[ci] [python-package] [R-package] adapt to scikit-learn check_sample_weight_equivalence changes, stop testing against R 3.6 on Linux

[jameslamb]

More changes to estimator checks have been made in scikit-learn, and those broke CI here.

CI is failing like this when using the latest scikit-learn nightlies:

=========================== short test summary info ============================
FAILED tests/python_package_test/test_sklearn.py::test_sklearn_integration[LGBMClassifier()-check_sample_weight_equivalence_on_dense_data]
FAILED tests/python_package_test/test_sklearn.py::test_sklearn_integration[LGBMClassifier()-check_sample_weight_equivalence_on_sparse_data]
===== 2 failed, 767 passed, 40 skipped, 2 xfailed, 584 warnings in 36.86s ======

(build link)

Looks like scikit-learn/scikit-learn#30137 removed check_sample_weight_equivalence, in favor of 2 new functions names check_sample_weight_equivalence_on_{dense,sparse}_data. This updates lightgbm's xfail_checks tag to include all 3 names, so those tests are correctly xfail'd for the full range of scikit-learn versions lightgbm supports.

update: this also removes the R 3.6 Linux CI job to fix another blocking CI issue, see #6733 (comment)

[jameslamb]

Noticing that the R 3.6 CI job has been failing for a couple days like this:

Post job cleanup.
/usr/bin/docker exec 0f363447ec94ed26e9ae21b628f3850fe9f1e15a4c8a341b96fcdc540018e374 sh -c "cat /etc/*release | grep ^ID"
/__e/node20/bin/node: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.28' not found (required by /__e/node20/bin/node)

(build link)

That's happening here:

LightGBM/.github/workflows/r_package.yml

Lines 176 to 180 in 83c0ff3

	- name: Checkout repository
	uses: actions/checkout@v3
	with:
	fetch-depth: 5
	submodules: true

Will have to fix that in this PR too. I'll try that.

Related prior conversations:

• checkout@v4 is not working in containers actions/checkout#1487
• [R-package] [ci] newer versions of actions/setup-pandoc are incompatible with Ubuntu 18.04 #6298
• /__e/node20/bin/node: /lib/x86_64-linux-gnu/libc.so.6: version GLIBC_2.28' not found (required by /__e/node20/bin/node)` actions/checkout#1590 (comment)

[jameslamb]

Trying to fix #6733 (comment), it seems that the workaround from actions/checkout#1590 (comment) is no longer working.

See actions/checkout#1590 (comment).

Between this and all the work that was required with package-pinning in #6718, I think we should just fully stop testing R 3.6 on Linux in CI here. As we did for macOS in #5859.

Note that we'll still have test coverage on Windows:

LightGBM/.github/workflows/r_package.yml

Lines 81 to 87 in 83c0ff3

	- os: windows-latest
	task: r-package
	compiler: MINGW
	toolchain: MINGW
	r_version: 3.6
	build_type: cmake
	container: null

LightGBM/.github/workflows/r_package.yml

Lines 95 to 102 in 83c0ff3

	# Visual Studio 2019
	- os: windows-2019
	task: r-package
	compiler: MSVC
	toolchain: MSVC
	r_version: 3.6
	build_type: cmake
	container: null

Dropping this testing gets us the following:

• reduces CI configuration complexity (see all the code removed in this PR)
• allows upgrading to actions/checkout@v4 (no more skipping PRs like [ci]: Bump actions/checkout from 3 to 4 in the ci-dependencies group #6712)
• reduced ongoing maintenance burden, via avoiding things like these:
  • [python-package][R-package] adapt to scikit-learn 1.6 testing changes, pin more packages in R 3.6 CI jobs #6718
  • [R-package] [ci] newer versions of actions/setup-pandoc are incompatible with Ubuntu 18.04 #6298
  • [ci] use an MRAN snapshot for R 3.6 Linux jobs (fixes #5898) #5903

[StrikerRUS]

LGTM! Thank you very much for quick fix! Nice to see this simplification diff for R.

[jameslamb]

Thanks very much for the quick review! Merging this to unblock CI.