brew update followed by brew upgrade fails for Python's 2to3 conflict (December 2022)

[traversaro]

Description

If one has on a job:

brew update
brew upgrade

the job fails with error:

 ==> Upgrading python@3.10
  3.10.8 -> 3.10.9 

==> Pouring python@3.10--3.10.9.big_sur.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

This is similar to old issues:

• brew upgrade fails for Python's 2to3 conflict  #2322
• Issue with brew #4020

Platforms affected

• Azure DevOps
• GitHub Actions - Standard Runners
• GitHub Actions - Larger Runners

Runner images affected

• Ubuntu 18.04
• Ubuntu 20.04
• Ubuntu 22.04
• macOS 11
• macOS 12
• Windows Server 2019
• Windows Server 2022

Image version and build link

Image Version: 20221215.1
Link: https://github.com/traversaro/github-actions-brew-update-upgrade-check/actions/runs/3742142787

Is it regression?

20221211.1

Expected behavior

The brew upgrade should exit fine.

Actual behavior

The brew upgrade fails with the error message in the top of the issue.

Repro steps

See https://github.com/traversaro/github-actions-brew-update-upgrade-check/blob/2fa847c627c643716ba10d681ea18c86c0b54dec/.github/workflows/brew-update.yml for a MWE .

[traversaro]

Possibly related to #6459 .

[igorboskovic3]

Hi @traversaro , thank you, we will take a look.

[david-engelmann]

I'm observing this as well

[ryancurrah]

Also observed this here https://github.com/ryancurrah/lima-and-qemu/actions/runs/3745432855/jobs/6359863993 and here https://github.com/mook-as/lima-and-qemu/actions/runs/3743467832/jobs/6356414606.

EDIT:

I was able to get it working by removing the existing symlinks.

rm /usr/local/bin/2to3
rm /usr/local/bin/idle3
rm /usr/local/bin/pydoc3
rm /usr/local/bin/python3
rm /usr/local/bin/python3-config

[mikhailkoliada]

It looks like it the universal python's package used in actions/setup-python is installing its symlinks to /usr/local, while I think it should not.

@marko-zivic-93 @dsame @dmitry-shibanov could you please take a look?

[ni4]

Got the same issue, and find out that something similar we had previously. Now it looks like:

  # homebrew fails to update python 3.9.1 to 3.9.1.1 due to unlinking failure
  rm /usr/local/bin/2to3 || true
  # homebrew fails to update python from 3.9 to 3.10 due to another unlinking failure
  rm /usr/local/bin/idle3 || true
  rm /usr/local/bin/pydoc3 || true
  rm /usr/local/bin/python3 || true
  rm /usr/local/bin/python3-config || true

[Flamefire]

It looks like it the universal python's package used in actions/setup-python is installing its symlinks to /usr/local, while I think it should not.

That is not the case for us and the OP:

/usr/local/bin/2to3 -> /Library/Frameworks/Python.framework/Versions/3.11/bin/2to3

There is seemingly a non-brew installed Python from somewhere else

[dsame]

@Flamefire the workflow does not use action/setup-python. It seems the links are created by the macos python package - i see them on the "almost" clean machine with the XCode installed.

[dsame]

@traversaro actully it is a normal behaviour. As you see from the log the installation continues normally with just a warning the links were not overwritten. The problem is brew upgrade exits with non-zero exit code and bash shell runs with set -e option. Thus the step signals the error condition despite brew upgrade is the very last command or not.

The easiest way to make the step to success is to add true after brew upgrade:

      - run: |
          brew update
          brew upgrade || true