[BioC] rcmd check does not recognize generic function definitions

Laurent Gautier laurent@cbs.dtu.dk
Tue, 18 Feb 2003 06:41:10 +0100

On Tue, Feb 18, 2003 at 12:16:02AM -0500, Robert Gentleman wrote:
> On Tue, Feb 18, 2003 at 04:08:51PM +1100, Gordon Smyth wrote:
> > Dear all,
> > 
> > I am trying to package up some microarray data analysis code into a 
> > bioconductor package and, naturally, I want to define some new generic 
> > functions using the methods library. I have not been able to get my package 
> > to pass rcmd check.  In particular, generic functions which I have defined 
> > are not recognized when rcmd check tries out the examples.  However, all 
> > the examples work correctly if I actually build the library using rcmd 
> > build, then install it and load it in my R session using library.  The 
> > examples then work correctly if I paste them into my R session.

Looks like a variant of "forget 'where=where'". As Robert said, pick
one package in bioC (say Biobase). .First.lib is
defined in a file called zzz.R (seems to be a tacit convention to call
files that do that this way in packages). Forgeting the argument 'where'
when defining a S4-style method is something I remember doing quite few 
times in the begining (and it made R check not so happy while the stuff
was working when doing copy/paste).

Hopin' it helps,