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• ran brew update and can still reproduce the problem?
• ran brew doctor, fixed all issues and can still reproduce the problem?
• ran brew config and brew doctor and included their output with your issue?

What you were trying to do (and why)

This error is occurred when I was dealing with this issue:
Homebrew/homebrew-core#54260

What happened (include command output)

It is upgraded to the same version.

And the error message is shown up:
Error: File exists @ dir_s_mkdir - /usr/local/opt/bison/.brew

==> Upgrading 1 outdated package:
bison 3.5.4 -> 3.5.4
==> Upgrading bison 3.5.4 -> 3.5.4
==> Downloading https://ftp.gnu.org/gnu/bison/bison-3.5.4.tar.xz
Already downloaded: /Users/mt/Library/Caches/Homebrew/downloads/0cd0b972eeb61898d808838afbf7d7142f74bab484acb305448d24e60dd18dce--bison-3.5.4.tar.xz
==> ./configure --prefix=/usr/local/Cellar/bison/3.5.4
==> make install
Error: File exists @ dir_s_mkdir - /usr/local/opt/bison/.brew

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

Reproduce steps:

1. cd /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula
2. brew remove bison to ensure you don't have bison installed.
3. git checkout 348a8a58f2bc665f5c75be6febefc23f13605bc4 bison.rb for bison version 3.5.4
4. HOMEBREW_NO_AUTO_UPDATE=1 brew install bison to install the specified version of bison.
5. git checkout 0058caaa5159082c9ec689983925dd79c5b21639 bison.rb for bison version 3.5.4 (downgraded)
6. HOMEBREW_NO_AUTO_UPDATE=1 brew upgrade bison to upgrade bison to the downgraded one.

cd /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula
brew remove bison
git checkout 348a8a58f2bc665f5c75be6febefc23f13605bc4 bison.rb
HOMEBREW_NO_AUTO_UPDATE=1  brew install bison
git checkout 0058caaa5159082c9ec689983925dd79c5b21639 bison.rb
HOMEBREW_NO_AUTO_UPDATE=1 brew upgrade bison

Cleaning up:

1. cd /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula
2. git reset --hard HEAD to switch to the latest Formula list and ignore changes.
3. brew remove bison && brew install bison to reinstall latest bison

cd /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula
git reset --hard HEAD
brew remove bison && brew install bison