You have uncommitted modifications to Homebrew/brew. If this is a surprise to you, then you should stash these modifications. Stashing returns Homebrew to a pristine state but can be undone should you later need to do so for some reason. cd /opt/homebrew && git stash -u && git clean -d -f Uncommitted files: D Library/Homebrew/vendor/bundle/ruby/3.3.0/gems/benchmark-0.4.0/lib/benchmark.rb