colin@colinsmith.org
2003-Sep-02 22:14 UTC
[Rd] completeSubclasses() methods bug (PR#4051)
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
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 > > ______________________________________________ > R-devel@stat.math.ethz.ch mailing list > https://www.stat.math.ethz.ch/mailman/listinfo/r-devel-- 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 Murray Hill, NJ 07974 web: http://www.cs.bell-labs.com/~jmc