[Bioc-devel] Importing generic functions from other pkgs and defining methods on them?
huber at ebi.ac.uk
Fri Mar 9 12:34:10 CET 2007
thanks! That solves the problem. I had never understood what the
idiom was good for, but I am pretty sure that at the time when I
initially wrote the package it was necessary. Good thing it's gone now.
I followed all your recommendation, exported plotPenLL and added more
Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber
> Hello again,
> I think I have a solution for you. You need to remove the conditional
> definition of the generics.
> I know that at some point in the past one needed to do things like
> if (!isGeneric("someFunc"))
> setGeneric("someFunc", ...)
> But this is no longer required and it seems to cause problems if it is
> there. I simply removed the if's in your AllGenerics.R and then the
> package built and checked for me.
> I don't completely understand what was going on, but some parts of
> your code were not getting the generic when it was needed.
> The if (!isGeneric) idiom is rather odd if you think about it. The
> only sensible way to define a method on a generic is if you know a
> fair bit about that generic (e.g., what its formal arguments are).
> When you optionally don't define your own generic and then set a
> method, who knows what the generic will be....
> So. Remove the if(!isGeneric) and things should improve.
> Also, since I spent some time looking at the code:
> * You should add a .onLoad function that does require("methods") as
> per Writing R Extensions and use of S4 + NAMESPACE
> * If you call plotPenLL in the vignette, perhaps you should export it
> instead of using ':::'.
> * You should add a Collate field to the DESCRIPTION file. You are
> getting a reasonable order at present, but since you have a lot of
> R files, that luck is going to run out sooner or later.
> * It is probably also worth adding import(method) to the NAMESPACE
> file. The rule, it seems, with the methods package, is that if
> there is a place where you could possible ask to use it, then you
> should (DESCRIPTION, .onLoad, NAMESPACE).
> Best Wishes,
> + seth
More information about the Bioc-devel