Thanks so much Hervé! That appears to have solved the problem. And I will
definitely keep in mind for the future Michael’s suggestion of duck typing for
matrix-like objects.
All of the best,
Elizabeth
> On Oct 10, 2018, at 9:33 PM, Hervé Pagès <hpa...@fredhutch.org> wrote:
>
> 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
>> _______________________________________________
>> Bioc-devel@r-project.org mailing list
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=4le20lkIbxVE8gFC4uH_tCGjq9qX1garrTomLOEFN6A&s=VePKILIDYgQk9KdF7u7hJQJLglF5ga8I6M5u99inEyo&e=
>
> --
> Hervé Pagès
>
> 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: hpa...@fredhutch.org
> Phone: (206) 667-5791
> Fax: (206) 667-1319
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