On 11/02/2017 05:00 AM, Martin Maechler wrote:
"ML" == Michael Lawrence <lawrence.mich...@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
> <hpa...@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.
>>
>>
[............]
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
This email message may contain legally privileged and/or...{{dropped:2}}
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
