brew upgrade fails for Python's 2to3 conflict #2322

traversaro · 2020-12-21T13:05:03Z

Description
If I run the commands brew update and brew upgrade, the job fails. This is similar to #2248 and #1811, but the specific error is different and is probably due to some other Python being installed.

Area for Triage:

Question, Bug, or Feature?:
Bug

Virtual environments affected

Expected behavior
I would expect that brew upgrade works fine.

Actual behavior
brew upgrade is failing with error:

2020-12-21T12:59:17.7407310Z The formula built, but is not symlinked into /usr/local
2020-12-21T12:59:17.7430550Z Could not symlink bin/2to3
2020-12-21T12:59:17.7443870Z Target /usr/local/bin/2to3
2020-12-21T12:59:17.7446720Z already exists. You may want to remove it:
2020-12-21T12:59:17.7452220Z   rm '/usr/local/bin/2to3'
2020-12-21T12:59:17.7482600Z 
2020-12-21T12:59:17.7485390Z To force the link and overwrite all conflicting files:
2020-12-21T12:59:17.7547210Z   brew link --overwrite python@3.9
2020-12-21T12:59:17.7599790Z 
2020-12-21T12:59:17.7652130Z To list all files that would be deleted:
2020-12-21T12:59:17.7663330Z   brew link --overwrite --dry-run python@3.9
2020-12-21T12:59:17.7667290Z 
2020-12-21T12:59:17.7678030Z Possible conflicting files are:

Repro steps

Run the following commands in a macos image:

brew update
brew upgrade

See https://github.com/traversaro/github-actions-brew-update-upgrade-check/actions/runs/435789601 for a minimal job that is failing.

The text was updated successfully, but these errors were encountered:

sunjayBhatia · 2020-12-21T20:04:42Z

Running into the same issue in Envoy CI

sunjayBhatia · 2020-12-21T20:12:30Z

Looks like it is coming from the system python?

$ which 2to3
/usr/local/bin/2to3
$ ls -la $(which 2to3)
lrwxr-xr-x  1 root  wheel  66 Dec 12 21:22 /usr/local/bin/2to3 -> ../../../Library/Frameworks/Python.framework/Versions/2.7/bin/2to3

maxim-lobanov · 2020-12-21T20:49:12Z

Most likely caused by #2217 where we switched Python 2 installation from to official pkg. This pkg brings this symlink and brew can't override it later

maxim-lobanov · 2020-12-21T20:50:28Z

@miketimofeev I guess we should leave default MacOS Python 2 without any updates (just install pip) to avoid issues with brew

miketimofeev · 2020-12-21T21:40:36Z

@maxim-lobanov there are some issues with pip installation in this case. I suggest removing the 2to3 symlink created by python2 before the python3 installation.
@traversaro as a workaround you can add rm -rf /usr/local/bin/2to3 as a first step until we've fixed it. Sorry for the inconvenience.

traversaro · 2020-12-22T09:02:49Z

Thanks a lot @miketimofeev @maxim-lobanov !

See actions/runner-images#2322

adds the `rm -rf /usr/local/bin/2to3` workaround as suggested in actions/runner-images#2322

* starts 2.3.0 release cycle updates versions in the configuration tools, bumps up copyright dates (also normalizes the MIT license to make it recognizable for github), and updates the release.sh script for the release automation. * fixes build on macOS adds the `rm -rf /usr/local/bin/2to3` workaround as suggested in actions/runner-images#2322

- brew install octave failing due to trouble overwriting things installed by existing versions of python and gcc. Ref: actions/runner-images#2322 Ref: actions/runner-images#2391

* Add rm '/usr/local/bin/2to3' in macOS jobs to fix symlink issue when brew upgrades Python (cf actions/runner-images#2322) * Add brew upgrade step preceded by unlinking gcc@8 and gcc@9 due to other symlink failures (cf actions/runner-images#2391)

This way each time a new Python version is installed via Homebrew , we don't get CI failures due to the upstream Python distribution also being installed. Ref: actions/runner-images#6459 Ref: actions/runner-images#2322

… on macOS This way each time a new Python version is installed via Homebrew , we don't get CI failures due to the upstream Python distribution also being installed. Ref: actions/runner-images#6459 Ref: actions/runner-images#2322

… on macOS This way each time a new Python version is installed via Homebrew , we don't get CI failures due to the upstream Python distribution also being installed. Ref: actions/runner-images#6459 Ref: actions/runner-images#6507 Ref: actions/runner-images#2322

CI has started failing again recently and I found this solution while going over: actions/runner-images#2322

The github mac runner images added python 3.11 but, unlike 3.10, not via brew. This causes brew install to fail with link conflict errors now that boost-python3 switched over to 3.11. Workaround this, and future python brew link errors, by ovewriting all links for python packages. Homebrew/homebrew-core@8c79089 https://github.com/orgs/Homebrew/discussions/3895 actions/setup-python#577 actions/runner-images#6459 actions/runner-images#6507 actions/runner-images#2322

The github mac runner images added python 3.11 but, unlike 3.10, not via brew. This causes brew install to fail with link conflict errors now that boost-python3 switched over to 3.11. Workaround this, and future python brew link errors, by overwriting all links for python packages. Homebrew/homebrew-core@8c79089 https://github.com/orgs/Homebrew/discussions/3895 actions/setup-python#577 actions/runner-images#6459 actions/runner-images#6507 actions/runner-images#2322

MacOS CI build started to fail in the PRs because when upgrading python it was not possible to override one existing file (related to 2to3 package). Apparently this happens because MacOS runners some times have python versions not installed/compatible with brew. Example of the failure: https://github.com/coturn/coturn/actions/runs/3850951324 The proposed workaround is taken from here: actions/runner-images#2322

The github mac runner images added python 3.11 but, unlike 3.10, not via brew. This causes brew install to fail with link conflict errors now that boost-python3 switched over to 3.11. Workaround this, and future python brew link errors, by overwriting all links for python packages. Homebrew/homebrew-core@8c79089 https://github.com/orgs/Homebrew/discussions/3895 actions/setup-python#577 actions/runner-images#6459 actions/runner-images#6507 actions/runner-images#2322

… on macOS This way each time a new Python version is installed via Homebrew , we don't get CI failures due to the upstream Python distribution also being installed. Ref: actions/runner-images#6459 Ref: actions/runner-images#6507 Ref: actions/runner-images#2322

…actions/runner-images#2322 (comment))

…ctions/runner-images#2322 (comment)

louwers · 2023-12-13T08:03:54Z

This is still an issue. Can it be reopened or should I create a new issue?

traversaro added the needs triage label Dec 21, 2020

traversaro mentioned this issue Dec 21, 2020

macOS Homebrew CI failing robotology/robotology-superbuild#565

Closed

div72 mentioned this issue Dec 21, 2020

ci: Fix python symlink issue & remove travis gridcoin-community/Gridcoin-Research#1990

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sunjayBhatia mentioned this issue Dec 21, 2020

macos build: Fix ninja install envoyproxy/envoy#14495

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Darleev added Area: Python OS: macOS investigate Collect additional information, like space on disk, other tool incompatibilities etc. and removed needs triage labels Dec 21, 2020

Darleev assigned Darleev and miketimofeev Dec 21, 2020

miketimofeev mentioned this issue Dec 21, 2020

[macOS] Fix the issue with Python 2to3 symlink #2326

Merged

4 tasks

miketimofeev added the awaiting-deployment Code complete; awaiting deployment and/or deployment in progress label Dec 23, 2020

soonho-tri added a commit to soonho-tri/dreal4 that referenced this issue Dec 23, 2020

github(main.yml): Remove /usr/local/bin/2to3

27fa79a

See actions/runner-images#2322

soonho-tri mentioned this issue Jan 3, 2021

brew 'glib' (in /setup/mac/binary_distribution/Brewfile is forcing python@3.9 RobotLocomotion/drake#14481

Closed

ivg added a commit to ivg/bap that referenced this issue Jan 4, 2021

fixes build on macOS

b461b3e

adds the `rm -rf /usr/local/bin/2to3` workaround as suggested in actions/runner-images#2322

ivg added a commit to ivg/bap that referenced this issue Jan 4, 2021

fixes build on macOS

3cbf22a

adds the `rm -rf /usr/local/bin/2to3` workaround as suggested in actions/runner-images#2322

ivg mentioned this issue Jan 5, 2021

brew upgrade fails on gcc #2391

Closed

7 tasks

tlestang mentioned this issue Jan 6, 2021

Fix GitHub actions MacOS pybamm-team/PyBaMM#1319

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traversaro mentioned this issue Jan 7, 2021

Pipeline example robotology/robometry#27

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ulupo mentioned this issue Jan 8, 2021

Fix brew symlinking in CI giotto-ai/giotto-tda#554

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traversaro mentioned this issue Jan 8, 2021

Implement the skeleton of the OptimalControlElement class and SE3Task ami-iit/bipedal-locomotion-framework#167

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jeeb mentioned this issue Nov 11, 2022

github/workflows: force deletion of existing upstream python symlinks on macOS mpv-player/mpv#10849

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banach-space added a commit to banach-space/llvm-tutor that referenced this issue Nov 18, 2022

[CI] Re-implement the fix to the brew install lit issue

a9eb52e

CI has started failing again recently and I found this solution while going over: actions/runner-images#2322

banach-space added a commit to banach-space/clang-tutor that referenced this issue Nov 18, 2022

[CI] Re-implement the fix to the brew install lit issue

bfffdf2

CI has started failing again recently and I found this solution while going over: actions/runner-images#2322

traversaro mentioned this issue Dec 26, 2022

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

Open

10 tasks

zjeffer mentioned this issue Dec 25, 2022

Qmake to cmake migration nuttyartist/notes#421

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q3aiml mentioned this issue Jan 8, 2023

fix brew link error on mac CI ledger/ledger#2161

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ggarber mentioned this issue Jan 8, 2023

Fix brew for MacOS CI build coturn/coturn#1136

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vpolikarpov-akvelon mentioned this issue Jun 15, 2023

[macos]: strange error during homebrew install #7725

Closed

10 tasks

akikuno added a commit to akikuno/cstag that referenced this issue Nov 23, 2023

add rm -rf /usr/local/bin/2to3 to avoid errors during brew update (…

179e336

…actions/runner-images#2322 (comment))

akikuno added a commit to akikuno/cstag that referenced this issue Nov 23, 2023

add rm -rf /usr/local/bin/2to3* to avoid errors during brew update a…

4a486a6

…ctions/runner-images#2322 (comment)

Jolg42 mentioned this issue Dec 13, 2023

ci(macos): overwrite conflicting files rather than ignore errors prisma/prisma#22369

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brew upgrade fails for Python's 2to3 conflict #2322

brew upgrade fails for Python's 2to3 conflict #2322

traversaro commented Dec 21, 2020 •

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sunjayBhatia commented Dec 21, 2020

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maxim-lobanov commented Dec 21, 2020

maxim-lobanov commented Dec 21, 2020

miketimofeev commented Dec 21, 2020

traversaro commented Dec 22, 2020

louwers commented Dec 13, 2023

brew upgrade fails for Python's 2to3 conflict #2322

brew upgrade fails for Python's 2to3 conflict #2322

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traversaro commented Dec 21, 2020 • edited Loading

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