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Automatic cleanup on install/upgrade removes resouce data used by multiple formula (e.g., 3.13-sysconfig.diff for both python@3.{13,14}) #21327

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#21358
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Automatic cleanup on install/upgrade removes resouce data used by multiple formula (e.g., 3.13-sysconfig.diff for both python@3.{13,14})#21327
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#21358
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help wantedWe want help addressing this
@XuehaiPan

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@XuehaiPan
XuehaiPan
opened on Dec 26, 2025

brew doctor output

Warning: Your Homebrew's prefix is not /home/linuxbrew/.linuxbrew.

Most of Homebrew's bottles (binary packages) can only be used with the default prefix.
Consider uninstalling Homebrew and reinstalling into the default prefix.

This is a Tier 3 configuration:
  https://docs.brew.sh/Support-Tiers#tier-3
You can report Tier 3 unrelated issues to Homebrew/* repositories!
Read the above document before opening any issues or PRs.

Verification

  • I ran brew update twice and am still able to reproduce my issue.
  • My "brew doctor output" above says Your system is ready to brew or a definitely unrelated Tier message.
  • This issue's title and/or description do not reference a single formula e.g. brew install wget. If they do, open an issue at https://github.com/Homebrew/homebrew-core/issues/new/choose instead.

brew config output

HOMEBREW_VERSION: 5.0.7-86-ga3338c7
ORIGIN: https://mirrors.tuna.tsinghua.edu.cn/git/homebrew/brew.git
HEAD: a3338c79dba64639b01683cc33ac39f9774b8098
Last commit: 12 hours ago
Branch: main
Core tap origin: https://mirrors.tuna.tsinghua.edu.cn/git/homebrew/homebrew-core.git
Core tap HEAD: 43734178bf6cf81d11e5b218834d0b1f39135bb1
Core tap last commit: 2 hours ago
Core tap JSON: 13 Sep 17:31 UTC
HOMEBREW_PREFIX: /home/panxuehai/.linuxbrew
HOMEBREW_REPOSITORY: /home/panxuehai/.linuxbrew/Homebrew
HOMEBREW_CELLAR: /home/panxuehai/.linuxbrew/Cellar
HOMEBREW_API_DOMAIN: https://mirrors.tuna.tsinghua.edu.cn/homebrew-bottles/api
HOMEBREW_BAT: set
HOMEBREW_BAT_THEME: Monokai Extended
HOMEBREW_BOTTLE_DOMAIN: https://mirrors.tuna.tsinghua.edu.cn/homebrew-bottles
HOMEBREW_BREW_GIT_REMOTE: https://mirrors.tuna.tsinghua.edu.cn/git/homebrew/brew.git
HOMEBREW_CASK_OPTS: []
HOMEBREW_CLEANUP_MAX_AGE_DAYS: 7
HOMEBREW_CORE_GIT_REMOTE: https://mirrors.tuna.tsinghua.edu.cn/git/homebrew/homebrew-core.git
HOMEBREW_DISPLAY: localhost:11.0
HOMEBREW_DOWNLOAD_CONCURRENCY: 176
HOMEBREW_EDITOR: vim
HOMEBREW_FORBID_PACKAGES_FROM_PATHS: set
HOMEBREW_FORCE_VENDOR_RUBY: set
HOMEBREW_GITHUB_API_TOKEN: set
HOMEBREW_MAKE_JOBS: 88
HOMEBREW_NO_ANALYTICS: set
HOMEBREW_PIP_INDEX_URL: https://pypi.tuna.tsinghua.edu.cn/simple
HOMEBREW_SORBET_RUNTIME: set
all_proxy: socks5://127.0.0.1:7891
ftp_proxy: http://127.0.0.1:7890
http_proxy: http://127.0.0.1:7890
https_proxy: http://127.0.0.1:7890
Homebrew Ruby: 3.4.8 => /home/panxuehai/.linuxbrew/Homebrew/Library/Homebrew/vendor/portable-ruby/3.4.8/bin/ruby
CPU: 88-core 64-bit broadwell
Clang: 21.1.8
Git: 2.52.0 => /home/panxuehai/.linuxbrew/bin/git
Curl: 8.5.0 => /bin/curl
Kernel: Linux 6.14.0-36-generic x86_64 GNU/Linux
OS: Ubuntu 24.04.3 LTS (noble)
Host glibc: 2.39
Host libstdc++: 6.0.33
/usr/bin/gcc: 13.3.0
/usr/bin/ruby: 3.2.3
glibc: N/A
gcc@12: N/A
gcc: 15.2.0
xorg: N/A

What were you trying to do (and why)?

I'm runing brew ugprade which upgading python@3.14 and python@3.13.

python@3.14 and python@3.13 downloads the same patch:

  patch do
    url "https://raw.githubusercontent.com/Homebrew/homebrew-core/1cf441a0/Patches/python/3.13-sysconfig.diff"
    sha256 "9f2eae1d08720b06ac3d9ef1999c09388b9db39dfb52687fc261ff820bff20c3"
  end

brew upgrade automatically runs brew cleanup python@3.14 after upgrading python@3.14. However, the patch file is removed after that and then the subsequent python@3.13 upgrade fails due to missing files.

What happened (include all command output)?

$ brew upgrade
==> Feching downloads for: python@3.14, python@3.13, ... and ...
Warning: Building python@3.14 from source as the bottle needs:
- `HOMEBREW_CELLER=/home/linuxbrew/.linuxbrew/Celler` (yours is /home/panxuehai/.linuxbrew/Cellar)
- `HOMEBREW_PREFIX=/home/linuxbrew/.linuxbrew` (yours is /home/panxuehai/.linuxbrew)
==> Verifying checksum for ...
...

==> Upgrading python@3.14
  3.14.0_1 -> 3.14.2
...
==> Caveats
...
==> Summary
...
==> Running `brew cleanup python@3.14` ...
Removing: /home/panxuehai/.linuxbrew/Cellar/python@3.14/3.14.0_1... (9,198 files, 239.5MB)
Removing: /home/panxuehai/.cache/HOmebrew/python@3.14--patch--9f2eae1d08720b06ac3d9ef1999c09388b9db39dfb52687fc261ff820bff20c3.diff... (1.8KB)
==> Upgrading python@3.13
  3.13.9_1 -> 3.13.11
...
Error: An exception occurred withing a child process:
  Errno::ENOENT: No such file or directory @ rb_sysopen - f72a2b1bbc0689505bf1f874e0081c68fc125dfe72b6746325074af29fa84897--3.13-sysconfig.diff

What did you expect to happen?

Successfully upgrade python@3.13.

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

$ brew install python@3.14 python@3.13

...

$ brew upgrade  # upgrade python@3.14 python@3.13

Simluation for auto cleanup, which removes the patch file in $(brew --cache)/downloads:

$ brew fetch --build-from-source python@3.14 python@3.13
Fetching: python@3.14, python@3.13
✔︎ Formula python@3.14 (3.14.2)                                                                 Verified     30.6MB/ 30.6MB
✔︎ Resource python@3.14--flit-core                                                              Verified     53.7KB/ 53.7KB
✔︎ Resource python@3.14--pip                                                                    Verified      1.8MB/  1.8MB
✔︎ Resource python@3.14--wheel                                                                  Verified    107.5KB/107.5KB
✔︎ Patch 3.13-sysconfig.diff                                                                    Verified      1.8KB/  1.8KB
✔︎ Formula python@3.13 (3.13.11)                                                                Verified     29.4MB/ 29.4MB

$ ls "$(brew --cache)/downloads"
1b008eaca53d469b6110de5cddda0574c58ebcd4465c56c398c92abb3957ffc5--Python-3.13.11.tgz
1e1011b3ce5323399f018a4fcdf9c860d74244bf7be9d30ad2ae686f6a37f57a--wheel-0.45.1.tar.gz
2ef2f28d5350a4addbfdd0b311c016b6cab946dae59a20d91a6475ff529ede74--flit_core-3.12.0.tar.gz
456348759b7490f3822ecf2e43efc8cede32952ab6c7d9bf79812587c97164ae--Python-3.14.2.tgz
e2c0c18ff7954d85c54e25dc323bfca3cbda5548a905ba8fda24e81f1b0ae98d--pip-25.3.tar.gz
f72a2b1bbc0689505bf1f874e0081c68fc125dfe72b6746325074af29fa84897--3.13-sysconfig.diff

$ brew cleanup python@3.14
Removing: /home/panxuehai/.cache/Homebrew/python@3.14--patch--9f2eae1d08720b06ac3d9ef1999c09388b9db39dfb52687fc261ff820bff20c3.diff... (1.8KB)
==> This operation has freed approximately 1.8KB of disk space.

$ ls "$(brew --cache)/downloads"
1b008eaca53d469b6110de5cddda0574c58ebcd4465c56c398c92abb3957ffc5--Python-3.13.11.tgz
1e1011b3ce5323399f018a4fcdf9c860d74244bf7be9d30ad2ae686f6a37f57a--wheel-0.45.1.tar.gz
2ef2f28d5350a4addbfdd0b311c016b6cab946dae59a20d91a6475ff529ede74--flit_core-3.12.0.tar.gz
456348759b7490f3822ecf2e43efc8cede32952ab6c7d9bf79812587c97164ae--Python-3.14.2.tgz
e2c0c18ff7954d85c54e25dc323bfca3cbda5548a905ba8fda24e81f1b0ae98d--pip-25.3.tar.gz

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