Hi Michael,
Did you get a chance to make this change?
Thanks,
H.
On 2/11/19 08:07, Michael Lawrence wrote:
> I propose that we just fix the signatures in the methods package and
> deal with the consequences. If Martin's OK with that, I'll make the
> change.
>
> Michael
>
> On Mon, Feb 11, 2019 at 7:45 AM McDavid, Andrew
> <andrew_mcda...@urmc.rochester.edu> wrote:
>> As a casual observer of this thread, my takeaway is that 1. the current
>> situation is untenable (e.g. it means that Aaron would have to essentially
>> reimplement S4 method dispatch) 2. Given the long history, and extent of
>> reverse dependencies to Matrix, there are good reasons to not mess with the
>> signature of its implicit generic (though I don't see much utility in
>> multiple dispatch here) and 3. therefore the least-bad alternative may be
>> to eliminate the call to setGeneric('colSums'), etc, in BiocGenerics,
>> hopefully with some fixes to the help system to make it more tolerant to S4
>> method naming. I appreciate that until these fixes are forthcoming it means
>> more work maintaining the help aliases for some methods. How often do we
>> think the aliases would be break?
>>
>> Andrew McDavid
>> Biostatistics and Computational Biology
>> Office: SRB 4.206 Ph: 585.275.5983
>>
>> Message: 1
>> Date: Sun, 10 Feb 2019 13:36:43 +0000
>> From: Aaron Lun
>> <infinite.monkeys.with.keyboa...@gmail.com<mailto:infinite.monkeys.with.keyboa...@gmail.com>>
>> To: "Pages, Herve" <hpa...@fredhutch.org<mailto:hpa...@fredhutch.org>>,
>> Martin Maechler
>> <maech...@stat.math.ethz.ch<mailto:maech...@stat.math.ethz.ch>>
>> Cc: Michael Lawrence
>> <lawrence.mich...@gene.com<mailto:lawrence.mich...@gene.com>>,
>> "bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>"
>> <bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>>
>> Subject: Re: [Bioc-devel] Pushing towards a better home for matrix
>> generics
>> Message-ID:
>> <1549805803.3935.11.ca...@gmail.com<mailto:1549805803.3935.11.ca...@gmail.com>>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Returning to this topic:
>>
>> It's good to hear some of the rationale behind the current state of
>> affairs. That said, the set-up we have now is quite difficult to work
>> with; as mentioned before, I've had to hack around it like:
>>
>> # Example from "BiocSingular",
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_LTLA_BiocSingular&d=DwIGaQ&c=4sF48jRmVAe_CH-k9mXYXEGfSnM3bY53YSKuLUQRxhA&r=YOujD4cGNGWN0ZskTj96dUHU2a4CkraklBd4BndS21sf3_emyYLIG1llnUarWCda&m=VBZgu2tHS9vBNQ2d8RSG4ijIcp3jyZkfCsRnA1mk7XI&s=FN4WdWx8gfnjFoLRQuBaIHaKrAjONVa9hsbAyIXSwGo&e=
>> .safe_colSums <- function(x) {
>> if (is(x, "Matrix")) {
>> Matrix::colSums(x)
>> } else {
>> colSums(x)
>> }
>> }
>>
>> ... which is ugly, and even worse, still incorrect, e.g., for non-
>> Matrix classes that have methods for the implicit colSums generic. This
>> situation is not sustainable for further package development.
>>
>> Is there a path forward that is palatable to everyone? Or perhaps these
>> conversations are already happening on R-devel?
>>
>> -A
>>
>> On Tue, 2019-01-29 at 18:46 +0000, Pages, Herve wrote:
>> Yes the help system could enforce the full signature for the aliases
>> but
>> that means the end user then will have to always do
>> ?`colSums,SomeClass,ANY,ANY-method`, which feels unnecessary
>> complicated
>> and confusing in the case of a generic where dispatching on the 2nd
>> and
>> 3rd arguments hardly makes sense.
>>
>> Or are you saying that the help system should enforce an alias that
>> strictly matches the signature explicitly used in the setMethod
>> statement? Problem with this is that then there is no easy way for
>> the
>> end user to know a priori which form to use to access the man page.
>> Is
>> it ?`colSums,dgCMatrix,ANY,ANY-method` or is it
>> ?`colSums,dgCMatrix-method`. Right now when you type colSums<ENTERN>
>> (after loading the Matrix package), you get this:
>>
>> > library(Matrix)
>> > colSums
>> standardGeneric for "colSums" defined from package "base"
>>
>> function (x, na.rm = FALSE, dims = 1, ...)
>> standardGeneric("colSums")
>> <bytecode:0x591c7d0>
>> <environment:0x591a408>
>> Methods may be defined for arguments: x, na.rm, dims
>> Use showMethods("colSums") for currently available ones.
>>
>> This suggests that the correct form is ?`colSums,dgCMatrix,ANY,ANY-
>> method`.
>>
>> All this confusion can be avoided by specifying signature="x" in the
>> definition of the implicit generic. It formalizes where dispatch
>> really
>> happens and sets expectations upfront. No loose ends.
>>
>> Hope this makes sense,
>>
>> H.
>>
>>
>> [[alternative HTML version deleted]]
>>
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--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
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