Issue with brew #4020

arttet · 2021-09-06T06:27:34Z

Description

When I use brew install cppcheck cpplint include-what-you-use, I get the error:

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@3.9

To list all files that would be deleted:
  brew link --overwrite --dry-run python@3.9

Possible conflicting files are:
/usr/local/bin/2to3 -> /Library/Frameworks/Python.framework/Versions/2.7/bin/2to3

This issue has emerged recently. That command worked well one week ago.

Virtual environments affected

Image version and build link

  Environment: macos-11
  Version: 20210831.3
  Included Software: https://github.com/actions/virtual-environments/blob/macOS-11/20210831.3/images/macos/macos-11-Readme.md
  Image Release: https://github.com/actions/virtual-environments/releases/tag/macOS-11%2F20210831.3

Is it regression?

https://github.com/actions/virtual-environments/releases/tag/macOS-10.15%2F20210814.1

Expected behavior

OK

Actual behavior

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@3.9

To list all files that would be deleted:
  brew link --overwrite --dry-run python@3.9

Possible conflicting files are:
/usr/local/bin/2to3 -> /Library/Frameworks/Python.framework/Versions/2.7/bin/2to3

Repro steps

brew install cppcheck cpplint include-what-you-use

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

al-cheb · 2021-09-06T07:30:57Z

Hello, @arttet
I couldn't reproduce the issue from my side. Or it failed when brew update&brew upgrade commands present(in that case you should run rm -rf /usr/local/bin/2to3 command before brew upgrade)?

macOS-10.15:

macOS-11:

lordgamez · 2021-09-06T08:12:46Z

I get the same issue if I want to manually install python on macos-10.15 with the command brew install python

Previously I did not need to install python as it should be present on the host machine, but today all the macos-10.15 builds started failing with the following (maybe it is connected to this issue):

-- Could NOT find PythonLibs (missing: PYTHON_LIBRARIES PYTHON_INCLUDE_DIRS) (Required is at least version "3.5")
CMake Error at /usr/local/Cellar/cmake/3.21.2/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:230 (message):
  Could NOT find PythonLibs (missing: PYTHON_LIBRARIES PYTHON_INCLUDE_DIRS)
  (Required is at least version "3.0")
Call Stack (most recent call first):
  /usr/local/Cellar/cmake/3.21.2/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:594 (_FPHSA_FAILURE_MESSAGE)
  /usr/local/Cellar/cmake/3.21.2/share/cmake/Modules/FindPythonLibs.cmake:310 (FIND_PACKAGE_HANDLE_STANDARD_ARGS)
  extensions/script/CMakeLists.txt:37 (find_package)


-- Configuring incomplete, errors occurred!

traversaro · 2021-09-06T08:39:31Z

Example of a minimum action that reproduces the problem: https://github.com/traversaro/github-actions-brew-update-upgrade-check/actions/runs/1204436581 .

arttet · 2021-09-06T10:09:06Z

It is my simple example to reproduce the bug.

mikhailkoliada · 2021-09-06T12:32:32Z

It happens due to python3.9.6 -> python3.9.7 upgrade

mikhailkoliada · 2021-09-07T13:44:09Z

We have found the root cause of this problem. Newly-generated images will make the problem gone (as updated images include an updated python version and no conflicts will happen). We are going to fix the problem until the next python release.

fredemmott · 2021-09-07T15:57:28Z

Also saw this, appears resolved by 20210905.2 image

mikhailkoliada · 2021-09-23T11:01:00Z

All the images have been updated by now.

joshua-auchincloss · 2023-11-30T07:52:05Z

Looks like this issue regressed - the dependency chain that errs is as follows:

2to3
idle3
pydoc3
python3
... stopped adding rm ... past here.

E.g. outputs:

Error: The `brew link` step did not complete successfully
The formula built, but is not symlinked into /usr/local
Could not symlink bin/python3
Target /usr/local/bin/python3
already exists. You may want to remove it:
  rm '/usr/local/bin/python3'

larseggert · 2024-02-14T09:03:35Z

This has recently (yesterday?) started happening on the macos-13 runner. The new macos-14 works (for now?), FWIW.

FirePing32 · 2024-02-26T16:30:50Z

Still persists on macos-12 and macos-13. Resolved on macos-14.
@mikhailkoliada any plans of fixing these images ?

Mukul1127 · 2024-02-29T01:34:04Z

It seems this is fixed on macos-14 because it just overwrote it

==> Installing python@3.12
==> Pouring python@3.12--3.12.2_1.arm64_sonoma.bottle.tar.gz
Warning: These files were overwritten during the `brew link` step:
/opt/homebrew/bin/2to3
/opt/homebrew/bin/idle3
/opt/homebrew/bin/pydoc3
/opt/homebrew/bin/python3
/opt/homebrew/bin/python3-config
/opt/homebrew/share/man/man1/python3.1
/opt/homebrew/lib/pkgconfig/python3-embed.pc
/opt/homebrew/lib/pkgconfig/python3.pc
/opt/homebrew/Frameworks/Python.framework/Headers
/opt/homebrew/Frameworks/Python.framework/Python
/opt/homebrew/Frameworks/Python.framework/Resources
/opt/homebrew/Frameworks/Python.framework/Versions/Current
They have been backed up to: /Users/runner/Library/Caches/Homebrew/Backup
==> /opt/homebrew/Cellar/python@3.12/3.12.2_1/bin/python3.12 -Im ensurepip
==> /opt/homebrew/Cellar/python@3.12/3.12.2_1/bin/python3.12 -Im pip install -v 
==> Summary
🍺  /opt/homebrew/Cellar/python@3.12/3.12.2_1: 3,239 files, 65.5MB

kchawla-linus · 2024-03-07T04:20:59Z

Looks like this issue regressed - the dependency chain that errs is as follows:

2to3

idle3

pydoc3

python3
... stopped adding rm ... past here.

E.g. outputs:
Error: The `brew link` step did not complete successfully
The formula built, but is not symlinked into /usr/local
Could not symlink bin/python3
Target /usr/local/bin/python3
already exists. You may want to remove it:
  rm '/usr/local/bin/python3'

I encountered this issue as well, when running brew install imagemagick via fastlane using macos-13 runner.
It tries to install `imagemagick 7.1.1-29_1 but fails when trying to pour the python bottle -

Pouring python@3.12--3.12.2_1.ventura.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'

Switching to the macos-14 runner somehow is installing an older version of imagemagick which skips installing python altogether.

Run brew install imagemagick
==> Downloading https://ghcr.io/v2/homebrew/core/imagemagick/manifests/7.1.1-26
==> Fetching dependencies for imagemagick: jbig2dec, libidn, openjpeg, ghostscript, highway, imath, openexr, webp, jpeg-xl, libvmaf, aom, libde265, shared-mime-info, x265, libheif, liblqr, jasper, libomp, libraw, m4 and libtool
==> Downloading https://ghcr.io/v2/homebrew/core/jbig2dec/manifests/0.20
...
🍺  /opt/homebrew/Cellar/libtool/2.4.7: 75 files, 3.8MB
==> Installing imagemagick
==> Pouring imagemagick--7.1.1-26.arm64_sonoma.bottle.tar.gz
🍺  /opt/homebrew/Cellar/imagemagick/7.1.1-26: 809 files, 31.3MB

actions/runner-images#4020 actions/runner-images#8838 hebasto/bitcoin@ae5f720 https://github.com/Cockatrice/Cockatrice/pull/4986/files

Due to a problem in the macos-13 runner image, installing python 3 via brew fails with a symlink error. This is a workaround to delete the symlinks before installing python 3. See actions/runner-images#4020

Currently there seems to be a issue with the macos-12 runner image when using brew. See [issue 4020](actions/runner-images#4020) for more information. So for now, support for the x86 architecture is on hold until the problem is resolved or a alternative is found macOS user's can now only use envio on the apple silicon chips.

alteredtech · 2024-06-14T19:11:55Z

Started having this issue just two hours apart from each other. Currently only happens on macos-13 runner. No changes were made to the actions. Only change was a typo in documentation.

Successful

Current runner version: '2.317.0'
Operating System
Runner Image
  Image: macos-13
  Version: 20240609.1
  Included Software: https://github.com/actions/runner-images/blob/macos-13/20240609.1/images/macos/macos-13-Readme.md
  Image Release: https://github.com/actions/runner-images/releases/tag/macos-13%2F20240609.1

Installing dependencies for repo/internal-tap/toolstools: libgit2, z3, llvm, rust, mozjpeg, libxml2, libxslt and openjpeg
==> Installing repo/internal-tap/tools dependency: libgit2
==> Downloading https://ghcr.io/v2/homebrew/core/libgit2/manifests/1.7.2
Already downloaded: /Users/runner/Library/Caches/Homebrew/downloads/9671856ced457ee95383408b4c243c7f196b6f204228b11a53735a8a561e2abb--libgit2-1.7.2.bottle_manifest.json
==> Pouring libgit2--1.7.2.ventura.bottle.tar.gz
🍺  /usr/local/Cellar/libgit2/1.7.2: 105 files, 4.5MB

Failed

Current runner version: '2.317.0'
Operating System
Runner Image
  Image: macos-13
  Version: 20240609.1
  Included Software: https://github.com/actions/runner-images/blob/macos-13/20240609.1/images/macos/macos-13-Readme.md
  Image Release: https://github.com/actions/runner-images/releases/tag/macos-13%2F20240609.1

Installing dependencies for repo/internal-tap/tools: python@3.12, libgit2, z3, llvm, rust, mozjpeg, libxml2, libxslt and openjpeg
==> Installing repo/internal-tap/tools dependency: python@3.12
==> Downloading https://ghcr.io/v2/homebrew/core/python/3.12/manifests/3.12.4
Already downloaded: /Users/runner/Library/Caches/Homebrew/downloads/2970a992f26f411cf71250ce54eb24411d8b065824b51819da7085559f09ce66--python@3.12-3.12.4.bottle_manifest.json
==> Pouring python@3.12--3.12.4.ventura.bottle.tar.gz
Error: The `brew link` step did not complete successfully
The formula built, but is not symlinked into /usr/local
Error: The `brew link` step did not complete successfully
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@3.12
To list all files that would be deleted:
  brew link --overwrite python@3.12 --dry-run
Possible conflicting files are:
/usr/local/bin/2to3 -> /Library/Frameworks/Python.framework/Versions/3.12/bin/2to3
/usr/local/bin/2to3-3.12 -> /Library/Frameworks/Python.framework/Versions/3.12/bin/2to3-3.12
/usr/local/bin/idle3 -> /Library/Frameworks/Python.framework/Versions/3.12/bin/idle3
/usr/local/bin/idle3.12 -> /Library/Frameworks/Python.framework/Versions/3.12/bin/idle3.12
/usr/local/bin/pydoc3 -> /Library/Frameworks/Python.framework/Versions/3.12/bin/pydoc3
/usr/local/bin/pydoc3.12 -> /Library/Frameworks/Python.framework/Versions/3.12/bin/pydoc3.12
/usr/local/bin/python3 -> /Library/Frameworks/Python.framework/Versions/3.12/bin/python3
/usr/local/bin/python3-config -> /Library/Frameworks/Python.framework/Versions/3.12/bin/python3-config
/usr/local/bin/python3.12 -> /Library/Frameworks/Python.framework/Versions/3.12/bin/python3.12
/usr/local/bin/python3.12-config -> /Library/Frameworks/Python.framework/Versions/3.12/bin/python3.12-config
==> /usr/local/Cellar/python@3.12/3.12.4/bin/python3.12 -Im ensurepip
==> /usr/local/Cellar/python@3.12/3.12.4/bin/python3.12 -Im pip install -v --no-
==> Summary
🍺  /usr/local/Cellar/python@3.12/3.12.4: 3,277 files, 63.9MB

The only difference I have found between the 3 images is macos-12 uses homebrew 4.3.2, macos-13 uses homebrew 4.3.3, and macos-14 uses homebrew 4.3.5.

Not how that would cause it to succeed once and then fail but something I noticed.

GitHub images already have maven installed, and upgrading to the latest version of maven via brew results in symlink conflicts of the python 3.12 dependency (earlier reported in actions/runner-images#4020).

arttet added the needs triage label Sep 6, 2021

al-cheb added investigate Collect additional information, like space on disk, other tool incompatibilities etc. OS: macOS and removed needs triage labels Sep 6, 2021

miketimofeev assigned mikhailkoliada Sep 6, 2021

traversaro mentioned this issue Sep 6, 2021

macOS Homebrew CI failure 2021/09/06 robotology/robotology-superbuild#879

Closed

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MINIFICPP-1635 Fix missing Python package issue in MacOS builds apache/nifi-minifi-cpp#1167

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8 tasks

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MacOS environment now provides a /usr/local/bin/2to3, conflicting with homebrew/homebrew dependencies #4033

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8 tasks

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MNT: hotfix CI yt-project/yt#3504

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Installing nginx now fails on macOS-10.14 #4049

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8 tasks

mikhailkoliada mentioned this issue Sep 9, 2021

[MacOS] fix python installation order #4052

Merged

4 tasks

miketimofeev added the awaiting-deployment Code complete; awaiting deployment and/or deployment in progress label Sep 15, 2021

mikhailkoliada closed this as completed Sep 23, 2021

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

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Mac CI is failing mozilla/neqo#1652

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Fix React Native CI issues breez/breez-sdk#835

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Symlink failures when installing azure-cli brew package installs dependency on Python 3.11 causes regression and build breaks. #9471

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13 tasks

njelich mentioned this issue Mar 10, 2024

CI bug fix - unlink 2to3 before installing python3 Cockatrice/Cockatrice#4986

Closed

Gelmo added a commit to Gelmo/warfork-qfusion that referenced this issue Mar 11, 2024

CI: Fix python issue for Mac runners

99f8be9

actions/runner-images#4020 actions/runner-images#8838 hebasto/bitcoin@ae5f720 https://github.com/Cockatrice/Cockatrice/pull/4986/files

Gelmo added a commit to Gelmo/warfork-qfusion that referenced this issue Mar 11, 2024

CI: Fix python issue for Mac runners

3986143

actions/runner-images#4020 actions/runner-images#8838 hebasto/bitcoin@ae5f720 https://github.com/Cockatrice/Cockatrice/pull/4986/files

Gelmo added a commit to Gelmo/warfork-qfusion that referenced this issue Mar 11, 2024

CI: Fix python issue for Mac runners

3ec5f8d

actions/runner-images#4020 actions/runner-images#8838 hebasto/bitcoin@ae5f720 https://github.com/Cockatrice/Cockatrice/pull/4986/files

Gelmo added a commit to Gelmo/warfork-qfusion that referenced this issue Mar 11, 2024

CI: Fix python issue for Mac runners

79f3dd0

actions/runner-images#4020 actions/runner-images#8838 hebasto/bitcoin@ae5f720 https://github.com/Cockatrice/Cockatrice/pull/4986/files

Gelmo mentioned this issue Mar 11, 2024

CI: Fix python issue for Mac runners TeamForbiddenLLC/warfork-qfusion#325

Merged

JCGoran mentioned this issue Mar 11, 2024

Try to fix homebrew CI issue. BlueBrain/nmodl#1212

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Fix broken MacOS and Ubuntu18.04 runs. p4lang/p4c#4517

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Fix MacOS CI setup phase PowerGridModel/power-grid-model#522

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[HOTFIX] Fix mobile CI builds MerginMaps/mobile#3142

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kduske mentioned this issue Mar 18, 2024

macOS CI currently broken TrenchBroom/TrenchBroom#4528

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Fix Github Actions ctags install issue AbanteAI/mentat#542

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CI: fix Python installation with brew SoundScapeRenderer/ssr#393

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Avoid brew symlink conflict in macos-13 diffblue/cbmc#8338

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Issue with brew #4020

Issue with brew #4020

arttet commented Sep 6, 2021

al-cheb commented Sep 6, 2021 •

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arttet commented Sep 6, 2021

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Issue with brew #4020

Issue with brew #4020

Comments

arttet commented Sep 6, 2021

Description

Virtual environments affected

Image version and build link

Is it regression?

Expected behavior

Actual behavior

Repro steps

al-cheb commented Sep 6, 2021 • edited Loading

lordgamez commented Sep 6, 2021

traversaro commented Sep 6, 2021

arttet commented Sep 6, 2021

mikhailkoliada commented Sep 6, 2021

mikhailkoliada commented Sep 7, 2021

fredemmott commented Sep 7, 2021

mikhailkoliada commented Sep 23, 2021

joshua-auchincloss commented Nov 30, 2023

larseggert commented Feb 14, 2024

FirePing32 commented Feb 26, 2024 • edited Loading

Mukul1127 commented Feb 29, 2024 • edited Loading

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