Re: [Rd] Class not found when search in .onLoad

From: Renaud Gaujoux <renaud_at_mancala.cbio.uct.ac.za>
Date: Fri, 24 Jun 2011 09:53:26 +0200

Thank you John for your response.

Things are a little bit more complicated though. The inheritance checks are not only made in .onLoad, they are part of a class validity method, which is called in .onLoad because some objects from this class are created at this stage. Such objects can also be created at any moment, not in a call from .onLoad.

More or less briefly:
class 'A' is in fact a virtual class defined in the package's namespace, with the purpose of defining a common interface. While the package does provide some derived classes (i.e. defined within the namespace), users too must be able to define derived classes from 'A' (i.e. not defined within the namespace).
In another class from the namespace, the validity method checks that one
of its character slot contains the name of a class that inherits from interface 'A'.

I was just expecting `isClass` and `extends` to also work in .onLoad without specifying the argument `where` (i.e. searching everywhere, starting by the package's namespace if called within a namespace). The argument `where` being there to allow finer search.

There is no argument pkgname to the validity method, to directly apply the work around. I guess I can always check the presence of the class in the some-how hard-coded namespace, and if it is not found there look for the class elsewhere:

#...
clref <- getClass('A', .Force=TRUE, where=THE.NAMESPACE) cl <- getClass(name, .Force=TRUE, where=THE.NAMESPACE) if( is.null(cl) )

     cl <- getClass(name, .Force=TRUE)

if( !extends(cl, clref) )

     return('invalid slot')
#...

I will use this, in last resort, although it feels strange as it will only be to deal with the case where objects are created within a call to .onLoad.

I am really interested in understanding why all this:

Could you please briefly give some explanations or pointers?

Thank you.

Bests,
Renaud

On 23/06/2011 18:44, John Chambers wrote:
> 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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