From jmc at research.bell-labs.com  Wed Sep  3 09:29:44 2003
From: jmc at research.bell-labs.com (John Chambers)
Date: Wed Sep  3 14:30:04 2003
Subject: [Rd] completeSubclasses() methods bug (PR#4051)
References: <200309022015.h82KFRJH015010@pubhealth.ku.dk>
Message-ID: <3F55DEB8.990C1A88@research.bell-labs.com>

Yes, thanks.  I have a corrected version checked out.  It has some other
changes--as soon as I make a cleaned-up version with this fix only, I'll
commit it.

John

colin@colinsmith.org wrote:
> 
> Full_Name: Colin A. Smith
> Version: 1.8.0
> OS: Mac OS X 10.2.6
> Submission from: (NULL) (128.102.184.81)
> 
> annaffy 1.0.1 (in BioC CVS) fails to load. annaffy 1.0 (on the BioC web site)
> has the same problem.
> 
> It looks like the load is failing because of a bug in completeSubclasses() in
> r-devel. It calls setIs() and doesn't specify an environment via the "where"
> argument. setIs() "where" defaults to topEnv() and fails because "aafGO" doesn't
> exist in that environment and "list" is sealed.
> 
> completeSubclasses should be specifying my package for "where" instead of using
> the default.
> 
> > library(annaffy)
> Error in setIs(class2, obji@superClass, extensionObject = obji, doComplete =
> FALSE) :
>         Cannot create a setIs relation when neither of the classes ("aafGO" and
> "list") is local and modifiable in this package
> Error in setClass("aafGO", "aafList", prototype = list(), where = where) :
>         Error in contained classes ("aafList") for class "aafGO"; class
> definition removed from "annaffy"
> Error in library(annaffy) : .First.lib failed
> 
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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] completeSubclasses() methods bug (PR#4051)
John Chambers