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

[Mikael Jagan]

 > There is a call to mosek and I assumed that this wasn’t going to be helpful 
for most R-devel recipients.  I tried Duncan’s very reasonable suggestion about 
options() but it didn’t produce the desired error, so perhaps this isn’t really 
a warning  but something else???
 >

The details are described in news(package="Matrix") under "Changes in version
1.5-0" and implemented in Matrix:::Matrix.DeprecatedCoerce.  That version was
released in Sep 2022.

At the time, it was too disruptive to signal a proper deprecation warning
with every as(., "d(g.|.C)Matrix") call, for every reverse dependency of
Matrix, so we decided that in those most common cases we would use message()
instead of warning().   A corollary was that options(warn=n) would not have
the usual effect, so we advertised an alternative to affected maintainers:

     in R:

         options(Matrix.warnDeprecatedCoerce=n)

     on the command line:

         R_MATRIX_WARN_DEPRECATED_COERCE=n R CMD check *.tar.gz

But maybe it is time to begin signaling warnings unconditionally ...

Mikael

 > For those who might have rmosek installed,  I’m doing:
 >
 > library(REBayes)
 > demo(GLmix1)
 >
 > Thanks,
 > Roger
 >
 >
 > > On Oct 3, 2023, at 6:17 PM, Martin Maechler <maechler using 
stat.math.ethz.ch> 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://urldefense.com/v3/__https://groups.google.com/g/mosek/c/yEwXmMfHBbg/m/l_mkeM4vAAAJ__;!!DZ3fjg!71re8ipw9fFStkMab0wGuPNSzSaAhPI5vwxd1BCQ7a55mYiRpAq2prn9-wREqKL_G2uBYboXISQfxZYCZ9AFxCnwxdzqTw$ 

 > >
 > >> 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.
 > >
 > > 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