From luke at stat.uiowa.edu  Fri Oct  3 22:35:18 2008
From: luke at stat.uiowa.edu (Luke Tierney)
Date: Fri, 3 Oct 2008 15:35:18 -0500 (CDT)
Subject: [Rd] Attributes of top level environments clobbered (was Re:
 [R] possible bug in function 'var' in R 2.7.2?)
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On Fri, 3 Oct 2008, Gabor Grothendieck wrote:

> On Fri, Oct 3, 2008 at 12:46 PM, Luke Tierney <luke at stat.uiowa.edu> wrote:
>> On Fri, 3 Oct 2008, Gabor Grothendieck wrote:
>>
>>> On Fri, Oct 3, 2008 at 11:43 AM, Luke Tierney <luke at stat.uiowa.edu> wrote:
>>>>
>>>> I will look into fixing it sometime if no one else feels like doing
>>>> it.  The environment aspect is not high priority; some other related
>>>> issues are more so (locking and active bindings as I recall).  But
>>>> even thoughs may not make it to the top of my queue any time soon.
>>>>
>>>> The issue of placing attributes on environments has come up before,
>>>> many times.  It is routinely advised against.  For better or worse,
>>>> the way environments were exposed to the R level is not designed to
>>>> support this properly.  Fixing this so that attributes are supported
>>>> reliably is non-trivial, and it is hard to justify the effort given
>>>> that there are standard work-arounds (such as putting the environment
>>>> in a list and attaching attributes to the list).  An alternative way
>>>> of removing the issues associated with attributes on environments, in
>>>> line with the way NULL works, is to disable placing attributes on
>>>> environments, at least from the R level.  This option is looking
>>>> increasingly attractive.
>>>
>>> These are not good options:
>>>
>>> - the workaround does not allow one to inherit methods.  This
>>> implies tediously rewriting or writing wrappers every inherited method
>>> in any such subclass.  Its really tantamount to eliminating OO for
>>> environments which is not a reasonable solution for a language that
>>> is supposed to be OO.
>>
>> It would mean sealing environments, making them final, pick your
>> favorite OO terminology.  Standard thing to do in many OO languages
>> when it is wararanted.
>
> I don't think this really addresses the problem.  The S3 model is
> in principle capable of handling environments and almost does
> so fully now.

Depends on your definitions.  Dispatch may work, but for me the show
stopper is unclass and related things.  Use of unclass inside code is
a fairly common idiom, and whenever an environment with a class gets
into a function that does an unclass on it, the environment ceases to
have a class.  You can argue that this should not be so but it is so,
it has been so for a long time, and it is lileky to remain so for a
long time.  To me this means that putting classes on environments is
too brittle to use in production code.  For this reason I would not use
a package that relies on doing this and would not encourage anyone
else to at this point.  I like prototype based OO, expecially for
graphics, which is why I wrote such a system for Lisp-Stat many years
ago. But using a variant of such a system in which the class can so
easily disappear seems ill-advised to me.

>>> - eliminating attributes on environments is even worse since widely
>>> used packages such as proto, ggplot2 and other packages would suffer.
>>> Maintaining reasonable compatiblity should be a goal of the core
>>> development.  It would be better to document the current situation than
>>> to make such a retrograde change.

While these packages may be widely used their authors have disregarded
repeated advice on this.  Inheritance just does not work reliably for
environments. Encapsulation does work. (One could argue that
encapsulation would be a better choice even if reliable inheritance
was available, but that is a moot point).

>>
>> The authors of proto would finally need to bite the bullet and address
>> this issue.  This would make proto more reliable in the end.
>
> The fact that environment attributes get clobbered at top level
> when defined in packages with lazy loading (but not outside packages
> nor in packages without lazy loading) is clearly a deficiency of R,
> not proto.

There is a bug in lazy loading in that some important features of
environments are not preserved.  Given that attributes on environments
are not reliable however I would argue that the fact that they are not
preserved is not particularly important.  While fixing the more
important bugs it is probably not hard to fix the attribute issue as
well (that is a conditional statement -- fixing the more imortant bugs
is going to be fairly painful, which is why it hasn't happened yet.)
Once that is done, lazy loading may "work" for proto but using
attributes on environments is still a Bad Idea given the way R works.

>
> Furthermore, the suggstion that this deficiency in R somehow reflects
> any unreliably in proto is likewise not accurate.  proto is extremely
> reliable, particularly in
> comparison to R.  In fact there are no known bugs in the development
> version of proto and large widely used packages use proto.  (If you are aware
> of any bugs let me know.) The fact that it is so solid is quite
> understandable because
> even if some of its code is necessarily complex the code is so short that its
> readily possible to accomplish this apprent bug-free status with reasonble
> effort.  Furthermore, the proto home page documents the problems -- mostly
> problems with R itself, not proto.
>
> I do appreciate the excellent R software; however, there are a few points like
> those addressed on the proto home page which do need to be addressed in R
> for it to be fully functional.

There are some interesting poins on that page that are worth looking
into.  Over time I suspect all but the current 3. will be addressed,
but 3., which is a variant on the unclass issue, is not likely to be.
You can call this a deficiency in R if you like, and I would agree in
the sense that I think it is inappropriate to allow attributes to be
set but not in a reliable way because they can be inadvertenly
removed.  We should have done this differently.  THere were/are two
choices:

     Make reference values, including environments, special in that they
     may not have attributes. This woud have been fairly easy (modulo one
     use made in decorating the frames on the search path) and could be
     done now to clean things up.

     Make R-visible environments in two parts--a wrapper that is passed by
     value like standard R objects and could have attributes, and an
     internal part that is essentially the current environment object.
     This is analogous to the way that character vectors, even of length 1,
     consist of an STRSXP wrapper containing CHARSXPs that hold the string.
     The STRSXP's are visible at the R level, the CHARSXPs are not.  This
     would have been messier to implement, and unfortunately would be very
     messy to retro-fit at this point, so it isn't likely to happen unless
     there is some other compelling reason to do so.

The bottom line is that this situation isn't likely to change any time
soon as far as I can see.  If that means that for you R will not be
"fully functional" then so be it.  Attributes on environments are not
reliable and hence it is a Bad Idea to try to use them.  This is a
feature of R as it is now, has been for a while, and will be for a
while. If you write code for language X, you can write it for
X-as-it-s or X-as-you-wish-it-to-be; but if you chose
X-as-you-wish-it-to-be and find things don't work out it's hard to
argue that the fault is with X.

luke

>
>>
>> luke
>>
>>> - if time is a problem perhaps the core group needs to add resources
>>> to reasonably address the problems in R.  Traditional economics
>>> do not apply to an open source project.  There is no monetary cost to
>>> adding additional developers.
>>>>
>>>> luke
>>>>
>>>> On Fri, 3 Oct 2008, Gabor Grothendieck wrote:
>>>>
>>>>> On Fri, Oct 3, 2008 at 3:23 AM, Martin Maechler
>>>>> <maechler at stat.math.ethz.ch> wrote:
>>>>>>
>>>>>> a much better (and much less error-prone) idea would be to install
>>>>>> R 2.8.0 alpha  even now.
>>>>>> It will become 'beta' early next week.
>>>>>>
>>>>>> We are asking the R community to please install and use
>>>>>> pre-release versions of R  (if you can / are allowed to)
>>>>>> at least from beta onwards, and report problems you see early on
>>>>>> *before* the final release.
>>>>>
>>>>> The bug discussed in the following year-old post suggested that
>>>>> the problem of clobbering attributes of top level environment objects
>>>>> would be fixed for 2.7 but its still in R version 2.7.2 (2008-08-25)"
>>>>> and also still in  "R version 2.8.0 alpha (2008-10-01 r46589)"
>>>>>
>>>>>  https://stat.ethz.ch/pipermail/r-devel/2007-October/047184.html
>>>>>
>>>>> The Avoiding R Bugs section of this page:
>>>>>
>>>>>  http://r-proto.googlecode.com
>>>>>
>>>>> has more discussion as well as a list of some other R bugs.
>>>>>
>>>>> This can be tested by creating a package with these two files only:
>>>>>
>>>>> ---DESCRIPTION---
>>>>> Package: testlazy
>>>>> Version: 1.0-0
>>>>> Date: 2008-10-03
>>>>> Title: Test lazy loading
>>>>> Author: G Grothendieck
>>>>> Maintainer: G Grothendieck <ggrothendieck at gmail.com>
>>>>> Description: Test lazy loading with top level objects.
>>>>> Depends: proto
>>>>> LazyLoad: yes
>>>>> License: GPL-2
>>>>> ---R/testlazy.R---
>>>>> TopLevel <- proto()
>>>>> ---
>>>>>
>>>>> And then testing it:
>>>>>
>>>>> library(testlazy)
>>>>> class(TopLevel)
>>>>>
>>>>> If its class is "environment" only then the class attribute was
>>>>> stripped.
>>>>>
>>>>> ______________________________________________
>>>>> R-devel at r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>>>
>>>>
>>>> --
>>>> Luke Tierney
>>>> Chair, Statistics and Actuarial Science
>>>> 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 at stat.uiowa.edu
>>>> Iowa City, IA 52242                 WWW:  http://www.stat.uiowa.edu
>>>>
>>>
>>
>> --
>> Luke Tierney
>> Chair, Statistics and Actuarial Science
>> 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 at stat.uiowa.edu
>> Iowa City, IA 52242                 WWW:  http://www.stat.uiowa.edu
>>
>

-- 
Luke Tierney
Chair, Statistics and Actuarial Science
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 at stat.uiowa.edu
Iowa City, IA 52242                 WWW:  http://www.stat.uiowa.edu



[Rd] Attributes of top level environments clobbered (was Re: [R] possible bug in function 'var' in R 2.7.2?)
Luke Tierney