Re: [Rd] R 4.4.0 has version of Matrix 1.7-0, but it's not available on CRAN
Everyone, take a deep breath - there have been many disruptions in last few
days - some obvious, others associated with the R release and the BioC
disruptions on CRAN, so there is no need to panic and start devising
"solutions" for issues that are temporary. Things are being sorted out and some
may take longer than others to settle. Feel free to report, but please don't
speculate or try to "help". That said, you may find that this thread is
obsolete by now (thanks to Kurt!), so no need to respond.
Cheers,
Simon
> On Apr 26, 2024, at 11:15 PM, Gábor Csárdi wrote:
>
> On Fri, Apr 26, 2024 at 1:06 PM Ivan Krylov wrote:
>>
>> On Fri, 26 Apr 2024 12:32:59 +0200
>> Martin Maechler wrote:
>>
>>> Finally, I'd think it definitely would be nice for
>>> install.packages("Matrix") to automatically get the correct
>>> Matrix version from CRAN ... so we (R-core) would be grateful
>>> for a patch to install.packages() to achieve this
>>
>> Since the binaries offered on CRAN are already of the correct version
>> (1.7-0 for -release and -devel), only source package installation needs
>> to concern itself with the Recommended subdirectory.
>>
>> Would it be possible to generate the PACKAGES* index files in the
>> 4.4.0/Recommended subdirectory? Then on the R side it would be needed
>> to add a new repo (adjusting chooseCRANmirror() to set it together with
>> repos["CRAN"]) and keep the rest of the machinery intact.
>
> That's not how this worked in the past AFAIR. Simply, the packages in
> the x.y.z/Recommended directories were included in
> src/contrib/PACKAGES*, metadata, with the correct R version
> dependencies, in the correct order, so that `install.packages()`
> automatically installed the correct version without having to add
> extra repositories or manually search for package files.
> E.g. right now we have
>
> Package: Matrix
> Version: 1.7-0
> Priority: recommended
> Depends: R (>= 4.5), methods
> Path: 4.5.0/Recommended
>
> for R 4.5.0. IMHO what we would need for R 4.4.0 is adding
> something like
>
> Package: Matrix
> Version: 1.7-0
> Priority: recommended
> Depends: R (>= 4.4), methods
> Path: 4.4.0/Recommended
>
> *after* that.
>
> G.
>
> [...]
>
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Re: [Rd] R 4.4.0 has version of Matrix 1.7-0, but it's not available on CRAN
On Fri, 26 Apr 2024 13:15:47 +0200 Gábor Csárdi wrote: > That's not how this worked in the past AFAIR. Simply, the packages in > the x.y.z/Recommended directories were included in > src/contrib/PACKAGES*, metadata, with the correct R version > dependencies, in the correct order, so that `install.packages()` > automatically installed the correct version without having to add > extra repositories or manually search for package files. That's great, then there is no need to patch anything. Thanks for letting me know. Should we be asking c...@r-project.org to add 4.4.0/Recommended to the index, then? -- Best regards, Ivan __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R 4.4.0 has version of Matrix 1.7-0, but it's not available on CRAN
On Fri, Apr 26, 2024 at 1:06 PM Ivan Krylov wrote:
>
> On Fri, 26 Apr 2024 12:32:59 +0200
> Martin Maechler wrote:
>
> > Finally, I'd think it definitely would be nice for
> > install.packages("Matrix") to automatically get the correct
> > Matrix version from CRAN ... so we (R-core) would be grateful
> > for a patch to install.packages() to achieve this
>
> Since the binaries offered on CRAN are already of the correct version
> (1.7-0 for -release and -devel), only source package installation needs
> to concern itself with the Recommended subdirectory.
>
> Would it be possible to generate the PACKAGES* index files in the
> 4.4.0/Recommended subdirectory? Then on the R side it would be needed
> to add a new repo (adjusting chooseCRANmirror() to set it together with
> repos["CRAN"]) and keep the rest of the machinery intact.
That's not how this worked in the past AFAIR. Simply, the packages in
the x.y.z/Recommended directories were included in
src/contrib/PACKAGES*, metadata, with the correct R version
dependencies, in the correct order, so that `install.packages()`
automatically installed the correct version without having to add
extra repositories or manually search for package files.
E.g. right now we have
Package: Matrix
Version: 1.7-0
Priority: recommended
Depends: R (>= 4.5), methods
Path: 4.5.0/Recommended
for R 4.5.0. IMHO what we would need for R 4.4.0 is adding
something like
Package: Matrix
Version: 1.7-0
Priority: recommended
Depends: R (>= 4.4), methods
Path: 4.4.0/Recommended
*after* that.
G.
[...]
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Re: [Rd] R 4.4.0 has version of Matrix 1.7-0, but it's not available on CRAN
On Fri, 26 Apr 2024 12:32:59 +0200
Martin Maechler wrote:
> Finally, I'd think it definitely would be nice for
> install.packages("Matrix") to automatically get the correct
> Matrix version from CRAN ... so we (R-core) would be grateful
> for a patch to install.packages() to achieve this
Since the binaries offered on CRAN are already of the correct version
(1.7-0 for -release and -devel), only source package installation needs
to concern itself with the Recommended subdirectory.
Would it be possible to generate the PACKAGES* index files in the
4.4.0/Recommended subdirectory? Then on the R side it would be needed
to add a new repo (adjusting chooseCRANmirror() to set it together with
repos["CRAN"]) and keep the rest of the machinery intact.
--
Best regards,
Ivan
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Re: [Rd] R 4.4.0 has version of Matrix 1.7-0, but it's not available on CRAN
On Fri, 26 Apr 2024, at 11:32 AM, Martin Maechler wrote: >> Gábor Csárdi >> on Fri, 26 Apr 2024 11:55:36 +0200 writes: > > > I don't know if this is a bug, but it is certainly weird. AFAICT R > > 4.4.0 has Matrix 1.7-0. > > Yes, it *is* available from CRAN: You can see it when looking into the > > 4.4.0/ , specifically the > 4.4.0/Recommended/ sub directory. > > Recommended packages should be built as part of R > unless *you* really want to *not* get them by choosing at > configure time, not to get them via extra flag > --without-recommended-packages. > > So, well, you got what you wanted. > > > However, currently CRAN has > > > Package: Matrix > > Version: 1.6-5 > > Priority: recommended > > Depends: R (>= 3.5.0), methods > > ... > . > Yes, because it has to provide Matrix to R versions before 4.4.0 > and Matrix 1.7-0 has 'Depends: R (>= 4.4.0)' > > > (plus another version for R >= 4.5.0 only). > > > Which has some weird consequences, e.g. if I have an R 4.4.0 > > installation without the recommended packages, > > (why would you explicitly choose *not* to have the > recommended packages when they *are* recommended .. :-b ) > ... Hi Martin. I appreciate the efforts you are going to balance these Matrix updates across CRAN versions. Related, but a little tangential, to the installation situation, I'd still expect the canonical CRAN link (https://cran.r-project.org/package=Matrix) to provide links to the *current* version. Currently links to a source tarball and the reference manual is for 1.6.5 (I'm guessing vignettes are also from 1.6.5.). Best Tim __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R 4.4.0 has version of Matrix 1.7-0, but it's not available on CRAN
> Gábor Csárdi
> on Fri, 26 Apr 2024 11:55:36 +0200 writes:
> I don't know if this is a bug, but it is certainly weird. AFAICT R
> 4.4.0 has Matrix 1.7-0.
Yes, it *is* available from CRAN: You can see it when looking into the
4.4.0/ , specifically the
4.4.0/Recommended/ sub directory.
Recommended packages should be built as part of R
unless *you* really want to *not* get them by choosing at
configure time, not to get them via extra flag
--without-recommended-packages.
So, well, you got what you wanted.
> However, currently CRAN has
> Package: Matrix
> Version: 1.6-5
> Priority: recommended
> Depends: R (>= 3.5.0), methods
> ...
Yes, because it has to provide Matrix to R versions before 4.4.0
and Matrix 1.7-0 has 'Depends: R (>= 4.4.0)'
> (plus another version for R >= 4.5.0 only).
> Which has some weird consequences, e.g. if I have an R 4.4.0
> installation without the recommended packages,
(why would you explicitly choose *not* to have the
recommended packages when they *are* recommended .. :-b )
> I don't have a way of installing Matrix 1.7-0.
That's not true (see above), but it maybe true that
install.packages() does not work directly -- I guess you
should get it to work with correct function arguments;
if not, you'd definitely have found a missing feature...
.. *and* Rstudio button clicking works even less, because it does
not allow to specify the install.packages() call.
.. and yes, ideally install.packages() would be smart enough to
figure that Matrix is recommended *and* that it should therefore
try the same location ( ./4.4.0/Recommended/ in this case) as
R's own tools/rsync-recommended script does.
Finally, I'd think it definitely would be nice for
install.packages("Matrix") to automatically get the correct
Matrix version from CRAN ... so we (R-core) would be grateful
for a patch to install.packages() to achieve this (unless that
patch is too large or too much involved for reliable
maintenance).
Martin
> Whereas R 4.4.0 installations with
> recommended packages come with Matrix 1.7-0.
> Gabor
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