[ci] R-package macOS jobs failing due to Homebrew errors

[jameslamb]

Description

I'm not sure exactly which of the warnings and errors I see in logs are the relevant ones, but the R-package macOS CI jobs are failing somewhere in here:

LightGBM/.ci/test_r_package.sh

Lines 87 to 89 in c2d2c99

	brew install --cask basictex || exit -1
	export PATH="/Library/TeX/texbin:$PATH"
	sudo tlmgr --verify-repo=none update --self || exit -1

Reproducible example

Tried 3 runs of these jobs on latest master, e.g. https://github.com/microsoft/LightGBM/actions/runs/3886554693/jobs/6637875169

Additional Comments

I do see errors like the following:

==> Pouring python@3.10--3.10.9.monterey.bottle.tar.gz
Error: The `brew link` step did not complete successfully
The formula built, but is not symlinked into /usr/local
Could not symlink bin/2to3
Target /usr/local/bin/2to3
already exists. You may want to remove it:
  rm '/usr/local/bin/2to3'

To force the link and overwrite all conflicting files:
  brew link --overwrite python@3.10

To list all files that would be deleted:
  brew link --overwrite --dry-run python@3.10

Possible conflicting files are:
/usr/local/bin/2to3 -> /Library/Frameworks/Python.framework/Versions/3.11/bin/2to3
/usr/local/bin/idle3 -> /Library/Frameworks/Python.framework/Versions/3.11/bin/idle3
/usr/local/bin/pydoc3 -> /Library/Frameworks/Python.framework/Versions/3.11/bin/pydoc3
/usr/local/bin/python3 -> /Library/Frameworks/Python.framework/Versions/3.11/bin/python3
/usr/local/bin/python3-config -> /Library/Frameworks/Python.framework/Versions/3.11/bin/python3-config

==> Pouring python@3.11--3.11.1.monterey.bottle.tar.gz
Error: The `brew link` step did not complete successfully
The formula built, but is not symlinked into /usr/local
Could not symlink bin/2to3-3.11
Target /usr/local/bin/2to3-3.11
already exists. You may want to remove it:
  rm '/usr/local/bin/2to3-3.11'

To force the link and overwrite all conflicting files:
  brew link --overwrite python@3.11

To list all files that would be deleted:
  brew link --overwrite --dry-run python@3.11

Possible conflicting files are:
/usr/local/bin/2to3-3.11 -> /Library/Frameworks/Python.framework/Versions/3.11/bin/2to3-3.11
/usr/local/bin/idle3.11 -> /Library/Frameworks/Python.framework/Versions/3.11/bin/idle3.11
/usr/local/bin/pydoc3.11 -> /Library/Frameworks/Python.framework/Versions/3.11/bin/pydoc3.11
/usr/local/bin/python3.11 -> /Library/Frameworks/Python.framework/Versions/3.11/bin/python3.11
/usr/local/bin/python3.11-config -> /Library/Frameworks/Python.framework/Versions/3.11/bin/python3.11-config

[jameslamb]

Based on my testing so far in #5671, looks like this is actually failing earlier, at this line:

LightGBM/.ci/test_r_package.sh

Line 80 in c2d2c99

brew update-reset && brew update

That was added in #4161.

[jameslamb]

Found some related discussions.

These say that basically homebrew is trying to create links to files that conflict with other, non-Homebrew methods of installing Python:

• brew update followed by brew upgrade fails for Python's 2to3 conflict (December 2022) actions/setup-python#577
• Add Python 3.11 support for runners actions/runner-images#6459

...and that even if the issue might have been fixed in homebrew-core, it's still problematic because some of those links have been baked into the GitHub Actions runner images:

• brew update followed by brew upgrade fails for Python's 2to3 conflict (December 2022) actions/setup-python#577 (comment)

[jameslamb]

This exact situation is happening again: https://github.com/microsoft/LightGBM/actions/runs/5245110302/jobs/9472087143?pr=5923

==> Pouring python@3.11--3.11.4.monterey.bottle.tar.gz
Error: The `brew link` step did not complete successfully
The formula built, but is not symlinked into /usr/local
Could not symlink bin/2to3
Target /usr/local/bin/2to3
already exists. You may want to remove it:
  rm '/usr/local/bin/2to3'

To force the link and overwrite all conflicting files:
  brew link --overwrite python@3.11

To list all files that would be deleted:
  brew link --overwrite --dry-run python@3.11

Possible conflicting files are:
/usr/local/bin/2to3 -> /Library/Frameworks/Python.framework/Versions/3.11/bin/2to3
/usr/local/bin/2to3-3.11 -> /Library/Frameworks/Python.framework/Versions/3.11/bin/2to3-3.11
/usr/local/bin/idle3 -> /Library/Frameworks/Python.framework/Versions/3.11/bin/idle3
/usr/local/bin/idle3.11 -> /Library/Frameworks/Python.framework/Versions/3.11/bin/idle3.11
/usr/local/bin/pydoc3 -> /Library/Frameworks/Python.framework/Versions/3.11/bin/pydoc3
/usr/local/bin/pydoc3.11 -> /Library/Frameworks/Python.framework/Versions/3.11/bin/pydoc3.11
/usr/local/bin/python3 -> /Library/Frameworks/Python.framework/Versions/3.11/bin/python3
/usr/local/bin/python3-config -> /Library/Frameworks/Python.framework/Versions/3.11/bin/python3-config
/usr/local/bin/python3.11 -> /Library/Frameworks/Python.framework/Versions/3.11/bin/python3.11
/usr/local/bin/python3.11-config -> /Library/Frameworks/Python.framework/Versions/3.11/bin/python3.11-config

🙃

[github-actions]

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