Unable to update formulas due to Homebrew detecting a non-existent untapped formula

[Kreeblah]

Output of brew config

HOMEBREW_VERSION: 4.6.3-56-gac160c7
ORIGIN: https://github.com/Homebrew/brew
HEAD: ac160c7f88640c287599d388d6924fa039becbe9
Last commit: 60 minutes ago
Branch: main
Core tap HEAD: 6459e6e64fcb1296eaf2bac13cda045fc409b4a4
Core tap last commit: 6 minutes ago
Core tap JSON: 25 Jul 05:21 UTC
Core cask tap HEAD: 58d9945d956c4ad0dab7c07ee4dda670a02c9af8
Core cask tap last commit: 23 minutes ago
Core cask tap JSON: 25 Jul 05:21 UTC
HOMEBREW_PREFIX: /opt/homebrew
HOMEBREW_CASK_OPTS: []
HOMEBREW_DISPLAY: /private/tmp/com.apple.launchd.n20kwXzxQV/org.xquartz:0
HOMEBREW_FORBID_PACKAGES_FROM_PATHS: set
HOMEBREW_GITHUB_API_TOKEN: set
HOMEBREW_MAKE_JOBS: 10
HOMEBREW_NO_INSTALL_FROM_API: set
HOMEBREW_NO_VERIFY_ATTESTATIONS: set
HOMEBREW_SORBET_RUNTIME: set
Homebrew Ruby: 3.4.5 => /opt/homebrew/Library/Homebrew/vendor/portable-ruby/3.4.5/bin/ruby
CPU: deca-core 64-bit arm_firestorm_icestorm
Clang: 17.0.0 build 1700
Git: 2.50.1 => /opt/homebrew/bin/git
Curl: 8.7.1 => /usr/bin/curl
macOS: 15.6-arm64
CLT: 16.4.0.0.1.1747106510
Xcode: 16.4
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:
  86box
  gstreamer-development
  gstreamer-runtime
  mkvtoolnix-app
  openrct2
  schism-tracker
  xemu
  xld

Warning: Some installed formulae are deprecated or disabled.
You should find replacements for the following formulae:
  icu4c@76
  libassuan@2
  six

Warning: You have the following deprecated, official taps tapped:
  Homebrew/homebrew-bundle
Untap them with `brew untap`.

Warning: The following casks have the same name as core casks:
  marsanne/cask/cork
Their taps are in use, so you must use these full names throughout Homebrew.

Warning: The following formulae have the same name as core formulae:
  justinschuldt/virt-manager/libvirt-glib
  justinschuldt/virt-manager/spice-gtk
  justinschuldt/virt-manager/spice-protocol
  justinschuldt/virt-manager/usbredir
  justinschuldt/virt-manager/virt-manager
  kreeblah/sdl-tap/sdl_gfx
  zegervdv/zathura/girara
Their taps are in use, so you must use these full names throughout Homebrew.

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

Unexpected dylibs:
  /usr/local/lib/libCAPSImage.dylib
  /usr/local/lib/libMoltenVK.dylib
  /usr/local/lib/libMuseSamplerCoreLib.dylib
  /usr/local/lib/libSPIRV-Tools-shared.dylib
  /usr/local/lib/libVkLayer_api_dump.dylib
  /usr/local/lib/libVkLayer_device_simulation.dylib
  /usr/local/lib/libVkLayer_khronos_profiles.dylib
  /usr/local/lib/libVkLayer_khronos_synchronization2.dylib
  /usr/local/lib/libVkLayer_khronos_validation.dylib
  /usr/local/lib/libdxcompiler.3.7.dylib
  /usr/local/lib/libshaderc_shared.1.dylib
  /usr/local/lib/libspirv-cross-c-shared.0.48.0.dylib
  /usr/local/lib/libvulkan.1.3.204.dylib

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

Unexpected '.pc' files:
  /usr/local/lib/pkgconfig/SPIRV-Tools-shared.pc
  /usr/local/lib/pkgconfig/SPIRV-Tools.pc
  /usr/local/lib/pkgconfig/shaderc.pc
  /usr/local/lib/pkgconfig/spirv-cross-c-shared.pc
  /usr/local/lib/pkgconfig/vulkan.pc

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

Unexpected static libraries:
  /usr/local/lib/libGenericCodeGen.a
  /usr/local/lib/libHLSL.a
  /usr/local/lib/libMachineIndependent.a
  /usr/local/lib/libOGLCompiler.a
  /usr/local/lib/libOSDependent.a
  /usr/local/lib/libSPIRV-Tools-link.a
  /usr/local/lib/libSPIRV-Tools-lint.a
  /usr/local/lib/libSPIRV-Tools-opt.a
  /usr/local/lib/libSPIRV-Tools-reduce.a
  /usr/local/lib/libSPIRV-Tools.a
  /usr/local/lib/libSPIRV.a
  /usr/local/lib/libSPVRemapper.a
  /usr/local/lib/libglslang-default-resource-limits.a
  /usr/local/lib/libglslang.a
  /usr/local/lib/libshaderc.a
  /usr/local/lib/libshaderc_combined.a
  /usr/local/lib/libshaderc_util.a
  /usr/local/lib/libspirv-cross-c.a
  /usr/local/lib/libspirv-cross-core.a
  /usr/local/lib/libspirv-cross-cpp.a
  /usr/local/lib/libspirv-cross-glsl.a
  /usr/local/lib/libspirv-cross-hlsl.a
  /usr/local/lib/libspirv-cross-msl.a
  /usr/local/lib/libspirv-cross-reflect.a
  /usr/local/lib/libspirv-cross-util.a

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:
  node
Error: Rejecting formula at /Users/myuser/z3 because it's not in a tap.
       Homebrew requires formulae to be in a tap.

To create a tap, run e.g.
  brew tap-new <user|org>/<repository>
To create a formula in a tap run e.g.
  brew create <url> --tap=<user|org>/<repository>

Description of issue

That bit at the end of brew doctor is what I'm having trouble with. That command was run in my user's home directory.

This error only happens in some directories, but when it does, it happens with that, with brew upgrade, brew install, etc., and blocks operations. Problem is, there's no formula there. For instance, in that z3 subdirectory, I have this:

myuser@myhost ~
fsh " ls -al z3
total 5528
drwxr-xr-x    6 myuser  staff      192 Sep 17  2024 ./
drwxr-xr--@ 355 myuser  staff    11360 Aug 13 11:27 ../
drwxr-xr-x    3 myuser  staff       96 Sep 17  2024 saves/
-rwxr-xr-x    1 myuser  staff  2136936 Apr 10  2024 zelda3*
-rw-r--r--    1 myuser  staff   683888 Apr 10  2024 zelda3_assets.dat
-rw-r--r--@   1 myuser  staff     6361 Sep 17  2024 zelda3.ini

So, when this happens, it's grabbing a seemingly-random (though consistent between commands) subdirectory, claiming there's an untapped formula in there, and erroring out.

What might be causing this?

[daeho-ro]

What is the output of brew tap?

[Kreeblah]

myuser@myhost ~ 
fsh " brew tap
akeru-inc/tap
apple/apple
draftbrew/tap
enigmaticdb/super-secret-tap
he3-app/he3
homebrew/bundle
homebrew/cask
homebrew/core
jorgelbg/tap
justinschuldt/virt-manager
kegworks-app/kegworks
kreeblah/16bo-tap
kreeblah/blissbox-updator-tap
kreeblah/flexigif-tap
kreeblah/gnupgosx-tap
kreeblah/kryoflux-tap
kreeblah/pololu-tap
kreeblah/redumper-tap
kreeblah/reflex-adapt-tap
kreeblah/sctools-tap
kreeblah/sdl-tap
kreeblah/smpq-tap
kreeblah/umskt-tap
kreeblah/unrar-tap
marsanne/cask
minacle/chntpw
nicowald/subtlesoft
osx-cross/avr
paninihouse/brewer-cmd
teamookla/speedtest
vcmi/vcmi
zegervdv/zathura

[carlocab]

I take it this is the error you're referring to:

Error: Rejecting formula at /Users/myuser/z3 because it's not in a tap.
       Homebrew requires formulae to be in a tap.

Can you identify which commands result in this error? Does the error always happen for those commands, or does it happen only when your current directory is ~? What happens if you navigate to other directories, or temporarily rename ~/z3?

[Kreeblah]

It happens when I'm in some other directories, and in those cases, it complains about a subdirectory one level below the one I'm in, just like with this.

It doesn't seem to happen if I rename ~/z3 to ~/z4, though, which is interesting. It happens again if I rename it back to ~/z3.

For specific commands, I've observed it with brew doctor, brew upgrade (when there's a formula to upgrade), and brew install.

[Kreeblah]

And, yes, that's the error.

[Kreeblah]

This was resolved with Homebrew/brew#20457