[Bioc-devel] generics from Biobase not found during package installation

[Florian Hahne]

Hi everyone,
with the new bioC release I encounter a strange problem in my prada package:
I'm using some of the generics from Biobase (e.g. exprs, pData, 
phenoData, description) to build methods for my own objects of class 
cytoFrame (which describe data from FACS measurements).
e.g.
setMethod("description", signature="cytoFrame", 
definition=function(object) object at description, valueClass="character")

This used to work fine with all recent bioC releases, but now I get the 
following error when trying to install prada (and the same thing happens 
on the build test machines in Seattle):

* Installing *source* package 'prada' ...
** R
** inst
** save image
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

        Vignettes contain introductory material.
        To view, simply type 'openVignette()' or start with 'help(Biobase)'.
        For details on reading vignettes, see the openVignette help page.

Loading required package: RColorBrewer
Loading required package: grid
KernSmooth 2.22 installed
Copyright M. P. Wand 1997

** preparing package for lazy loading
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
Error in methods:::mlistMetaName(mi, ns) :
        the methods object name for 'description' must include the name 
of the package that contains the generic function, but there is no 
generic function of this name
Execution halted
ERROR: lazy loading failed for package 'prada'

Obviously R can't find the generics from Biobase although it is 
attached. As a quick fix I tried to redefine those "missing" generics in 
my own package. By doing so I get rid of the error message during 
installation but I also break all functionality from Biobase. When 
adding require(Biobase) in my R code before setting the new methods this 
evaluates to TRUE but isGeneric(description) evaluates to FALSE during 
installation.
When starting R interactively an after attaching Biobase I can set my 
new methods without any problem simply by pasting in the code.

Does anybody have any idea what might be going wrong here?

My system setup is i686-pc-linux-gnu running with R 2.2.0 release and a 
fresh installation of bioC 1.7 release (Biobase 1.8.0, prada 1.6.1)

Thank's in advance,
Florian