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

[Martin Morgan]

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@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

PkgAB.tar
Description: Unix tar archive

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