R devel - Jan 2021 - Unexpected behavior with inheritance and using S3 classes as slots in S4 class

Hi all,

I have a situation where I'm trying to use S3 classes as slots in an S4
class and am running into some problems with inheritance.

My example:
## with S3 classes
a <- function(x) structure(x, class = "a")
b <- function(x) structure(x, class = c("b", "a"))
setOldClass(c("a", "b"))

a_1 <- a("hello")
b_1 <- b("world")
n <- setClass("n", slots = c(s1 = "a"))
n(s1 = a_1) # works as expected
is(b_1, "a") # yields TRUE
n(s1 = b_1) # doesn't work-- unexpected

Error message is:
Error in validObject(.Object) :
invalid class ?n? object: invalid object for slot "s1" in class
"n": got class "b", should be or extend class "a"

Digging in, validObject looks like it's calling getClassDef, which gives
me
> getClassDef("b")
Virtual Class "b" [in ".GlobalEnv"]

Slots:

Name: .S3Class
Class: character

Extends: "oldClass"

-- it extends "oldClass" but it doesn't extend class "a"
despite the fact the S3 version does.

Now, In this simple example, I could have defined a and b as s4 classes, but in
the real world, I didn't define them and have to use setOldClass.
I'm currently getting around this issue by doing
setClassUnion("ab", c("a", "b")) and then specify
to use "ab" as the type for the slot, but since I already know b
inherits from a, this ought not to be necessary (and there are other reasons
this is undesirable).

1. Is there anything I missed, in setting up this simple example, that would
cause n(s1 = b_1) to work properly? Or is there anything I should do other than
setClassUnion?
2. Is this a shortcoming of validObject or getClassDef?

Thank you all!
-Ezra
	[[alternative HTML version deleted]]

Ezra,

I think it's just the fact the you specified the wrong class inheritance in
setOldClass() - it has to match you S3 definition, so it should be:

setOldClass(c("b","a"))

In which case it works:
> n(s1 = b_1)
An object of class "n"
Slot "s1":
[1] "world"
attr(,"class")
[1] "b" "a"

Cheers,
Simon


> On Jan 28, 2021, at 15:55, Ezra Tucker <ezra at landtucker.com>
wrote:
> 
> Hi all,
> 
> I have a situation where I'm trying to use S3 classes as slots in an S4
class and am running into some problems with inheritance.
> 
> My example:
> ## with S3 classes
> a <- function(x) structure(x, class = "a")
> b <- function(x) structure(x, class = c("b", "a"))
> setOldClass(c("a", "b"))
> 
> a_1 <- a("hello")
> b_1 <- b("world")
> n <- setClass("n", slots = c(s1 = "a"))
> n(s1 = a_1) # works as expected
> is(b_1, "a") # yields TRUE
> n(s1 = b_1) # doesn't work-- unexpected
> 
> Error message is:
> Error in validObject(.Object) :
> invalid class ?n? object: invalid object for slot "s1" in class
"n": got class "b", should be or extend class "a"
> 
> Digging in, validObject looks like it's calling getClassDef, which
gives me
>> getClassDef("b")
> Virtual Class "b" [in ".GlobalEnv"]
> 
> Slots:
> 
> Name: .S3Class
> Class: character
> 
> Extends: "oldClass"
> 
> -- it extends "oldClass" but it doesn't extend class
"a" despite the fact the S3 version does.
> 
> Now, In this simple example, I could have defined a and b as s4 classes,
but in the real world, I didn't define them and have to use setOldClass.
> I'm currently getting around this issue by doing
setClassUnion("ab", c("a", "b")) and then specify
to use "ab" as the type for the slot, but since I already know b
inherits from a, this ought not to be necessary (and there are other reasons
this is undesirable).
> 
> 1. Is there anything I missed, in setting up this simple example, that
would cause n(s1 = b_1) to work properly? Or is there anything I should do other
than setClassUnion?
> 2. Is this a shortcoming of validObject or getClassDef?
> 
> Thank you all!
> -Ezra
> 	[[alternative HTML version deleted]]
> 
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