From kevinushey at gmail.com  Fri Jul 29 20:37:04 2016
From: kevinushey at gmail.com (Kevin Ushey)
Date: Fri, 29 Jul 2016 11:37:04 -0700
Subject: [Rd] strange behavior in 'inherits' check for loaded S4 object
In-Reply-To: <CAJXgQP3ap2QSemxr533=AAHNKA+J_xMWns6EB_ky7FPGpSsQwg@mail.gmail.com>
References: <CAJXgQP3ap2QSemxr533=AAHNKA+J_xMWns6EB_ky7FPGpSsQwg@mail.gmail.com>
Message-ID: <CAJXgQP1qDaBc9dEW8J9H7xYonzJGtOjhs-fBVWtA5RgUG7aW7A@mail.gmail.com>

I have a small idea as to what's going on now; at least, why exporting
the class resolves this particular issue.

Firstly, when an S4 class is not exported, the associated
'.__C__<class>' object is not made part of the package environment.
For example, I see:

    > getAnywhere(".__C__SubMatrix")
    A single object matching '.__C__SubMatrix' was found
    It was found in the following places
      namespace:s4inherits
    with value
    < ... >

Note that the symbol is only discovered in the package namespace. When
the class is exported (e.g. with 'exportClasses(SubMatrix)' in the
NAMESPACE file), it's found both in 'package:s4inherits' and
'namespace:s4inherits'.

Secondly, when R attempts to resolve the superclasses for an S3 class,
the function 'methods:::.extendsForS3' is called. Tracing that code
eventually gets us here:

https://github.com/wch/r-source/blob/trunk/src/library/methods/R/SClasses.R#L255

Note that we reach this code path as the S3 class cache has not been
populated yet; ie, this code returns NULL:

https://github.com/wch/r-source/blob/trunk/src/library/methods/R/SClasses.R#L238-L240

So, the class hierarchy is looked up using this code:

    if(isTRUE(nzchar(package))) {
       whereP <- .requirePackage(package)
       value <- get0(cname, whereP, inherits = inherits)
    }

However, because the '.__C__SubMatrix' object is only made available
in the package's namespace, not within the package environment, it is
not resolved, and so lookup fails. (Presumedly, that lookup is done
when initially building a cache for S3 dispatch?) So, I wonder if that
class lookup should occur within the package's namespace instead?

Thanks for your time,
Kevin

On Sat, Jun 25, 2016 at 12:46 PM, Kevin Ushey <kevinushey at gmail.com> wrote:
> Hi,
>
> (sorry for the wall of text; the issue here appears to be rather complicated)
>
> I'm seeing a somewhat strange case where checking whether an S4 object
> inherits from a parent class defined from another package with
> 'inherits' fails if that object is materialized through a call to
> 'load'. That's a mouthful, so I've put together a relatively small
> reproducible example online here:
>
> https://github.com/kevinushey/s4inherits
>
> This package, 's4inherits', defines an S4 class, 'SubMatrix', that
> inherits from the 'dsyMatrix' class defined in the Matrix package.
> After installing the package, I run some simple tests:
>
> $ R -f test-save.R
>
>> library(s4inherits)
>> data <- SubMatrix(1)
>>
>> is(data, "SubMatrix")
> [1] TRUE
>> inherits(data, "SubMatrix")
> [1] TRUE
>>
>> is(data, "dsyMatrix")
> [1] TRUE
>> inherits(data, "dsyMatrix")
> [1] TRUE
>>
>> save(data, file = "test.RData")
>>
>
> All the inheritance checks report as we would expect. I check that the
> inheritance reports are as expected, then save that object to
> 'test.RData'. I then load that data file in a new R session and run
> the same checks:
>
> $ R -f test-load.R
>
>> library(methods)
>> load("test.RData")
>>
>> inherits(data, "SubMatrix")
> Loading required package: s4inherits
> [1] TRUE
>> is(data, "SubMatrix")
> [1] TRUE
>>
>> inherits(data, "dsyMatrix")
> [1] FALSE # (??)
>> is(data, "dsyMatrix")
> [1] TRUE
>>
>
> Note that R now reports that my loaded object does _not_ inherit from
> "dsyMatrix", yet this occurs only when checked with 'inherits()' --
> 'is' produces the expected result.
>
> I do not see the behavior if I explicitly load / attach the
> 's4inherits' package before loading the associated data file; it only
> occurs if the package namespace is loaded in response to loading the
> data object hosting a 'SubMatrix' object.
>
> More precisely, the package namespace is loaded when the promise
> hosting the data object is evaluated; that promise being generated by
> 'load', if I understand correctly. Somehow, evaluation of that promise
> within the call to 'inherits' in this very special case causes the
> unexpected behavior -- ie, if the first thing that you do with the
> loaded object is check its class with 'inherits', then you get this
> unexpected result.
>
> Even more, this behavior seems to go away if the 's4inherits' package
> explicitly exports the class -- however, you could imagine this class
> normally being internal to the package, and so it may be undesirable
> to export it.
>
> I checked a bit into the C code, and IIUC the check here looks up the
> class hierarchy in the R_S4_extends_table object defined in
> 'attrib.c', so it seems like that mapping is potentially not getting
> constructed with the full hierarchy (although hopefully someone with
> more knowledge of the S4 internals + interaction with S3 can
> elaborate).
>
> (FWIW, this was distilled from a case where S3 dispatch on a similar
> loaded S4 object failed, due to failure to resolve the class hierarchy
> for the S3 dispatch context.)
>
> Thanks,
> Kevin
>
> ---
>
> $ R --slave -e "utils::sessionInfo()"
> R Under development (unstable) (2016-06-13 r70769)
> Platform: x86_64-apple-darwin15.5.0 (64-bit)
> Running under: OS X 10.11.5 (El Capitan)



[Rd] strange behavior in 'inherits' check for loaded S4 object
Kevin Ushey