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

Taras Zakharko t@r@@@z@kh@rko @end|ng |rom uzh@ch
Wed Jun 30 15:20:07 CEST 2021


Thanks Duncan, I will submit a bug report to R core then. 

Best, 

Taras

> On 30 Jun 2021, at 14:16, Duncan Murdoch <murdoch.duncan using gmail.com> wrote:
> 
> On 30/06/2021 7:37 a.m., Taras Zakharko wrote:
>> 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.
> 
> Yes, I think you're right:  the method is registered in the environment of the generic.  I think by default it is searched for in the topenv() of that environment.
> 
> In most cases those are the same thing, but in your code they aren't the same:  the topenv is the global environment.
> 
> So I think I'd agree this is a bug.  I'd say the bug is in registerS3method, which should pay attention to the _R_S3_METHOD_LOOKUP_USE_TOPENV_AS_DEFENV_ setting when it computes defenv.
> 
> Here's a workaround that copies methods to the appropriate place:
> 
> fixS3registrations <- function(genericname, envir = parent.frame()) {
>  generic <- get(genericname, envir=envir)
>  genenv <- environment(generic)
>  top <- topenv(genenv)
> 
>  if (!identical(genenv, top)) {
>    toptable <- top[[".__S3MethodsTable__."]]
>    if (is.null(toptable)) {
>      toptable <- new.env(hash = TRUE, parent = baseenv())
>      top[[".__S3MethodsTable__."]] <- toptable
>    }
>    table <- genenv[[".__S3MethodsTable__."]]
>    if (!is.null(table)) {
>      methodnames <- ls(table, pattern = paste0(genericname, "[.][^.]*$"))
>      for (m in methodnames)
>        toptable[[m]] <- table[[m]]
>    }
>  }
> }
> 
> env <- local({
>  # define the generic function and the method
>  myfun <- function(x) UseMethod("myfun")
>  myfun.myclass <- function(x) print("called myfun.myclass")
> 
>     # register the method
>     .S3method("myfun", "myclass", myfun.myclass)
>     fixS3registrations("myfun")
> 
>     environment()
>  })
> 
> env$myfun(structure(0, class = "myclass"))
> #> [1] "called myfun.myclass"
> 
> 
> Duncan Murdoch
> 
>> 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
> 



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