From mtmorgan at fhcrc.org  Fri Dec 16 15:05:34 2011
From: mtmorgan at fhcrc.org (Martin Morgan)
Date: Fri, 16 Dec 2011 06:05:34 -0800
Subject: [Rd] R CMD check fails to warn about undocumented classes and
 methods
In-Reply-To: <20203.5957.7651.175889@stat.math.ethz.ch>
References: <4EEA8560.9020102@fhcrc.org>	<4EEA86D3.1000203@fhcrc.org>
	<20203.5957.7651.175889@stat.math.ethz.ch>
Message-ID: <4EEB502E.9080907@fhcrc.org>

On 12/16/2011 02:02 AM, Martin Maechler wrote:
>> 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  ?

Earlier (2-11, 2-13, 2-14 & devel checked)

>
> 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.

Attached.

Thanks Martin, Martin

>
> Martin Maechler, ETH Zurich


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