Re: [Rd] R CMD check fails to warn about undocumented classes and methods

From: Martin Morgan <mtmorgan_at_fhcrc.org>
Date: Fri, 16 Dec 2011 06:05:34 -0800

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

Location: M1-B861
Telephone: 206 667-2793


______________________________________________ R-devel_at_r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Received on Fri 16 Dec 2011 - 14:10:29 GMT

This quarter's messages: by month, or sorted: [ by date ] [ by thread ] [ by subject ] [ by author ]

All messages

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.2.0, at Fri 16 Dec 2011 - 15:00:18 GMT.

Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-devel. Please read the posting guide before posting to the list.

list of date sections of archive