From maechler at stat.math.ethz.ch  Fri Dec 16 11:02:45 2011
From: maechler at stat.math.ethz.ch (Martin Maechler)
Date: Fri, 16 Dec 2011 11:02:45 +0100
Subject: [Rd] R CMD check fails to warn about undocumented classes and
 methods
In-Reply-To: <4EEA86D3.1000203@fhcrc.org>
References: <4EEA8560.9020102@fhcrc.org>
	<4EEA86D3.1000203@fhcrc.org>
Message-ID: <20203.5957.7651.175889@stat.math.ethz.ch>

> 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 Morgan

Thank you, Martin.
I don't have time to delve into this, before Monday, but I agree 
that things could/should be improved.

Two quick questions/requests:

1) Is this new in R-2.14.x or R-devel, but does not happen
   earlier  ?

2) As the 'R-devel' list allows attachments of MIME type
   application/x-tar
   application/x-compressed-tar
   application/x-gzip
it would be most convenient to most readers of this list, and
notably to R core members, if you included the packages maybe
as one *.tar containing the two <pkg>.tar.gz files.

Martin Maechler, ETH Zurich



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