[Bioc-devel] any interest in a BiocMatrix core package?

[Martin Morgan]

On 11/02/2017 05:00 AM, Martin Maechler wrote:
>>>>>> "ML" == Michael Lawrence <lawrence.michael at gene.com>
>>>>>>      on Wed, 1 Nov 2017 14:13:54 -0700 writes:
> 
>      > Probably way easier to add the generics to the Matrix
>      > package and everyone just depends on that.
> 
> Yes!  It is 'Recommended' and comes with every R installation,
> and has had many such matrix S4 methods in place for > 10 years,
> notably for dealing with (large) sparse matrices.
> 
> Honestly, I (as co-maintainer of Matrix, principal maintainer
> 	     for several years now)
> had been a bit surprised and frustrated that the 'matrixStats'
> initiative had started w/o any contact with the Matrix package
> maintainers and initially has not ever tried to use Matrix
> package classes or functionality
> (and this is still the case now AFAICS).
> 
> I'm happy to coordinate with maintainers of bioc packages about
> which generics (and classes !) to use and export, etc.

One issue is that Matrix is a relatively large package (well, I wonder 
if that's a reasonable statement, given the Bioc dependencies and data 
involved, but perhaps in general...) and hence 'overkill' to obtain a 
collection of generics. Is there any prospect for factoring out the 
definition of the generics from implementation of the methods? 
Re-purposing stats4 ?

Martin Morgan

> 
> Best,
> Martin Maechler
> ETH Zurich (and R core team)
> 
> 
> 
>      > On Wed, Nov 1, 2017 at 1:59 PM, Hervé Pagès
>      > <hpages at fredhutch.org> wrote:
> 
>      >> That's probably a good idea but a clean solution would
>      >> need to involve all players, including the Matrix
>      >> package. Right now there are conflicts for some S4
>      >> generics defined in Matrix and in BiocGenerics
>      >> (e.g. rowSums). I'm not sure that moving rowSums from
>      >> BiocGenerics to a new MatrixGenerics package would
>      >> address this.  Unless MatrixGenerics is on CRAN and
>      >> Matrix depends on it ;-)
>      >>
>      >> How likely is this to happen?
>      >>
>      >> H.
>      >>
>      >>
> [............]
> 
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