[Rd] as(<dgCMatrix>, "dgTMatrix")' is deprecated.

[Hervé Pagès]

Hi Martin,

On 10/3/23 10:17, Martin Maechler wrote:
>>>>>> Duncan Murdoch
>>>>>>      on Tue, 3 Oct 2023 12:59:10 -0400 writes:
>      > On 03/10/2023 12:50 p.m., Koenker, Roger W wrote:
>      >> I’ve been getting this warning for a while now (about
>      >> five years if memory serves) and I’m finally tired of it,
>      >> but also too tired to track it down in Matrix.  As far as
>      >> I can grep I have no reference to either deprecated
>      >> object, only the apparently innocuous Matrix::Matrix(A,
>      >> sparse = TRUE).  Can someone advise, Martin perhaps?  I
>      >> thought it might come from Rmosek, but mosek folks don’t
>      >> think so.
>      >>https://groups.google.com/g/mosek/c/yEwXmMfHBbg/m/l_mkeM4vAAAJ
>
>      > A quick scan of that discussion didn't turn up anything
>      > relevant, e.g. a script to produce the warning.  Could you
>      > be more specific, or just post the script here?
>
>      > In general, a good way to locate the source of a warning
>      > is to set options(warn=2) to turn it into an error, and
>      > then trigger it.  The traceback from the error will
>      > include a bunch of junk from the code that catches the
>      > warning, but it will also include the context where it was
>      > triggered.
>
>      > Duncan Murdoch
>
> Indeed.
>
> But Roger is right that it in the end, (almost surely) it is
> from our {Matrix} package.
>
> Indeed for several years now, we have tried to make the setup
> leaner (and hence faster) by not explicitly define coercion
> from <everything> to <everything>  because  the size of
> <everything> is here about 200, and we don't want to have to provide
> 200^2 = 40'000  coercion methods.

40,000 coercion methods sounds indeed crazy. But have you considered 
having 200 coercions from ANY to <everything>?

For example the coercion from ANY to dgTMatrix would do as(as(as(from, 
"dMatrix"), "generalMatrix"), "TsparseMatrix").

Maybe the ANY->xyzMatrix methods could even be generated programmatically?

Best,

H.

>
> Rather, Matrix package users should use to high level abstract Matrix
> classes such as "sparseMatrix" or "CsparseMatrix" or
> "TsparseMatrix" or "dMatrix", "symmetricMatrix".
>
> In the case of  as(<dgCMatrix>, "dgTMatrix") , if you
> replace "dgTMatrix" by "TsparseMatrix"
> the result will be the same but also work in the future when the
> deprecation may have been turned into a defunctation ...
>
> Martin
>
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-- 
Hervé Pagès

Bioconductor Core Team
hpages.on.github using gmail.com

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