Reduce R to a dummy package, upgrade rpy2 to 3.4.5

[mkoeppe]

We reduce the unmaintained r package (stuck at 3.6.3) so that we detect a system installation of R (>= 3.5) but do not attempt to install it ourselves.

When R is found as a system package, rpy2 will be built; otherwise it won't.

rpy2 3.5.x only supports R >= 4.0 according to
https://rpy2.github.io/doc/v3.5.x/html/overview.html#requirements

Here we upgrade rpy2 to 3.4.5, the latest that still supports R >= 3.5 according to https://rpy2.github.io/doc/v3.4.x/html/overview.html#requirements

Support for R < 3.5 was already dropped in the rpy 3.3.x series (our current version of rpy2 is 3.3.6).

According to https://repology.org/project/r/versions, we will thus drop support for R on the ancient platforms:

• ubuntu-trusty (R 3.0.2; past End of Standard Support; EOL April 2024]),
• ubuntu-xenial (R 3.2.3; past End of Standard Support; EOL April 2026),
• ubuntu-bionic (R 3.4.4; End of Standard Support: April 2023)
• debian-stretch (R 3.3.3; past EOL)
• fedora-26 (R 3.4.4; past EOL),
  as well as on Cygwin. (See Meta-ticket: Remove support for outdated distros #32074)

Depends on #34193

CC: @EmmanuelCharpentier @videlec @dimpase @isuruf @jhpalmieri @novoselt @williamstein

Component: packages: standard

Author: Matthias Koeppe

Branch/Commit: a50460e

Reviewer: John Palmieri

Issue created by migration from https://trac.sagemath.org/ticket/34268

[dimpase]

comment:1

good idea

[mkoeppe]

Branch: u/mkoeppe/reduce_r_to_a_dummy_package__upgrade_rpy2

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. New commits:

cbcff37

build/pkgs/rpy2: Mark as not required when there is no R

[sagetrac-git]

Commit: cbcff37

[sagetrac-git]

Changed commit from cbcff37 to 004bac5

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. New commits:

004bac5

build/pkgs/r: Restore spkg-legacy-uninstall as spkg-uninstall script

[mkoeppe]

Dependencies: #34193

[sagetrac-git]

Changed commit from 004bac5 to 77a2474

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. Last 10 new commits:

1b61561	m4/sage_spkg_collect.m4: Display installed package version
215fbbc	m4/sage_spkg_collect.m4: Omit 'version none' in messages
8273456	m4/sage_spkg_collect.m4: Show installed versions / upgrade information
9574e8c	m4/sage_spkg_collect.m4: Handle multiple installation records better
b1a4aac	build/make/Makefile.in: For script packages, remove old installation records
515a785	m4/sage_spkg_collect.m4: Update comment regarding multiple installation records of script packages
46a0870	m4/sage_spkg_collect.m4: Actually find installation records in SAGE_VENV when that is set implicitly
7bda1cb	m4/sage_spkg_collect.m4: Restore uninstall message
551b2a2	Merge #34193
77a2474	build/make/Makefile.in: When uninstalling script packages, remove all versions of stamp files

[sagetrac-git]

Changed commit from 77a2474 to 5e3e4be

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. New commits:

7069512	build/pkgs/rpy2: Update to 3.5.3
5e3e4be	build/pkgs/r/spkg-configure.m4: Remove depcheck

[sagetrac-git]

Changed commit from 5e3e4be to 9887c7e

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. New commits:

54c0b55	build/pkgs/rpy2/patches/716.patch: Remove (upstreamed)
9887c7e	build/pkgs/rpy2/patches/setup-no-pytest.patch: Remove, obsolete

[mkoeppe]

Author: Matthias Koeppe

[sagetrac-git]

Changed commit from 9887c7e to e54b60c

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. New commits:

e54b60c

build/pkgs/r/spkg-configure.m4: Bump required r version for rpy2

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. New commits:

83a751a

build/pkgs/rpy2: Downgrade to 3.4.5

[sagetrac-git]

Changed commit from e54b60c to 83a751a

[jhpalmieri]

comment:46

Right, and of course it doesn't matter whether rpy2 has been built, the same message appears, because this branch installs version 3.4.5 of rpy2, and that does not satisfy rpy2<3.4,>=3.3.

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. New commits:

7ab9370

build/pkgs/rpy2/install-requires.txt: Remove upper version bound

[sagetrac-git]

Changed commit from 83a751a to 7ab9370

[jhpalmieri]

comment:48

./configure says

    notice: the following SPKGs did not find equivalent system packages:

        rpy2   4ti2 _recommended cbc coxeter3 ffmpeg gp2c igraph libsemigroups lrslib pandoc pdf2svg perl_mongodb perl_term_readline_gnu polymake

Do you know why there seems to be extra space after rpy2?

[jhpalmieri]

comment:49

With ./configure --with-system-r=no, rpy2 is not built and I see lots of warnings in docbuilding:

pkg_resources.DistributionNotFound: The 'rpy2>=3.3' distribution was not found and is required by sagemath-standard

The scipy log file says

sagemath-standard 9.7b8 requires networkx<3.0,>=2.4, which is not installed.
sagemath-standard 9.7b8 requires rpy2>=3.3, which is not installed.

(networkx-2.8.4 had not yet finished installing at this point.)

[mkoeppe]

comment:50

Replying to @jhpalmieri:

./configure says

    notice: the following SPKGs did not find equivalent system packages:

        rpy2   4ti2 _recommended cbc coxeter3 ffmpeg gp2c igraph libsemigroups lrslib pandoc pdf2svg perl_mongodb perl_term_readline_gnu polymake

Do you know why there seems to be extra space after rpy2?

I think I put this space there to separate standard packages from optional packages

[sagetrac-git]

Changed commit from 7ab9370 to 5d66432

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. New commits:

5d66432

src/setup.cfg.m4: Move rpy2 from install-requires to extras-require

[jhpalmieri]

comment:52

Looks okay to me. Passes tests with and without using the system installation of R.

[jhpalmieri]

Reviewer: John Palmieri

[mkoeppe]

comment:53

Thank you!

[jhpalmieri]

comment:54

Replying to @mkoeppe:

Replying to @jhpalmieri:

Since the downloading timeouts can take a while, is there any way to tell Sage to skip the standard mirrors and just jump straight to the option given by --enable-download-from-upstream-url?)

You can edit the file upstream/mirror_list to remove most mirrors

Would it be useful to be able to add $UPSTREAM (or something like that) to the mirror list, which would have the effect of turning on --enable-download-from-upstream-url?

[mkoeppe]

comment:55

I think it would make sense to limit the number of mirrors it tries to some small number (5?) before it tries the upstream.

[mkoeppe]

comment:56

I've opened #34411 for this

[mkoeppe]

comment:57

Also see #32390

[mkoeppe]

Changed dependencies from #34193, #32074 to #34193

[vbraun]

comment:59

Merge failure on top of:

024b81f Trac #33812: Refactor distributions sagemath-{objects,categories} through sagemath-{environment,repl}

e4d3004 Trac #33805: use Homebrew's primecount

5076cd5 Trac #34110: numpy 1.23.x

025fdd4 Trac #34532: modernize super in manifolds/

f9129b1 Trac #34531: some details in LS paths crystals

7f7088d Trac #34529: remove deprecated method spring_layout_fast_split from src/sage/graphs/generic_graph_pyx.pyx

12890b6 Trac #34520: Remove randomly failing doctest in src/sage/graphs/generators/random.py

c8511ab Trac #34512: compute list CRT via tree

3f4e544 Trac #34508: Improve documentation of JoinFeature

cb5e1af Trac #34493: Make TrivialFamily.map return a TrivialFamily

c036ccc Trac #34486: VectorFieldModule: Faster fast path for tensor_module, exterior_power, dual_exterior_power

89b4155 Trac #34469: modern super in matrix_space

4f3a9b0 Trac #34468: fix W605 in all pyx files inside matroids/

bfa6342 Trac #34465: Invalid escape sequence in special.py

cd65d44 Trac #34462: Uniformize the headline: finite rings

7736a49 Trac #34435: Add method to trim trailing zeros from IntegerVector

154baa5 Trac #34432: Upgrade: jupyter-packaging 0.12.3

bfc2ccf Trac #34409: remove experimental warning for composite elliptic-curve isogenies

89b0d28 Trac #34375: Replace sage.algebras.yangian.GeneratorIndexingSet with cartesian_product

ce82f81 Trac #34358: pycodestyle cleanup in src/sage/graphs/generic_graph.py (part 4)

c8c541f Trac #34578: standard error messages in pbori

721c4c1 Trac #34573: Remove binary_function from ginac's code in sage

5fc16f5 Trac #34571: fix typo in docstring

b836c6c Trac #34562: refactor multiple zeta values

1366a0d Trac #34528: Installation guide: Improve section on prerequisites/recommendations

ad97e1b Trac #34413: implement derivatives of lazy series

a802d07 Trac #31664: Add package msolve 0.4.4 (multivariate polynomial system solver)

4541564 Updated SageMath version to 9.8.beta0

merge was not clean: conflicts in build/make/Makefile.in

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. New commits:

091e0af	Merge tag '9.8.beta0' into t/34268/reduce_r_to_a_dummy_package__upgrade_rpy2
a50460e	Merge tag '9.8.beta1' into t/34268/reduce_r_to_a_dummy_package__upgrade_rpy2

[sagetrac-git]

Changed commit from 5d66432 to a50460e

[vbraun]

Changed branch from u/mkoeppe/reduce_r_to_a_dummy_package__upgrade_rpy2 to a50460e