From mtmorgan at fhcrc.org  Fri Dec 16 00:40:16 2011
From: mtmorgan at fhcrc.org (Martin Morgan)
Date: Thu, 15 Dec 2011 15:40:16 -0800
Subject: [Rd] R CMD check fails to warn about undocumented classes and
	methods
Message-ID: <4EEA8560.9020102@fhcrc.org>

In

 > R.version.string
[1] "R Under development (unstable) (2011-12-15 r57901)"

PkgA promotes 'unique' to a generic and exports that

   DESCRIPTION:
   Imports: methods

   R/f.R:
   setGeneric("unique")

   NAMESPACE:
   export(unique)

and PkgB creates and exports a method on unique

   DESCRIPTION
   Imports: methods, PkgA

   R/f.R:
   setClass("B", representation(b="numeric"))
   setMethod(unique, "B",
             function(x, incomparables=FALSE, ...) unique(x at b))

   NAMESPACE:
   importFrom(PkgA, unique)
   exportClasses(B)
   exportMethods(unique)

There is a man/ page for each package, but no other documentation. Yet

    R CMD check PkgA_1.0.tar.gz

says

* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK

and for Pkg B we only get

* checking for missing documentation entries ... WARNING
Undocumented code objects:
   ?bunique?
All user-level objects in a package should have documentation entries.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK

Martin
-- 
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793



[Rd] R CMD check fails to warn about undocumented classes and methods
Martin Morgan