Re: [Rd] as(, "dgTMatrix")' is deprecated.
Thanks, Ivan, I should have had the initiative to do this myself. I’ve now
written to the Mosek folks in the hope that they will update this in Rmosek.
Best
Roger
> On Oct 3, 2023, at 8:47 PM, Ivan Krylov wrote:
>
> On Tue, 3 Oct 2023 16:50:55 +
> "Koenker, Roger W" wrote:
>
>> I thought it might come from Rmosek, but mosek folks don’t think so.
>
> I downloaded the Rmosek source package using
>
> download.packages(
> 'Rmosek', '.',
> repos='https://urldefense.com/v3/__https://download.mosek.com/R/10.1__;!!DZ3fjg!-J68cgVdf_vRXm7yhSxSNzoDv6i6681nySXG9qhE808C3UTKTWGNCfZEWchGfsh2FZbBpQJuWa8Tr8_mo3f2xFo$
> '
> )
>
> ...and there are the deprecated calls:
>
>
> Rmosek/R$ grep -C2 -r as\(.*dgT
> toCSCMatrix.R- }
> toCSCMatrix.R- else if (is(obj,"dgCMatrix")) {
> toCSCMatrix.R:obj <- as(obj,"dgTMatrix")
> toCSCMatrix.R- }
> toCSCMatrix.R- else if (is(obj,"list") &&
> setequal(names(obj),c("i","j","v","ncol","nrow"))) {
> --
> toCSCMatrix.R- x=obj[['v']],
> toCSCMatrix.R- dims=c(obj[['nrow']], obj[['ncol']]) )
> toCSCMatrix.R:obj <- as(tmp, "dgTMatrix")
> toCSCMatrix.R- }
> toCSCMatrix.R- else if (canCoerce(obj,"dgTMatrix")) {
> toCSCMatrix.R-# Assume coercion is meaningful, and that
> toCSCMatrix.R-# users are aware of computational overhead.
> toCSCMatrix.R:obj <- as(obj,"dgTMatrix")
> toCSCMatrix.R- }
> toCSCMatrix.R- else {
>
>
> --
> Best regards,
> Ivan
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Re: [Rd] as(, "dgTMatrix")' is deprecated.
> 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 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 to because the size of
> > 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(, "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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Re: [Rd] as(, "dgTMatrix")' is deprecated.
thanks, good to know, although at my age this is the sort of knowledge that has
a very short half-life. ;-)
R
> On Oct 4, 2023, at 9:57 AM, Mikael Jagan wrote:
>
> > 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 > > 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 to because the size of
> > > 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(, "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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Re: [Rd] as(, "dgTMatrix")' is deprecated.
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 to because the size of
> 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 ?
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(, "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.git...@gmail.com
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Re: [Rd] [R-pkg-devel] Problem with "compacting" pdf files.
> Ivan Krylov writes:
Thanks: committed now.
Best
-k
> Dear Rolf,
> (Moving this one to R-devel...)
> On Sun, 1 Oct 2023 21:01:13 +
> Rolf Turner wrote:
>> I *really* think that the instructions from CRAN could have been
>> clearer! Without your guidance I'd have been at a total loss.
> Since the CRAN e-mails quote the R CMD check messages verbatim, would
> it have been enough if R CMD check suggested using --compact-vignettes?
> Index: src/library/tools/R/check.R
> ===
> --- src/library/tools/R/check.R (revision 85249)
> +++ src/library/tools/R/check.R (working copy)
> @@ -3079,7 +3079,8 @@
> " 'qpdf' made some significant size reductions:\n",
> paste(" ", res, collapse = "\n"),
> "\n",
> - " consider running tools::compactPDF() on these
> files\n")
> + " consider running tools::compactPDF() on these
> files,\n",
> + " or build the source package with
> --compact-vignettes\n")
> }
> if (R_check_doc_sizes2) {
> gs_cmd <- find_gs_cmd()
> @@ -3093,7 +3094,8 @@
> " 'gs+qpdf' made some significant size
> reductions:\n",
> paste(" ", res, collapse = "\n"),
> "\n",
> - ' consider running
> tools::compactPDF(gs_quality = "ebook") on these files\n')
> + ' consider running
> tools::compactPDF(gs_quality = "ebook") on these files,\n',
> + ' or build the source package with
> --compact-vignettes=both\n')
> }
> } else {
> if (!any) noteLog(Log)
> Or is there anything else you would prefer to be reworded? Should the
> message link to Writing R Extensions, section 1.4? Recently there was a
> project to improve the R CMD check messages [*], but I managed to miss
> almost all of it.
> --
> Best regards,
> Ivan
> [*] https://github.com/r-devel/r-project-sprint-2023/issues/55
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