[Rd] :: and ::: as .Primitives?

Hervé Pagès hpages at fredhutch.org
Fri Jan 23 19:11:47 CET 2015


On 01/23/2015 07:01 AM, luke-tierney at uiowa.edu wrote:
> On Thu, 22 Jan 2015, Michael Lawrence wrote:
>> On Thu, Jan 22, 2015 at 11:44 AM,  <luke-tierney at uiowa.edu> wrote:
>>> For default methods there ought to be a way to create those so the
>>> default method is computed at creation or load time and stored in an
>>> environment.
>> We had considered that, but we thought the definition of the function
>> would be easier to interpret if it explicitly specified the namespace,
>> instead of using tricks with environments. The same applies for
>> memoizing the lookup in front of a loop.
> interpret in what sense (human reader or R interpreter)? In either
> case I'm not convinced.

 From a developer perspective, especially when debugging, when we do
selectMethod("match", ...) and it turns out that this returns the
default method, it's good to see:

   Method Definition (Class "derivedDefaultMethod"):

   function (x, table, nomatch = NA_integer_, incomparables = NULL,
   base::match(x, table, nomatch = nomatch, incomparables = incomparables,
   <environment: namespace:BiocGenerics>

           x           table
   target  "DataFrame" "ANY"
   defined "ANY"       "ANY"

rather than some obscure/uninformative body. I hope we can keep that.

>> The implementation of these functions is almost simpler in C than it
>> is in R, so there is relatively little risk to this change. But I
>> agree the benefits are also somewhat minor.
> I don't disagree, but it remains that even calling the C version has
> costs that should not need to be paid. But maybe we can leave that to
> the compiler/byte code engine. Optimizing references to symbols
> resolved statically to name spaces and imports is on the to do list,
> and with a little care that mechanism should work for foo::bar uses as
> well.

That would be great. Thanks!


> Best,
> luke
>>> For other cases if I want to use foo::bar many times, say
>>> in a loop, I would do
>>> foo_bar <- foo::bar
>>> and use foo_bar, or something along those lines.
>>> When :: and ::: were introduce they were intended primarily for
>>> reflection and debugging, so speed was not an issue. ::: is still
>>> really only reliably usable that way, and making it faster may just
>>> encourage bad practice. :: is different and there are good arguments
>>> for using it in code, but I'm not yet seeing good arguments for use in
>>> ways that would be performance-critical, but I'm happy to be convinced
>>> otherwise. If there is a need for a faster :: then going to a
>>> SPECIALSXP is fine; it would also be good to make the byte code
>>> compiler aware of it, and possibly to work on ways to improve the
>>> performance further e.g. through cacheing.
>>> Best,
>>> luke
>>> On Thu, 22 Jan 2015, Peter Haverty wrote:
>>>> Hi all,
>>>> When S4 methods are defined on base function (say, "match"), the
>>>> function becomes a method with the body "base::match(x,y)". A call to
>>>> such a function often spends more time doing "::" than in the function
>>>> itself.  I always assumed that "::" was a very low-level thing, but it
>>>> turns out to be a plain old function defined in base/R/namespace.R.
>>>> What would you all think about making "::" and ":::" .Primitives?  I
>>>> have submitted some examples, timings, and a patch to the R bug
>>>> tracker (https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=16134).
>>>> I'd be very interested to hear your thoughts on the matter.
>>>> Regards,
>>>> Pete
>>>> ____________________
>>>> Peter M. Haverty, Ph.D.
>>>> Genentech, Inc.
>>>> phaverty at gene.com
>>>> ______________________________________________
>>>> R-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>> --
>>> Luke Tierney
>>> Ralph E. Wareham Professor of Mathematical Sciences
>>> University of Iowa                  Phone:             319-335-3386
>>> Department of Statistics and        Fax:               319-335-3017
>>>    Actuarial Science
>>> 241 Schaeffer Hall                  email:   luke-tierney at uiowa.edu
>>> Iowa City, IA 52242                 WWW:  http://www.stat.uiowa.edu
>>> ______________________________________________
>>> R-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel

Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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E-mail: hpages at fredhutch.org
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