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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