From jwiley.psych at gmail.com  Thu Oct  8 13:43:09 2015
From: jwiley.psych at gmail.com (Joshua Wiley)
Date: Thu, 8 Oct 2015 22:43:09 +1100
Subject: [Rd] Unexpected failure when calling new() with unnamed arg and
In-Reply-To: <22038.19866.92251.745312@stat.math.ethz.ch>
References: <55527C42.7090707@fredhutch.org>
	<21843.11818.477419.434062@stat.math.ethz.ch>
	<5553CC87.7080402@fredhutch.org>
	<CANz9Z_L4qY60RXOQuu_4DVc10Yxb0Hy8MzoDHkt4+-jQ7xPPcw@mail.gmail.com>
	<22038.19866.92251.745312@stat.math.ethz.ch>
Message-ID: <CANz9Z_Lp4=f_ttD5RTQoFcGu-Tck2nP9Na9xdDFfGLkFHp=Wbg@mail.gmail.com>

Hi Martin,

Thanks and apologies for not seeing that.  I had checked NEWS but not tried
it in R devel.

Thanks again.

Josh


On Thu, Oct 8, 2015 at 10:03 PM, Martin Maechler <maechler at stat.math.ethz.ch
> wrote:

> >>>>> Joshua Wiley <jwiley.psych at gmail.com>
> >>>>>     on Thu, 8 Oct 2015 12:19:16 +1100 writes:
>
>     > Hi, I realize this is an old thread, but just wondering
>     > whether a conclusion was ever reached on this issue?  I'm
>     > using formula(NULL) but it would be nice if default
>     > initialization worked for formula classes as well.
>
> Well,
> yes "of course", it was fixed quite a while ago ..
> as I had ("almost") promissed (below).
>
> Fixed only for R-devel though, e.g., because it potentially
> requires package re-installation, etc.
>
> Martin
>
>     > Cheers,
>     > Josh
>
>
>     > On Thu, May 14, 2015 at 8:13 AM, Herv? Pag?s
>     > <hpages at fredhutch.org> wrote:
>
>     >> Thanks Martin for looking into this.  H.
>     >>
>     >>
>     >> On 05/13/2015 03:57 AM, Martin Maechler wrote:
>     >>
>     >>> Herv? Pag?s <hpages at fredhutch.org>
>     >>>>>>>> on Tue, 12 May 2015 15:18:42 -0700 writes:
>     >>>>>>>>
>     >>>>>>>
>     >>> Hi,
>     >>>>
>     >>>
>     >>> The man page for new() suggests that if 'a' is an object
>     >>> with slots
>     >>>> "slot1" and "slot2" and C is a class that extends the
>     >>>> class of 'a', then the 2 following calls should be
>     >>>> equivalent:
>     >>>>
>     >>>
>     >>> new("C", a, ...)
>     >>>> new("C", slot1=a at slot1, slot2=a at slot2, ...)
>     >>>>
>     >>>
>     >>> This is generally the case but I just ran into a
>     >>> situation where it's
>     >>>> not. In the following example the former fails while
>     >>>> the latter works:
>     >>>>
>     >>>
>     >>> setClass("A", representation(slot1="numeric",
>     >>> slot2="logical"))
>     >>>> setClass("B", contains="A",
>     >>>> representation(design="formula")) setClass("C",
>     >>>> contains="B") a <- new("A", slot1=77, slot2=TRUE)
>     >>>>
>     >>>
>     >>> new("C", a, design=x ~ y) # fails
>     >>>> new("C", slot1=a at slot1, slot2=a at slot2, design=x ~ y) #
>     >>>> works
>     >>>>
>     >>>
>     >>> Note that new("B", a, design=x ~ y) works so the 3-level
>     >>> class
>     >>>> hierarchy is really needed in order to reproduce.
>     >>>>
>     >>>
>     >>> Probably related to this, I also noted that new("B")
>     >>> and/or new("C")
>     >>>> return invalid objects:
>     >>>>
>     >>>
>     >>> c <- new("C")
>     >>>>
>     >>>
>     >>> validObject(c)
>     >>>> # Error in validObject(c) : # invalid class ?C? object:
>     >>>> invalid object for slot "design" # in class "C": got
>     >>>> class "S4", should be or extend class "formula"
>     >>>>
>     >>>
>     >>> is(c at design, "formula")
>     >>>> # [1] FALSE
>     >>>>
>     >>>
>     >>> class(c at design)
>     >>>> # [1] "S4"
>     >>>>
>     >>>
>     >>> Note that 'c' can be fixed:
>     >>>>
>     >>>
>     >>> c at design <- formula(NULL)
>     >>>>
>     >>>
>     >>> validObject(c)
>     >>>> # [1] TRUE
>     >>>>
>     >>>
>     >>> Maybe something that the default "initialize" method
>     >>> should take care
>     >>>> of?
>     >>>>
>     >>>
>     >>> Another singularity that is maybe at the root of all of
>     >>> this is that
>     >>>> the "formula" S4 class is virtual:
>     >>>>
>     >>>
>     >>> showClass("formula")
>     >>>> # Virtual Class "formula" [package "methods"]
>     >>>> #
>     >>>> # Slots:
>     >>>> #
>     >>>> # Name: .S3Class # Class: character
>     >>>> #
>     >>>> # Extends: "oldClass"
>     >>>>
>     >>>
>     >>> so a bare call to new("formula") fails:
>     >>>>
>     >>>
>     >>> new("formula")
>     >>>> # Error in new("formula") : # trying to generate an
>     >>>> object from a virtual class ("formula")
>     >>>>
>     >>>
>     >>> Shouldn't new("formula") just return an "empty" S3
>     >>> formula (like
>     >>>> formula(NULL) does), in the same way that
>     >>>> new("integer") returns an empty ordinary integer
>     >>>> vector?
>     >>>>
>     >>>
>     >>> Interesting .. and at least worth following.
>     >>>
>     >>> One problem and historical reason for the current setup
>     >>> seems that the "formula" S3 class is not from 'base' but
>     >>> 'stats' :
>     >>>
>     >>> R's source, src/library/methods/R/BasicClasses.R, lines
>     >>> 524 ff has the following comment block
>     >>>
>     >>> | .OldClassesPrototypes is a list of S3 classes for
>     >>> which prototype | objects are known & reasonable.  The
>     >>> classes will reappear in | .OldClassesList, but will
>     >>> have been initialized first in | .InitBasicClasses.  NB:
>     >>> the methods package will NOT set up | prototypes for S3
>     >>> classes except those in package base and for "ts" | (and
>     >>> would rather not do those either).  The package that
>     >>> owns the | S3 class should have code to call setOldClass
>     >>> in its | initialization.
>     >>>
>     >>> So, when John Chambers wrote this, he envisioned that
>     >>> the 'stats' package would do "the correct thing" for its
>     >>> own classes.  OTOH, as history went, the stats package
>     >>> was never allowed to depend on methods.  There are many
>     >>> other S3 classes from 'stats' which also end up
>     >>> similarly, being defined via setOldClass() and that
>     >>> itself produces a VIRTUAL class.  Also, another part of
>     >>> the (R source) comment above is no longer quite
>     >>> accurate, e.g., "data.frame" is in .OldClassesPrototypes
>     >>> but not in .OldClassesList ...
>     >>>
>     >>> As I do agree that "formula" is much more basic than
>     >>> these other classes, I'm currently looking at tweaks to
>     >>> the methods (and stats) code, to get this to work.... as
>     >>> indeed - you mentioned above - we already allow "empty
>     >>> S3 formula" objects anyway.
>     >>>
>     >>> ... half an hour later : Indeed, I've been able to use
>     >>> the above information such that new("formula") and
>     >>> new("formula", y ~ x) work.
>     >>>
>     >>> However, your code above now --- with my changes ---
>     >>> would fail :
>     >>>
>     >>> > setClass("A", representation(slot1="numeric",
>     >>> slot2="logical")) > setClass("B", contains="A",
>     >>> representation(design="formula")) > setClass("C",
>     >>> contains="B") Error in
>     >>> reconcilePropertiesAndPrototype(name, slots, prototype,
>     >>> superClasses, : "B" is not eligible to be the data part
>     >>> of another class (must be a basic class or a virtual
>     >>> class with no slots)
>     >>> >
>     >>>
>     >>> So, I am not yet committing my changes to R-devel.
>     >>> Hopefully more on this, later today.
>     >>>
>     >>> Martin Maechler, ETH Zurich
>     >>>
>     >>>
>     >>> Thanks,
>     >>>> H.
>     >>>>
>     >>>
>     >>> > sessionInfo()
>     >>>> R version 3.2.0 Patched (2015-04-17 r68202) Platform:
>     >>>> x86_64-unknown-linux-gnu (64-bit) Running under: Ubuntu
>     >>>> 14.04.2 LTS
>     >>>>
>     >>>
>     >>> --
>     >>>> Herv? Pag?s Fred Hutchinson Cancer Research Center
>     >>>>
>     >>>
>     >>> [..................]
>     >>>
>     >>>
>     >>>
>     >> --
>     >> Herv? Pag?s
>     >>
>     >> Program in Computational Biology Division of Public
>     >> Health Sciences Fred Hutchinson Cancer Research Center
>     >> 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA
>     >> 98109-1024
>     >>
>     >> E-mail: hpages at fredhutch.org Phone: (206) 667-5791 Fax:
>     >> (206) 667-1319
>     >>
>     >> ______________________________________________
>     >> R-devel at r-project.org mailing list
>     >> https://stat.ethz.ch/mailman/listinfo/r-devel
>     >>
>
>
>
>     > --
>     > Joshua F. Wiley, Ph.D.  http://joshuawiley.com/
>     > ---
>     > Postdoctoral Research Fellow Mary MacKillop Institute for
>     > Health Research Australian Catholic University
>     > ---
>     > Senior Partner, Elkhart Group Ltd.
>     > http://elkhartgroup.com Office: 260.673.5518
>



-- 
Joshua F. Wiley, Ph.D.
http://joshuawiley.com/
---
Postdoctoral Research Fellow
Mary MacKillop Institute for Health Research
Australian Catholic University
---
Senior Partner, Elkhart Group Ltd.
http://elkhartgroup.com
Office: 260.673.5518

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[Rd] Unexpected failure when calling new() with unnamed arg and
Joshua Wiley