[Rd] S3 dispatch does not work for generics defined inside an environment

Wed Jun 30 13:37:23 CEST 2021

Thats not how I read the code? Consider this snippet from registerS3method:

genfun <- get(genname, envir = envir)
        if (.isMethodsDispatchOn() && methods::is(genfun, "genericFunction")) 
            genfun <- methods::finalDefaultMethod(genfun using default)
        if (typeof(genfun) == "closure") 
            environment(genfun)
        else .BaseNamespaceEnv

This is the environment where the method cache (.__S3MethodsTable__.) will be updated. The problem hoverer, the with the default setting of _R_S3_METHOD_LOOKUP_USE_TOPENV_AS_DEFENV_ this is *not* the environment where R will look for the method cache. Manually injecting the entry into the method cache of the top environment instead works like a charm. 

The envir argument is just for looking up the generic function. 

Best, 

Taras 

> On 30 Jun 2021, at 13:29, Duncan Murdoch <murdoch.duncan using gmail.com> wrote:
> 
> On 30/06/2021 7:23 a.m., Taras Zakharko wrote:
>> I had another glance at the code and now I’m convinced that this is the bug in registerS3method(). Default R behavior (in objects.c) appears to be to look for method definitions in the top environment, not the defining environment, but registerS3method() registers the method in the defining environment. I think registerS3method() should be changed to something like:
> 
> It registers wherever you ask it to.  The default is the defining environment.
> 
> .S3method is the one that always uses the defining environment, since it has no way to override the default.
> 
> Duncan Murdoch
> 
>> - if (typeof(genfun) == "closure”)
>> -            environment(genfun)
>> ------------
>> + if (typeof(genfun) == "closure”)
>> + if(isFALSE(Sys.getenv("_R_S3_METHOD_LOOKUP_USE_TOPENV_AS_DEFENV_”))  environment(genfun) else topenv(environment(genfun))
>> in order to match the behavior of do_usemethod()
>> Best,
>> Taras
>>> On 30 Jun 2021, at 12:51, Taras Zakharko <taras.zakharko using uzh.ch> wrote:
>>> 
>>> @Duncan: .S3method() calls registerS3method() with appropriate environmental argument under the good, so that’s not the problem.
>>> 
>>> Anyway, I’ve been doing some debugging and I think I have found the issue. The following snippet in src/objects.c (https://github.com/wch/r-source/blob/ecc633b37d77fdd1cb27dda74d7f6b3684f0c01c/src/main/objects.c#L525) sets the global lookup_use_topenv_as_defenv variable:
>>> 
>>> 
>>> if(lookup_use_topenv_as_defenv == -1) {
>>> 	lookup = getenv("_R_S3_METHOD_LOOKUP_USE_TOPENV_AS_DEFENV_");
>>> 	lookup_use_topenv_as_defenv =
>>> 	    ((lookup != NULL) && StringFalse(lookup)) ? 0 : 1;
>>> }
>>> 
>>> Isn’t that supposed to be
>>> 
>>> 	lookup_use_topenv_as_defenv =  ((lookup != NULL) && StringFalse(lookup)) ? 1 : 0;
>>> 
>>> instead?
>>> 
>>> The way the code works right now, methods will be looked up in top environment exactly if _R_S3_METHOD_LOOKUP_USE_TOPENV_AS_DEFENV_ is not set. This seems incompatible with what registerS3method() does (setting the .__S3MethodsTable__. on the defining environment instead of the topenv). When I change 0 and 1 around, everything works as expected.
>>> 
>>> In the meantime, I can work around it by manually injecting __S3MethodsTable__ into .GlobalEnv (which is my topenv here).
>>> 
>>> I can open a bug report, but I would like to wait for some more comments.
>>> 
>>> Best,
>>> 
>>> Taras
>>> 
>>>> On 30 Jun 2021, at 12:39, Joshua Ulrich <josh.m.ulrich using gmail.com> wrote:
>>>> 
>>>> On Wed, Jun 30, 2021 at 5:17 AM Duncan Murdoch <murdoch.duncan using gmail.com> wrote:
>>>>> 
>>>>> On 30/06/2021 5:22 a.m., Taras Zakharko wrote:
>>>>>> Dear all,
>>>>>> 
>>>>>> I have a generic function and a bunch of methods defined in a separate environment. Here is a reduced example:
>>>>>> 
>>>>>>   env <- local({
>>>>>>     # define the generic function and the method
>>>>>>     myfun <- function(x) UseMethod("myfun")
>>>>>>     myfun.myclass <- function(x) print("called myfun.myclass”)
>>>>>> 
>>>>>>     # register the method
>>>>>>     .S3method("myfun", "myclass", myfun.myclass)
>>>>>> 
>>>>>>     environment()
>>>>>>  })
>>>>>> 
>>>>>> Since the method has been registered, I hoped that invocation like this would work:
>>>>>> 
>>>>>>   env$myfun(structure(0, class = "myclass”))
>>>>>> 
>>>>>> However, this results in a “no applicable method" error.
>>>>>> 
>>>>>> It is my understanding that registerS3method (called by .S3method) will install the method string in the .__S3MethodsTable__. table of the environment where the generic function is defined, and this table is subsequently used by usemethod() inside R, so I am puzzled that the dispatch does not work. I checked and the  .__S3MethodsTable__. of env is indeed setup correctly. I also tried manually adding the method string to the global .__S3MethodsTable__. inside .BaseNamespaceEnv to no effect.
>>>>>> 
>>>>>> In fact, the only way to make it work is to define either myfun or  myfun.myclas in the global environment, which is something I would like to avoid.
>>>>>> 
>>>>>> Thank you in advance for any pointers!
>>>>>> 
>>>>> 
>>>>> registerS3method has an additional parameter "envir" which I believe
>>>>> would end up set to env in your code.  So this works:
>>>>> 
>>>>>> eval(expression(myfun(structure(0, class = "myclass"))), envir = env)
>>>>> [1] "called myfun.myclass"
>>>>> 
>>>>> You could probably also call registerS3method with envir specified
>>>>> appropriately and get your original expression to work.
>>>>> 
>>>> That doesn't seem to work on 4.1.0 for me. The code below worked for
>>>> me in Oct-2020, though I'm not sure what version of R I was using at
>>>> the time. I was slow to upgrade to 4.0, so it was probably the latest
>>>> 3.x version.
>>>> 
>>>> env <- new.env()
>>>> local({
>>>>  # define the generic function and the method
>>>>  myfun <- function(x) { UseMethod("myfun", x) }
>>>> 
>>>>  # register the method
>>>>  registerS3method("myfun", "myclass",
>>>>      function(x) { print("called myfun.myclass") },
>>>>      envir = env)
>>>> }, envir = env)
>>>> attach(env)
>>>> myfun(structure(0, class = "myclass"))
>>>> 
>>>> 
>>>>> Duncan Murdoch
>>>>> 
>>>>> ______________________________________________
>>>>> R-devel using r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>> 
>>>> 
>>>> 
>>>> -- 
>>>> Joshua Ulrich  |  about.me/joshuaulrich
>>>> FOSS Trading  |  www.fosstrading.com
>>> 
>> ______________________________________________
>> R-devel using r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel