[Bioc-devel] Pushing towards a better home for matrix generics

Thu Mar 28 17:57:24 CET 2019

Not yet. Too busy breaking other things ;) I'll move it up on my TODO list.

On Thu, Mar 28, 2019 at 9:16 AM Pages, Herve <hpages using fredhutch.org> wrote:

> 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_Mcdavid using 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.keyboards using gmail.com<mailto:
> infinite.monkeys.with.keyboards using gmail.com>>
> >> To: "Pages, Herve" <hpages using fredhutch.org<mailto:hpages using fredhutch.org>>,
> Martin Maechler
> >> <maechler using stat.math.ethz.ch<mailto:maechler using stat.math.ethz.ch>>
> >> Cc: Michael Lawrence <lawrence.michael using gene.com<mailto:
> lawrence.michael using gene.com>>,
> >> "bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>" <
> bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>>
> >> Subject: Re: [Bioc-devel] Pushing towards a better home for matrix
> >> generics
> >> Message-ID: <1549805803.3935.11.camel using gmail.com<mailto:
> 1549805803.3935.11.camel using 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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> >>
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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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> Seattle, WA 98109-1024
>
> E-mail: hpages using fredhutch.org
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>
>

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