Homebrew error during brew update run

[Justin24506]

Output of brew config

HOMEBREW_VERSION: 5.1.15-40-g8cf7601
ORIGIN: https://github.com/Homebrew/brew
HEAD: 8cf7601ec0b783ab1212143cadb50c3af929826c
Last commit: 4 hours ago
Branch: main
Core tap HEAD: 37a751947b9a27976f3541985a57da644dc08feb
Core tap last commit: 21 minutes ago
Core cask tap HEAD: dcdc5f99338da635f8df4d07e626928a0a5b723c
Core cask tap last commit: 70 minutes ago
HOMEBREW_PREFIX: /opt/homebrew
HOMEBREW_CASK_OPTS: []
HOMEBREW_DOWNLOAD_CONCURRENCY: 20
HOMEBREW_EDITOR: nvim
HOMEBREW_FORBID_PACKAGES_FROM_PATHS: set
HOMEBREW_MAKE_JOBS: 10
HOMEBREW_REQUIRE_TAP_TRUST: set
HOMEBREW_USE_INTERNAL_API: set
Homebrew Ruby: 4.0.5 => /opt/homebrew/Library/Homebrew/vendor/portable-ruby/4.0.5_1/bin/ruby
CPU: deca-core 64-bit arm_firestorm_icestorm
Clang: 21.0.0 build 2100
Git: 2.54.0 => /opt/homebrew/bin/git
Curl: 8.7.1 => /usr/bin/curl
macOS: 26.5-arm64
CLT: 26.5.0.0.1777544298
Xcode: 26.5
Metal Toolchain: N/A
Rosetta 2: false

Output of 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: Some installed casks are deprecated or disabled.
You should find replacements for the following casks:
  aegisub
  cakebrewjs
  gittyup
  headlamp
  koodo-reader
  logisim-evolution
  mark-text

Warning: Some installed formulae are deprecated or disabled.
You should find replacements for the following formulae:
  termshark
  vapoursynth-imwri

Warning: Unbrewed header files were found in /usr/local/include.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae and may need to be deleted.

Unexpected header files:
  /usr/local/include/fetch.h
  /usr/local/include/node/*

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:
  superset
  gascity

Warning: Some taps are not on the default git origin branch and may not receive
updates. If this is a surprise to you, check out the default branch with:
  git -C $(brew --repo duongductrong/snapzy) checkout master

Description of issue

When I run brew update, I see an error message along with it, like this:

brew update
==> Updating Homebrew...
Already up-to-date.
Error: can't modify frozen Array: []

I ran brew update because:

brew upgrade --greedy-auto-updates                                                                  ─╯
==> Auto-updating Homebrew...
Adjust how often this is run with `$HOMEBREW_AUTO_UPDATE_SECS` or disable with
`$HOMEBREW_NO_AUTO_UPDATE=1`. Hide these hints with `$HOMEBREW_NO_ENV_HINTS=1` (see `man brew`).
error: could not apply ddfc099... fix: Implement database recovery flow and enhance error handling for database operations (#223)
Could not apply ddfc099... # fix: Implement database recovery flow and enhance error handling for database operations (#223)
==> Auto-updated Homebrew!
Updated 2 taps (anomalyco/tap and duongductrong/snapzy).

You have 7 outdated formulae and 6 outdated casks installed.
Warning: Skipping shichizip/tap because it is not trusted. Run `brew trust shichizip/tap` to trust it.
Error: Cask 'flux-markdown-official' definition is invalid: Token 'flux-markdown' in header line does not match the file name.

I cancelled this run by Ctrl + c, which is why the output is cut off.

Can someone please help me out? Thanks

[botantony]

Can you run brew update with --verbose and --debug flags?

[Justin24506]

Yep, here you go. There were a lot of lines, so I made a file: update.txt.

[Justin24506]

But, now brew update runs without any errors,

brew update                                                                                                                                                                                                                                          
==> Updating Homebrew...
Already up-to-date.

and so does this:

brew outdated --greedy-auto-updates --verbose                                                                                                                                                                                                        
fastfetch (2.64.1) < 2.64.2

i'm not sure what changed, though.

[Extra-Citron-7630]

I am getting the same error

>> brew update
==> Updating Homebrew...
Already up-to-date.
Error: can't modify frozen Array: []

[Extra-Citron-7630]

brew-update1.log

Here is the log file

[Justin24506]

I am getting the error again, I need to run brew update-test every single time for it to fix

Same here. Running

brew update-reset

Only fixes the problem temporarily.

[Extra-Citron-7630]

Sorry to hear you are having the problem again.

[botantony]

This error seems to be caused by buo/homebrew-cask-upgrade tap. Can you run brew untap buo/cask-upgrade and run brew update again?

Related links:
buo/homebrew-cask-upgrade#308
buo/homebrew-cask-upgrade#307

[Extra-Citron-7630]

This error seems to be caused by buo/homebrew-cask-upgrade tap. Can you run brew untap buo/cask-upgrade and run brew update again?

Related links: buo/homebrew-cask-upgrade#308 buo/homebrew-cask-upgrade#307

This worked, does this mean this tool can no longer be used?

[Justin24506]

This worked, does this mean this tool can no longer be used?

@Extra-Citron-7630, I've since run brew tap buo/cask-upgrade and don't see the issue atleast for now.
If running this still brings up the issue for you, you could either choose to ignore it (I don't think it does anything other than display a warning, atleast from my limited understanding) or wait until buo/homebrew-cask-upgrade#308 and/or buo/homebrew-cask-upgrade#307 have been closed/merged.

[Justin24506]

@botantony

brew untap buo/cask-upgrade                                                     
Untapping buo/cask-upgrade...
Untapped 2 commands (113 files, 465.8KB).

brew update                                                                     
==> Updating Homebrew...
fatal: It seems that there is already a rebase-merge directory, and
I wonder if you are in the middle of another rebase.  If that is the
case, please try
        git rebase (--continue | --abort | --skip)
If that is not the case, please
        rm -fr ".git/rebase-merge"
and run me again.  I am stopping in case you still have something
valuable there.

Already up-to-date.

This is a new one, and came up when I ran brew update once more, before running brew untap buo/cask-upgrade, to check if the problem still existed.

[Justin24506]

Could this be because I ran brew tap --force homebrew/cask a while back, about 3weeks prior, to contribute to Homebrew/homebrew-cask.

[Justin24506]

So, I have some "findings":

cd /opt/homebrew/Library/Taps/duongductrong/homebrew-snapzy && git status                                                                      
On branch master
Your branch is behind 'origin/master' by 4 commits, and can be fast-forwarded.
  (use "git pull" to update your local branch)

Last command done (1 command done):
   pick ddfc099 # fix: Implement database recovery flow and enhance error handling for database operations (#223)
No commands remaining.
You are currently editing a commit while rebasing branch 'master' on 'fc0a303'.
  (use "git commit --amend" to amend the current commit)
  (use "git rebase --continue" once you are satisfied with your changes)

nothing to commit, working tree clean

This tap (duongductrong/snapzy) was causing the previous

brew upgrade --greedy-auto-updates                                                                  ─╯
==> Auto-updating Homebrew...
Adjust how often this is run with `$HOMEBREW_AUTO_UPDATE_SECS` or disable with
`$HOMEBREW_NO_AUTO_UPDATE=1`. Hide these hints with `$HOMEBREW_NO_ENV_HINTS=1` (see `man brew`).
error: could not apply ddfc099... fix: Implement database recovery flow and enhance error handling for database operations (#223)
Could not apply ddfc099... # fix: Implement database recovery flow and enhance error handling for database operations (#223)
==> Auto-updated Homebrew!
Updated 2 taps (anomalyco/tap and duongductrong/snapzy).

You have 7 outdated formulae and 6 outdated casks installed.
Warning: Skipping shichizip/tap because it is not trusted. Run `brew trust shichizip/tap` to trust it.
Error: Cask 'flux-markdown-official' definition is invalid: Token 'flux-markdown' in header line does not match the file name.

and probably also

brew update                                                                     
==> Updating Homebrew...
fatal: It seems that there is already a rebase-merge directory, and
I wonder if you are in the middle of another rebase.  If that is the
case, please try
        git rebase (--continue | --abort | --skip)
If that is not the case, please
        rm -fr ".git/rebase-merge"
and run me again.  I am stopping in case you still have something
valuable there.

Already up-to-date.