Hi Elizabeth,
I agree that the setClassUnion() warning is rather esoteric, especially
the "consider setClassUnion()" part.
library(DelayedArray)
setClassUnion("matrixOrHDF5", c("matrix", "DelayedArray"))
# Warning message:
# subclass "DelayedArray1" of class "DelayedArray" is not local and
# cannot be updated for new inheritance information; consider
Furthermore, showClass("DelayedArray") reports the correct inheritance
information:
showClass("DelayedArray1")
# Class "DelayedArray1" [package "DelayedArray"]
#
# Slots:
#
# Name: index delayed_ops seed
# Class: list list ANY
#
# Extends:
# Class "DelayedArray", directly
# Class "DelayedUnaryIsoOp", by class "DelayedArray", distance 2
# Class "matrixOrHDF5", by class "DelayedArray", distance 2
# Class "DelayedUnaryOp", by class "DelayedArray", distance 3
# Class "DelayedOp", by class "DelayedArray", distance 4
# Class "Array", by class "DelayedArray", distance 5
As well as extends():
extends("DelayedArray1")
# [1] "DelayedArray1" "DelayedArray" "DelayedUnaryIsoOp"
# [4] "matrixOrHDF5" "DelayedUnaryOp" "DelayedOp"
# [7] "Array"
extends("DelayedArray", "matrixOrHDF5")
# [1] TRUE
extends("DelayedArray1", "DelayedArray")
# [1] TRUE
extends("DelayedArray1", "matrixOrHDF5")
# [1] TRUE
So it might just be a spurious warning :-/
Anyway, I've exported the DelayedArray1 class in DelayedArray 0.7.48:
https://github.com/Bioconductor/DelayedArray/commit/26061a9b28b87b8a3ee26b8b81ff3334b55115c1
No more warning with this version:
library(DelayedArray)
setClassUnion("matrixOrHDF5", c("matrix", "DelayedArray"))
Cheers,
H.
On 10/10/2018 11:51 AM, Elizabeth Purdom wrote:
Hello,
I am using `setClassUnion` in my package `clusterExperiment` in the following
code to allow for either matrix or DelayedArray:
setClassUnion("matrixOrHDF5",members=c("matrix", "DelayedArray"))
This causes the following warning in checking my package:
Warning: subclass "DelayedArray1" of class "DelayedArray" is not local and
cannot be updated for new inheritance information; consider setClassUnion()
I’ve gotten this warning in other settings, and I believe it is due to the fact
that setClassUnion works on the subclasses of the members, so if you give the
argument `members=c(“X”,”Y”)` and you haven’t imported into your package all of
the subclasses of “X” and “Y” it is warning you those non-imported classes
haven’t been dealt with (though if so, I’d say the warning is awfully cryptic,
especially since it says to use `setClassUnion` as a solution). In my other
cases, I have just gone ahead and imported all of the subclasses from the
package that defines the member classes and have gotten rid of the message (in
the past it hasn’t been so many). But “DelayedArray1” is not an exported class
of the DelayedArray package so that is not an option here.
I have been just ignoring this warning, since I understand (I think) the
warning, I can’t do anything about it, and am not concerned about it since this
new class is only used internally by my function for the slot definition. And I
don’t think the user sees this generally. But given that we’re coming up on a
release I thought I would ask if there’s anything I can do to get rid of this
warning! Or can I go with my first instinct and safely ignore it?
Thanks,
Elizabeth Purdom
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