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

Florian Hahne f.hahne at dkfz.de
Fri Oct 21 12:43:34 CEST 2005

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).
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 
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,

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