers)
Date: Sat Sep  6 15:41:01 2003
Subject: [Rd] S4 Method Collisions with "[" (PR#4075)
References: <200309050955.h859t4JH016010@pubhealth.ku.dk>
Message-ID: <3F59E3DD.121EFFAA@research.bell-labs.com>

We have a fix for this bug, which will be comitted, probably later
today.  Be aware until then that some
methods for primitive functions may turn up missing if one package
requires() another.  If you must use last night's version, a workaround
is to do

getAllMethods(f)

for the offending functions, e.g., "[", abter the library() call.

John

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)
> > showMethods("[")
> 
> Function "[":
> x = "ANY"
> x = "aafList"
> x = "aafTable"
> 
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> R-devel@stat.math.ethz.ch mailing list
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-- 
John M. Chambers                  jmc@bell-labs.com
Bell Labs, Lucent Technologies    office: (908)582-2681
700 Mountain Avenue, Room 2C-282  fax:    (908)582-3340
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[Rd] S4 Method Collisions with "[" (PR#4075)
John Chambers