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

Martin Maechler maechler at stat.math.ethz.ch
Thu Nov 2 10:00:09 CET 2017

>>>>> "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.

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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