[Bioc-devel] methods package is not attached in .onLoad for Biobase

[Seth Falcon]

Hi Florian,

On  2 Feb 2006, fhahne at gmx.de wrote:
> I just noticed some strange behaviour when starting R with a saved
> workspace containing objects of class cytoFrame or cytoSet. These
> classes are defined in my own package prada and make heavy use of
> Biobase generics. I get the error
>
> Error in .initContents() : couldn't find function "isGeneric"
> Error: .onLoad failed in 'loadNamespace' for 'Biobase'
> Fatal error: unable to restore saved data in .RData
>
> When looking at the .onLoad function for Biobase I realized that the
> methods package is not attached thus isGeneric can not be found in
> the call to .initContents().  Adding a required(methods) to .onLoad
> fixed this for me. To my understanding, attaching methods is
> mandatory for every package that uses the S4 system (at least that's
> what's stated in the writing R extensions documentation), so I guess
> it should be fixed?!

Absolutely.  Thanks for the report.  A fix is in svn and will show up
in the devel repository within 24hrs or so.

Note to other package maintainers:

If your package has a NAMESPACE file and you define S4 classes or
methods, it is essential that you add a .onLoad function that looks
like this to your package:

  .onLoad <- function(libname, pkgname) {
      require("methods")
  }

Best,

+ seth