[SOLVED] Document S4 class and "undocumented code object" during R CMD check

Document S4 class and "undocumented code object" during R CMD check

After struggling with documenting a S4 class with roxygen2, I decided to take a step back and create a minimum example using package.skeleton, promptClass, and promptMethod.

My problem is that R CMD check still gives a warning about "undocumented code objects", although I think that I have documented them properly.

The files I have now are:

testClass.R:

setClass("testClass",
        slots = c(a = "numeric"),
        prototype = prototype( a = 0 ),         
        validity = function(object) return(TRUE))

setGeneric(name = "testMethod",
            def = function(object, ...) standardGeneric("testMethod") )

setMethod(f = "testMethod", signature = "testClass",
        definition=function(object, x) 
        {
            cat("testMethod:",x,"\n")
            invisible(object)
        }
)

testClass-class.Rd

\name{testClass-class}
\Rdversion{1.1}
\docType{class}
\alias{testClass-class}
%%\alias{testMethod,testClass-method}
\title{Class \code{"testClass"}}
\description{bla bla}
\section{Objects from the Class}{bla bla}
\section{Slots}{\describe{\item{\code{a}:}{Object of class \code{"numeric"} ~~ }}}
\section{Methods}{\describe{\item{testMethod}{\code{signature(object = "testClass")}: ... }}}
\keyword{classes}

and testMethod.Rd

\name{testMethod-methods}
\docType{methods}
\alias{testMethod-methods}
\alias{testMethod,testClass-method}
\title{ ~~ Methods for Function \code{testMethod}  ~~}
\description{blabla}
\section{Methods}{
\describe{\item{\code{signature(object = "testClass")}}{blabla}}}
\keyword{methods}

There is also a package documentation file, but I think it is not relevant here.

R CMD check gives:

* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘testMethod’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.

I have consulted these sections, and what I took from these is that I needed at least an alias to generic,signature-list-method, which in this case would be alias{testMethod,testClass-method} which was placed in the documentation file automatically by my call of promtMethod (I have commented it out from the class .Rd file because it was duplicated there).

What do I need to change in the .Rd file to get rid of this warning?

Solution

In the meanwhile, I figured out the problem. It seems that I also needed to ass \alias{testMethod} to the .Rd file. I find it strange, however, that the file generated by promptMethod did not include this alias.