A simple example is that I have created an extension to show
, which is a S4 base method. I don't want to cause a disambiguation fork by re-documenting show
in my package, and I also want to consolidate the documentation of my extension to show
in the documentation for the new class, myPkgSpClass
, by adding an alias for show,myPkgSpClass-method
.
#' @export
#' @aliases show,myPkgSpClass-method
#' @rdname myPkgSpClass-class
setMethod("show", "myPkgSpClass", function(object){ show(NA) })
The problem I'm having, is that this results in an serious warning during documentation-build by roxygen2, Rd files with duplicated alias 'show':
because there is more than one class extension to show
in this package, and roxygen2 has automatically added the generic term in the list of aliases to all the relevant *-class.Rd
files:
\alias{show}
\alias{show,myPkgSpClass-method}
But I think I don't want the generic alias in any of the instances, because it will force the need for disambiguation between show
in my package, and the base show
. This issue also applies to other S4 methods extended from other packages besides show
.
If I tag all class-specific methods to the same .Rd
file, then the warning goes away, but the ambiguity remains, because the show
alias still gets added automatically for that doc entry. If I manually remove \alias{show}
from the .Rd
file, then the problem seems solved, no warnings during roxygen or R CMD check pkgname
. So how do I get Roxygen2 to not-add the generic alias?
Other background:
This is a specific question building from a previous issue for exporting/documenting S4 extensions to base methods: Is it necessary to export base method extensions in an R package? Documentation implications?
It is more specific than, and not covered by, the following questions regarding documenting S4 methods / classes using Roxygen2:
How to properly document S4 methods using roxygen2
How to properly document S4 class slots using Roxygen2?
Seems to be fixed in roxygen2_3.1.0:
#' @export
#' @aliases show,myPkgSpClass-method
#' @rdname myPkgSpClass-class
setMethod("show", "myPkgSpClass", function(object){ show(NA) })
produces the myPkgSpClass-class.Rd:
\docType{methods}
\name{show,myPkgSpClass-method}
\alias{show,myPkgSpClass-method}
\usage{
\S4method{show}{myPkgSpClass}(object)
}
\arguments{
\item{object}{Any R object}
}
As Hadley stated, you do not need anymore to explicitly set the alias or the rd name, e.g.:
#' my title
#' @export
setMethod("show", "myPkgSpClass", function(object){ show(NA) })
will generate show-myPkgSpClass-method.Rd:
\docType{methods}
\name{show,myPkgSpClass-method}
\alias{show,myPkgSpClass-method}
\title{my title}
\usage{
\S4method{show}{myPkgSpClass}(object)
}
\arguments{
\item{object}{Any R object}
}
\description{
my title
}
Note that in that case you have to set the description. It will not generate a doc page if the documentation entry is empty.
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