From jmc at r-project.org  Thu Jun 23 18:44:30 2011
From: jmc at r-project.org (John Chambers)
Date: Thu, 23 Jun 2011 09:44:30 -0700
Subject: [Rd] Class not found when search in .onLoad
In-Reply-To: <4E0321DE.2020601@cbio.uct.ac.za>
References: <4E0321DE.2020601@cbio.uct.ac.za>
Message-ID: <4E036D6E.3000509@r-project.org>

The workaround is to use the package's namespace, as you did.  That's 
one of the reasons why pkgname is an argument to .onLoad().

Depending on what you want to do, you can either use the namespace as an 
argument where= or get the class definition from the namespace and use 
it in place of the class name.

A side advantage is that such checks work regardless of whether or not 
the classes, etc. are exported from the package.  Also, on the remote 
chance there is another class of the same name, the check works 
unambiguously on your package's version.

The relevant part of your script, modified accordingly, seems to work as 
desired.

John

############
# script.R
############

setClass('A', representation(data='numeric'))

setClass('B', contains='A') # the argument is contains=

check.classes <- function(where){

message("isClass('A', where = where): ", methods::isClass('A', where = 
where))

message("isClass('B', where = where): ", methods::isClass('B', where = 
where))

classA <- getClass('A', where = where)
classB <- getClass('B', where = where)
message("extends(classB, classA): ", methods::extends(classB, classA))
}

.onLoad <- function(libname, pkgname=NULL){
cat("\n## .onLoad ##\n")
check.classes(asNamespace(pkgname))
}

.onAttach <- function(libname, pkgname){
cat("\n## .onAttach ##\n")
check.classes(asNamespace(pkgname))
}




On 6/23/11 4:22 AM, Renaud Gaujoux wrote:
> Hi,
>
> I am facing with a strange behaviour of isClass and extends when these
> are called in .onLoad in both R 2.12.1 and R 2.13.0. This is preventing
> my package from doing some object initializations at a proper place
> (i.e. in .onLoad).
>
> Suppose one defines two S4 classes in a package, and that one needs to
> check the inheritance between these two when loading the package (e.g.
> to validate slots in objects).
> See package attached or code below (not sure attachments can go through).
>
> in R 2.13.0:
> At the loading check after installation, the classes are not found by
> `isClass` and `extends` when these are called in .onLoad, but are
> correctly found when called in .onAttach.
> However findClass correctly finds the class in both case, as well as
> isClass if it is called with the argument
> `where=asNamespace('<THE.PACKAGE.NAME>')`.
> When the package is loaded from an open R session, the behaviour is the
> same.
>
> in R 2.12.1:
> the classes are correctly found by isClass and extends when these are
> called in .onLoad or .onAttach, but only at installation (i.e. at the
> loading check after R CMD INSTALL).
> When the package is loaded from an open R session, one fails to find the
> classes only in .onLoad while in .onAttach they are correctly found.
>
> This is really an issue as up to now I was using .onAttach to do my
> checks and initialization, but it is not a wise thing as package that
> would only need to import my package (load and not attach) will not get
> internal objects properly initialized. All this should be done in
> .onLoad, but I cannot do it due to this behaviour of `extends`.
>
> Can someone provide some explanations or work around.
>
> Thank you,
> Renaud
>
>
> ############
> # script.R
> ############
>
> setClass('A', representation(data='numeric'))
>
> setClass('B', contain='A')
>
> check.classes <- function(){
>
> a <- new('A')
> b <- new('B')
>
> message("isClass('A'): ", methods::isClass('A'))
> message("isClass('A') in namespace: ", methods::isClass('A',
> where=asNamespace('anRpackage')))
> message("findClass('A'): ")
> print(methods::findClass('A'))
>
> message("isClass('B'): ", methods::isClass('B'))
> message("isClass('B') in namespace: ", methods::isClass('B',
> where=asNamespace('anRpackage')))
> message("findClass('B'): ")
> print(methods::findClass('B'))
>
> message("extends('B', 'A'): ", methods::extends('B', 'A'))
> message("is(a, 'A'): ", is(a, 'A'))
> message("inherits(a, 'A'): ", inherits(a, 'A'))
> message("is(b, 'A'): ", is(b, 'A'))
> }
>
> .onLoad <- function(libname, pkgname=NULL){
> cat("\n## .onLoad ##\n")
> check.classes()
> }
>
> .onAttach <- function(libname, pkgname){
> cat("\n## .onAttach ##\n")
> check.classes()
> }
> ############
>
>
..............
>
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[Rd] Class not found when search in .onLoad
John Chambers