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[email protected] overrides /usr/local/bin/python3 etc. installed by [email protected] #86520

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jwodder opened this issue Oct 5, 2021 · 2 comments
Closed
2 tasks done

[email protected] overrides /usr/local/bin/python3 etc. installed by [email protected] #86520

jwodder opened this issue Oct 5, 2021 · 2 comments
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bug Reproducible Homebrew/homebrew-core bug outdated PR was locked due to age

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@jwodder
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jwodder commented Oct 5, 2021 •
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brew gist-logs <formula> link OR brew config AND brew doctor output

brew config:

HOMEBREW_VERSION: 3.2.15
ORIGIN: https://github.com/Homebrew/brew
HEAD: 92749f9c5243691f8e576aa1227cb9ebba509cd4
Last commit: 2 hours ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: 7f9f35c8b47c0c7be433b608b5ca22adfd409c9b
Core tap last commit: 3 hours ago
Core tap branch: master
HOMEBREW_PREFIX: /usr/local
HOMEBREW_CASK_OPTS: []
HOMEBREW_CLEANUP_MAX_AGE_DAYS: 1
HOMEBREW_DISPLAY: /private/tmp/com.apple.launchd.RJVoZZ6LWA/org.xquartz:0
HOMEBREW_EDITOR: /usr/bin/vim
HOMEBREW_MAKE_JOBS: 8
Homebrew Ruby: 2.6.3 => /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/bin/ruby
CPU: octa-core 64-bit icelake
Clang: 12.0.5 build 1205
Git: 2.33.0 => /usr/local/bin/git
Curl: 7.64.1 => /usr/local/Homebrew/Library/Homebrew/shims/shared/curl
macOS: 11.6-x86_64
CLT: 12.5.0.22.9
Xcode: 13.0
XQuartz: 2.8.1 => /opt/X11

brew doctor:

Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry or file an issue; just ignore this. Thanks!

Warning: A newer Command Line Tools release is available.
Update them from Software Update in System Preferences or run:
  softwareupdate --all --install --force

If that doesn't show you any updates, run:
  sudo rm -rf /Library/Developer/CommandLineTools
  sudo xcode-select --install

Alternatively, manually download them from:
  https://developer.apple.com/download/all/.
You should download the Command Line Tools for Xcode 13.0.


Warning: Some installed formulae are deprecated or disabled.
You should find replacements for the following formulae:
  [email protected]

Warning: You have unlinked kegs in your Cellar.
Leaving kegs unlinked can lead to build-trouble and cause formulae that depend on
those kegs to fail to run properly once built. Run `brew link` on these:
  [email protected]

  • I ran brew update and am still able to reproduce my issue.
  • I have resolved all warnings from brew doctor and that did not fix my problem.

What were you trying to do (and why)?

brew install [email protected]. As the python formula is still an alias to [email protected], I expected that /usr/local/bin/python3 would continue to point to 3.9 after the upgrade, with 3.10 not symlinked into PATH.

What happened (include all command output)?

  • I installed Python 3.10. Homebrew complained along the way that /usr/local/bin/python3 etc. were overwritten during the brew link step.
  • I found that the /usr/local/bin/python3 symlink and friends (pip etc.) now pointed to Python 3.10, though individual python3.9 and python3.10 programs were both available and ran the respective versions.
  • I unlinked 3.10 and relinked 3.9. python3 is now 3.9, and there is no python3.10 in the PATH.
  • I suspect that this will repeat should 3.10 receive an update before 3.9.
Tue Oct 05 ~/work$ brew install [email protected]
Updating Homebrew...
==> Auto-updated Homebrew!
Updated 2 taps (homebrew/core and homebrew/cask).
==> New Formulae
libnghttp2
==> Updated Formulae
Updated 16 formulae.
==> Updated Casks
Updated 10 casks.

==> Downloading https://ghcr.io/v2/homebrew/core/ca-certificates/manifests/2021-
######################################################################## 100.0%
==> Downloading https://ghcr.io/v2/homebrew/core/ca-certificates/blobs/sha256:47
==> Downloading from https://pkg-containers.githubusercontent.com/ghcr1/blobs/sh
######################################################################## 100.0%
==> Downloading https://ghcr.io/v2/homebrew/core/openssl/1.1/manifests/1.1.1l_1
######################################################################## 100.0%
==> Downloading https://ghcr.io/v2/homebrew/core/openssl/1.1/blobs/sha256:64d4d8
==> Downloading from https://pkg-containers.githubusercontent.com/ghcr1/blobs/sh
######################################################################## 100.0%
==> Downloading https://ghcr.io/v2/homebrew/core/readline/manifests/8.1.1
######################################################################## 100.0%
==> Downloading https://ghcr.io/v2/homebrew/core/readline/blobs/sha256:c596199dc
==> Downloading from https://pkg-containers.githubusercontent.com/ghcr1/blobs/sh
######################################################################## 100.0%
==> Downloading https://ghcr.io/v2/homebrew/core/python/3.10/manifests/3.10.0
######################################################################## 100.0%
==> Downloading https://ghcr.io/v2/homebrew/core/python/3.10/blobs/sha256:f415f1
==> Downloading from https://pkg-containers.githubusercontent.com/ghcr1/blobs/sh
######################################################################## 100.0%
==> Installing dependencies for [email protected]: ca-certificates, [email protected] and readline
==> Installing [email protected] dependency: ca-certificates
==> Pouring ca-certificates--2021-09-30.all.bottle.1.tar.gz
==> Regenerating CA certificate bundle from keychain, this may take a while...
🍺  /usr/local/Cellar/ca-certificates/2021-09-30: 3 files, 203.5KB
==> Installing [email protected] dependency: [email protected]
==> Pouring [email protected]_1.big_sur.bottle.tar.gz
🍺  /usr/local/Cellar/[email protected]/1.1.1l_1: 8,073 files, 18.5MB
==> Installing [email protected] dependency: readline
==> Pouring readline--8.1.1.big_sur.bottle.tar.gz
🍺  /usr/local/Cellar/readline/8.1.1: 48 files, 1.6MB
==> Installing [email protected]
==> Pouring [email protected]_sur.bottle.tar.gz
Warning: These files were overwritten during the `brew link` step:
/usr/local/bin/2to3
/usr/local/bin/idle3
/usr/local/bin/pydoc3
/usr/local/bin/python3
/usr/local/bin/python3-config
/usr/local/share/man/man1/python3.1
/usr/local/lib/pkgconfig/python3-embed.pc
/usr/local/lib/pkgconfig/python3.pc
/usr/local/Frameworks/Python.framework/Headers
/usr/local/Frameworks/Python.framework/Python
/usr/local/Frameworks/Python.framework/Resources
/usr/local/Frameworks/Python.framework/Versions/Current

They have been backed up to: /Users/jwodder/Library/Caches/Homebrew/Backup
==> /usr/local/Cellar/[email protected]/3.10.0/bin/python3 -m ensurepip
==> /usr/local/Cellar/[email protected]/3.10.0/bin/python3 -m pip install -v --no-deps
==> Caveats
Python has been installed as
  /usr/local/bin/python3

Unversioned symlinks `python`, `python-config`, `pip` etc. pointing to
`python3`, `python3-config`, `pip3` etc., respectively, have been installed into
  /usr/local/opt/[email protected]/libexec/bin

You can install Python packages with
  pip3 install <package>
They will install into the site-package directory
  /usr/local/lib/python3.10/site-packages

tkinter is no longer included with this formula, but it is available separately:
  brew install [email protected]

See: https://docs.brew.sh/Homebrew-and-Python
==> Summary
🍺  /usr/local/Cellar/[email protected]/3.10.0: 3,133 files, 55.8MB
==> Upgrading 3 dependents:
imagemagick 7.1.0-8 -> 7.1.0-9, nghttp2 1.45.1 -> 1.45.1_1, unbound 1.13.2 -> 1.13.2_1
==> Downloading https://ghcr.io/v2/homebrew/core/libomp/manifests/13.0.0
######################################################################## 100.0%
==> Downloading https://ghcr.io/v2/homebrew/core/libomp/blobs/sha256:be00288f6f2
==> Downloading from https://pkg-containers.githubusercontent.com/ghcr1/blobs/sh
######################################################################## 100.0%
==> Downloading https://ghcr.io/v2/homebrew/core/openexr/manifests/3.1.2
######################################################################## 100.0%
==> Downloading https://ghcr.io/v2/homebrew/core/openexr/blobs/sha256:922846fff4
==> Downloading from https://pkg-containers.githubusercontent.com/ghcr1/blobs/sh
######################################################################## 100.0%
==> Downloading https://ghcr.io/v2/homebrew/core/imagemagick/manifests/7.1.0-9
######################################################################## 100.0%
==> Downloading https://ghcr.io/v2/homebrew/core/imagemagick/blobs/sha256:476959
==> Downloading from https://pkg-containers.githubusercontent.com/ghcr1/blobs/sh
######################################################################## 100.0%
==> Downloading https://ghcr.io/v2/homebrew/core/libnghttp2/manifests/1.45.1
######################################################################## 100.0%
==> Downloading https://ghcr.io/v2/homebrew/core/libnghttp2/blobs/sha256:6edccdb
==> Downloading from https://pkg-containers.githubusercontent.com/ghcr1/blobs/sh
######################################################################## 100.0%
==> Downloading https://ghcr.io/v2/homebrew/core/nghttp2/manifests/1.45.1_1
######################################################################## 100.0%
==> Downloading https://ghcr.io/v2/homebrew/core/nghttp2/blobs/sha256:4c27ecc896
==> Downloading from https://pkg-containers.githubusercontent.com/ghcr1/blobs/sh
######################################################################## 100.0%
==> Downloading https://ghcr.io/v2/homebrew/core/libnghttp2/manifests/1.45.1
Already downloaded: /Users/jwodder/Library/Caches/Homebrew/downloads/a10e8809f2b80ff379c8ac93e0e41e69e5a179b36e2ac19968bcfec8abe11b73--libnghttp2-1.45.1.bottle_manifest.json
==> Downloading https://ghcr.io/v2/homebrew/core/libnghttp2/blobs/sha256:6edccdb
Already downloaded: /Users/jwodder/Library/Caches/Homebrew/downloads/0ddc64f9fd99263fe024b4c46452c0f244578238ff5a2b0321e5742e8e08522e--libnghttp2--1.45.1.big_sur.bottle.tar.gz
==> Downloading https://ghcr.io/v2/homebrew/core/unbound/manifests/1.13.2_1
######################################################################## 100.0%
==> Downloading https://ghcr.io/v2/homebrew/core/unbound/blobs/sha256:7f411a6ec2
==> Downloading from https://pkg-containers.githubusercontent.com/ghcr1/blobs/sh
######################################################################## 100.0%
==> Upgrading imagemagick
  7.1.0-8 -> 7.1.0-9 

==> Installing dependencies for imagemagick: libomp and openexr
==> Installing imagemagick dependency: libomp
==> Pouring libomp--13.0.0.big_sur.bottle.tar.gz
🍺  /usr/local/Cellar/libomp/13.0.0: 9 files, 1.6MB
==> Installing imagemagick dependency: openexr
==> Pouring openexr--3.1.2.big_sur.bottle.tar.gz
🍺  /usr/local/Cellar/openexr/3.1.2: 194 files, 5.9MB
==> Installing imagemagick
==> Pouring imagemagick--7.1.0-9.big_sur.bottle.tar.gz
🍺  /usr/local/Cellar/imagemagick/7.1.0-9: 799 files, 30.3MB
Removing: /usr/local/Cellar/imagemagick/7.1.0-8... (799 files, 30.3MB)
==> Upgrading nghttp2
  1.45.1 -> 1.45.1_1 

==> Installing dependencies for nghttp2: libnghttp2
==> Installing nghttp2 dependency: libnghttp2
==> Pouring libnghttp2--1.45.1.big_sur.bottle.tar.gz
🍺  /usr/local/Cellar/libnghttp2/1.45.1: 13 files, 659.9KB
==> Installing nghttp2
==> Pouring nghttp2--1.45.1_1.big_sur.bottle.tar.gz
🍺  /usr/local/Cellar/nghttp2/1.45.1_1: 17 files, 2.2MB
Removing: /usr/local/Cellar/nghttp2/1.45.1... (23 files, 2.8MB)
Removing: /Users/jwodder/Library/Caches/Homebrew/nghttp2--1.45.1... (972.3KB)
==> Upgrading unbound
  1.13.2 -> 1.13.2_1 

==> Pouring unbound--1.13.2_1.big_sur.bottle.tar.gz
🍺  /usr/local/Cellar/unbound/1.13.2_1: 57 files, 5.7MB
Removing: /usr/local/Cellar/unbound/1.13.2... (57 files, 5.7MB)
==> Checking for dependents of upgraded formulae...
==> No broken dependents found!
==> Caveats
==> [email protected]
Python has been installed as
  /usr/local/bin/python3

Unversioned symlinks `python`, `python-config`, `pip` etc. pointing to
`python3`, `python3-config`, `pip3` etc., respectively, have been installed into
  /usr/local/opt/[email protected]/libexec/bin

You can install Python packages with
  pip3 install <package>
They will install into the site-package directory
  /usr/local/lib/python3.10/site-packages

tkinter is no longer included with this formula, but it is available separately:
  brew install [email protected]

See: https://docs.brew.sh/Homebrew-and-Python
Tue Oct 05 ~/work$ python3 -V
Python 3.10.0
Tue Oct 05 ~/work$ python3.9 -V
Python 3.9.7
Tue Oct 05 ~/work$ python3.10 -V
Python 3.10.0
Tue Oct 05 ~/work$ pip3 -V
pip 21.2.4 from /usr/local/lib/python3.10/site-packages/pip (python 3.10)
Tue Oct 05 ~/work$ brew unlink [email protected]
Unlinking /usr/local/Cellar/[email protected]/3.10.0... 24 symlinks removed.
Tue Oct 05 ~/work$ brew link [email protected]
Warning: Already linked: /usr/local/Cellar/[email protected]/3.9.7
To relink, run:
  brew unlink [email protected] && brew link [email protected]
Tue Oct 05 ~/work$ python3 -V
-bash: /usr/local/bin/python3: No such file or directory
[127]
Tue Oct 05 ~/work$ brew unlink [email protected]
Unlinking /usr/local/Cellar/[email protected]/3.9.7... 10 symlinks removed.
Tue Oct 05 ~/work$ brew link [email protected]
Linking /usr/local/Cellar/[email protected]/3.9.7... 24 symlinks created.
Tue Oct 05 ~/work$ python3 -V
Python 3.9.7
Tue Oct 05 ~/work$ python3.9 -V
Python 3.9.7
Tue Oct 05 ~/work$ python3.10 -V
-bash: /usr/local/bin/python3.10: No such file or directory
[127]
Tue Oct 05 ~/work$ pip3 --version
pip 21.2.4 from /usr/local/lib/python3.9/site-packages/pip (python 3.9)

What did you expect to happen?

[email protected] and [email protected] should not have gotten into a slap-fight over the ownership of /usr/local/bin/python3.

Step-by-step reproduction instructions (by running brew commands)

brew install [email protected]
brew install [email protected]
@jwodder jwodder added the bug Reproducible Homebrew/homebrew-core bug label Oct 5, 2021
@branchvincent
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sorry about that. #86469 should fix it

@branchvincent branchvincent mentioned this issue Oct 6, 2021
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@carlocab
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carlocab commented Oct 6, 2021

Fixed in #86469.

@carlocab carlocab closed this as completed Oct 6, 2021
@github-actions github-actions bot added the outdated PR was locked due to age label Nov 6, 2021
@github-actions github-actions bot locked as resolved and limited conversation to collaborators Nov 6, 2021
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[email protected]: make keg-only branchvincent/homebrew-core
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@jwodder @branchvincent @carlocab