[Bioc-devel] Versioned (Biobase) "initialize" method

2016-01-07 Thread Stravs, Michael
Hi, The "initialize" method of the Versioned class in Biobase is defined in a way that breaks when inheriting classes want to define a copy constructor. Code to reproduce: library(Biobase) setClass("A", representation = representation(var1="integer"), prototype=prototype(var1=

[Bioc-devel] Use of EnsDb in the AnnotationDbi framework

2016-01-07 Thread Rainer Johannes
Dear all, thanks to Vince’s suggestion I have now implemented the central AnnotationDbi methods “columns”, “keys”, “keytypes” and “select” for EnsDb objects in my ensembldb package version 1.3.11 (EnsDb are TxDb like annotation packages/objects tailored to Ensembl based annotations). Thus, EnsD