R devel - Dec 2011 - R CMD check fails to warn about undocumented classes and methods

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

On 12/15/2011 03:40 PM, Martin Morgan wrote:
> 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))
this also has

   bunique <- function(b) unique(b)
> NAMESPACE:
> importFrom(PkgA, unique)
> exportClasses(B)
> exportMethods(unique)
and

   export(bunique)
>
> 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