fatal: It seems that there is already a rebase-merge directory

[laiyewfai]

I encountered the following error. I can use "brew update-reset" to bypass the issue for a while. After a while, the issue will come back. Any idea why and how to resolve it? Thanks.

---

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.

[SMillerDev]

What does brew doctor say?

[laiyewfai]

Quite a lot of warnings from "brew doctor", but not sure which one is related to the problem above.

---

Warning: Some installed formulae are deprecated or disabled.
You should find replacements for the following formulae:
  ilmbase

Warning: You have installed Bitdefender. The "Traffic Scan" option interferes with
Homebrew's ability to download packages. See:
  https://github.com/Homebrew/brew/issues/5558

Warning: "config" scripts exist outside your system or Homebrew directories.
`./configure` scripts often look for *-config scripts to determine if
software packages are installed, and which additional flags to use when
compiling and linking.

Having additional scripts in your path can confuse software installed via
Homebrew if the config script overrides a system or Homebrew-provided
script of the same name. We found the following "config" scripts:
  /usr/local/Caskroom/miniconda/base/envs/python_threeten/bin/icu-config
  /usr/local/Caskroom/miniconda/base/envs/python_threeten/bin/krb5-config
  /usr/local/Caskroom/miniconda/base/envs/python_threeten/bin/libpng16-config
  /usr/local/Caskroom/miniconda/base/envs/python_threeten/bin/libpng-config
  /usr/local/Caskroom/miniconda/base/envs/python_threeten/bin/python3.10-config
  /usr/local/Caskroom/miniconda/base/envs/python_threeten/bin/xml2-config
  /usr/local/Caskroom/miniconda/base/envs/python_threeten/bin/python3-config
  /usr/local/Caskroom/miniconda/base/envs/python_threeten/bin/ncursesw6-config
  /usr/local/Caskroom/miniconda/base/envs/python_threeten/bin/pcre-config
  /usr/local/Caskroom/miniconda/base/envs/python_threeten/bin/nspr-config
  /usr/local/Caskroom/miniconda/base/envs/python_threeten/bin/nss-config
  /Library/Frameworks/Python.framework/Versions/3.10/bin/python3.10-config
  /Library/Frameworks/Python.framework/Versions/3.10/bin/python3-config

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/libtcl8.6.dylib
  /usr/local/lib/libtk8.6.dylib

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/fakemysql.h
  /usr/local/include/fakepq.h
  /usr/local/include/fakesql.h
  /usr/local/include/itcl.h
  /usr/local/include/itcl2TclOO.h
  /usr/local/include/itclDecls.h
  /usr/local/include/itclInt.h
  /usr/local/include/itclIntDecls.h
  /usr/local/include/itclMigrate2TclCore.h
  /usr/local/include/itclTclIntStubsFcn.h
  /usr/local/include/mysqlStubs.h
  /usr/local/include/odbcStubs.h
  /usr/local/include/pqStubs.h
  /usr/local/include/tcl.h
  /usr/local/include/tclDecls.h
  /usr/local/include/tclOO.h
  /usr/local/include/tclOODecls.h
  /usr/local/include/tclPlatDecls.h
  /usr/local/include/tclThread.h
  /usr/local/include/tclTomMath.h
  /usr/local/include/tclTomMathDecls.h
  /usr/local/include/tdbc.h
  /usr/local/include/tdbcDecls.h
  /usr/local/include/tdbcInt.h
  /usr/local/include/tk.h
  /usr/local/include/tkDecls.h
  /usr/local/include/tkPlatDecls.h

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/tcl.pc
  /usr/local/lib/pkgconfig/tk.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/libtclstub8.6.a
  /usr/local/lib/libtkstub8.6.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:
  hadoop

[SMillerDev]

Try git -C $(brew --prefix) status, git -C $(brew --prefix homebrew/core) status and git -C $(brew --prefix homebrew/cask) status

[laiyewfai]

❯ git -C $(brew --prefix) status
fatal: not a git repository (or any of the parent directories): .git
❯ git -C $(brew --prefix homebrew/core) status
Error: No available formula with the name "homebrew/core".
fatal: cannot change to 'status': No such file or directory
❯ git -C $(brew --prefix homebrew/cask) status
Error: No available formula with the name "homebrew/cask". Did you mean homebank?
fatal: cannot change to 'status': No such file or directory

[laiyewfai]

I managed to solve this issue by tracking the sub-directory using the command:

find /usr/local/Homebrew -name "rebase-merge"

It returns the following:

/usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/.git/rebase-merge

There are a few files under the sub-directory which are created on 2 May. This seems to correspond to the time when I started encountering the issue last week. I deleted all the files, and also the sub-directory.

Now "brew update" and "brew upgrade" are working fine now.

[noahhhi]

For Apple Sillicon devices it should be:
find /opt/Homebrew -name "rebase-merge"

[sei-dwtompkins]

I had this happen at the root level, not with a specific "tap". I was able to fix by:

cd /opt/homebrew &&
git rebase --abort &&
brew update