R help - Sep 2009 - package documentation of S4 methods

Hi,

I'm new to this mailing list and to R-programming so if the question is
stupid I apologize.

I have to create a package, which includes an S4-class called "BList".
For objects of this class I implemented a method "show", which
displays the first 15 data-lines of the object. I further implemented a method
"showall", which displays the whole data in the object. For the
"showall"-method i first defined a generic method:

setGeneric("showall",
    function(object){
        out<- standardGeneric("showall")
})

and then defined the method using

setMethod("showall", signature(object="BList"),
    function(object){
...
}

My problem: I don't know how to document the "showall"-method for
the package. If I just add the method in the documentation
'BList-class.Rd' as an alias using:

\alias{showall,BList-method}

and then add it to the list of methods:

\section{Methods}{
  \describe{
    \item{show}{\code{signature(object = "BList")}: Short output}
    \item{showall}{\code{signature(object = "BList")}: Long output}
    }
}

I get the following warning (when I check the package for installation):

* checking for missing documentation entries ... WARNING
Undocumented code objects:
  showall
All user-level objects in a package should have documentation entries.


I then used promptMethods() to build a seperate documentation-file
'showall-methods.Rd'. If I then run the check I get the warning:

* checking Rd files ... WARNING
Rd files with duplicated alias 'showall,BList-method':
  BList-class.Rd showall-methods.Rd

If I then remove the alias line '\alias{showall,BList-method}' from
either 'BList-class.Rd' or 'showall-methods.Rd' I get the first
warning ("Undocumented code objects...").

My question: how do you document methods of S4-classes in a package? It works
fine for the method "show" but it does not work for
"showall", for which I had to define the generic function first. What
can I do to fix this, or is it better to just define "showall" as a
function and not as a method?

Thanks a lot,

Elton G.




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El Gorgonzola <elgorgonzola <at> hotmail.com> writes:
> My question: how do you document methods of S4-classes in a package? 
> It works fine for the method "show" but it does not work for
"showall",
> for which I had to define the generic function first. What can I do to
> fix this, or is it better to just define "showall" as a function
and not
> as a method?
Hey I have this same problem and I too just started R. 
Did you ever found out how to make the warnings go away?

- Hassaan