brew update: The following untracked working tree files would be overwritten by merge:

Question

I tried to run brew update and I get an error about my local changes would be lost if I merged. I tried committing my local changes (don't remember making any, but it's been awhile), and that made things worse.

Here's the output:

MBP:Library User$ sudo brew update error: The following untracked working tree files would be overwritten by merge:     Library/Aliases/fastcgi     Library/Aliases/htop     Library/Aliases/nodejs     Library/Aliases/ocio     Library/Aliases/oiio     Library/Aliases/pgrep     Library/Aliases/pkill     Library/Contributions/cmds/brew-beer.rb     Library/Contributions/cmds/brew-dirty.rb     Library/Contributions/cmds/brew-graph     Library/Contributions/cmds/brew-grep     Library/Contributions/cmds/brew-leaves.rb     Library/Contributions/cmds/brew-linkapps.rb     Library/Contributions/cmds/brew-man     Library/Contributions/cmds/brew-mirror-check.rb     Library/Contributions/cmds/brew-missing.rb     Library/Contributions/cmds/brew-pull.rb     Library/Contributions/cmds/brew-readall.rb     Library/Contributions/cmds/brew-server     Library/Contributions/cmds/brew-services.rb     Library/Contributions/cmds/brew-switch.rb     Library/Contributions/cmds/brew-test-bot.commit.html.erb     Library/Contributions/cmds/brew-test-bot.css     Library/Contributions/cmds/brew-test-bot.index.html.erb     Library/Contributions/cmds/brew-test-bot.rb     Library/Contributions/cmds/brew-tests.rb     Library/Contributions/cmds/brew-unpack.rb     Library/Contributions/cmds/brew-which.rb     Library/Contributions/install_homebrew.rb     Library/Formula/abcl.rb     Library/Formula/abyss.rb     Library/Formula/akka.rb     Library/Formula/apollo.rb     Library/Formula/appledoc.rb     Library/Formula/arangodb.rb     Library/Formula/autoconf.rb     Library/Formula/automake.rb     Library/Formula/avidemux.rb     Library/Formula/bind.rb     Library/Formula/bsdconv.rb     Library/Formula/bsdmake.rb     Library/Formula/camellia.rb     Library/Formula/cbmbasic.rb     Library/Formula/cdo.rb     Library/Formula/checkstyle.rb     Library/Formula/cifer.rb     Library/Formula/clhep.rb     Library/Formula/collada-dom.rb     Library/Formula/crash.rb     Library/Formula/crossroads.rb     Library/Formula/css-crush.rb     Library/Formula/curlftpfs.rb     Library/Formula/dart.rb     Library/Formula/dasm.rb     Library/Formula/dfc.rb     Library/Formula/di.rb     Library/Formula/dsniff.rb     Library/Formula/dupx.rb     Library/Formula/dwatch.rb     Library/Formula/eprover.rb     Library/Formula/ext2fuse.rb     Library/Formula/ezlupdate.rb     Library/Formula/f3.rb     Library/Formula/fastx_toolkit.rb     Library/Formula/fceux.rb     Library/Formula/findbugs.rb     Library/Formula/freerdp.rb     Library/Formula/funcoeszz.rb     Library/Formula/fwknop.rb     Library/Formula/gabedit.rb     Library/Formula/gbdfed.rb     Library/Formula/gconf.rb     Library/Formula/git-encrypt.rb     Library/Formula/glm.rb     Library/Formula/gmap-gsnap.rb     Library/Formula/gnu-arch.rb     Library/Formula/gnunet.rb     Library/Formula/gobby.rb     Library/Formula/gptfdisk.rb     Library/Formula/griffon.rb     Library/Formula/grok.rb     Library/Formula/gtk-chtheme.rb     Library/Formula/gtkglextmm.rb     Library/Formula/gtmess.rb     Library/Formula/hg-flow.rb     Library/Formula/hqx.rb     Library/Formula/htop-osx.rb     Library/Formula/htpdate.rb     Library/Formula/imap-uw.rb     Library/Formula/iozone.rb     Library/Formula/ipbt.rb     Library/Formula/ipe.rb     Library/Formula/ispc.rb     Library/Formula/ispell.rb     Library/Formula/jigdo.rb     Library/Formula/jing.rb     Library/Formula/jless.rb     Library/Formula/jpeginfo.rb     Library/Formula/konoha.rb     Library/Formula/legit.rb     Library/Formula/libcouchbase.rb     Library/Formula/libcuefile.rb     Library/Formula/libextractor.rb     Library/Formula/libglademm.rb     Library/Formula/libgtextutils.rb     Library/Formula/libinfinity.rb     Library/Formula/libkate.rb     Library/Formula/libqalculate.rb     Library/Formula/libqglviewer.rb     Library/Formula/libreplaygain.rb     Library/Formula/libtool.rb     Library/Formula/libvbucket.rb     Library/Formula/libvo-aacenc.rb     Library/Formula/libxmi.rb     Library/Formula/lifelines.rb     Library/Formula/makeicns.rb     Library/Formula/mathgl.rb     Library/Formula/meld.rb     Library/Formula/mesalib-glw.rb     Library/Formula/minisat.rb     Library/Formula/minuit2.rb     Library/Formula/mobile-shell.rb     Library/Formula/movgrab.rb     Library/Formula/mp3cat.rb     Library/Formula/mpich2.rb     Library/Formula/mrfast.rb     Library/Formula/musepack.rb     Library/Formula/ndiff.rb     Library/Formula/net6.rb     Library/Formula/nrpe.rb     Library/Formula/nuttcp.rb     Library/Formula/oath-toolkit. Updating aa07533..3f070ef Aborting Error: Failed while executing git pull  origin refs/heads/master:refs/remotes/origin/master 

Answer 1

Don't forget to fetch the origin:

cd /usr/local/Homebrew git fetch origin git reset --hard origin/master 

What happens is that you are trying to update brew, but brew itself is either not up to date (likely), there is a permissions change via some OS update (also likely), or brew is slightly corrupt (unlikely). Since brew itself is a git repo, you have to update or reset brew to the master branch version. brew [by default] is located in the /usr/local/Homebrew folder, so you

1. Go to that folder [first command] which also should update permissions (if not see below)
2. Fetch the origin [second command] which means to update your LOCAL version of the remote branch of brew
3. Hard reset [3rd command] based on the REMOTE master branch (which also uses your current permissions).

You can also chown the first command if you are in a non sudo or admin profile

sudo chown -R `whoami` /usr/local/Homebrew cd /usr/local/Homebrew git reset --hard origin/master 

To understand git reset, take a look at this article.

Answer 2

I had a similar issue a couple weeks ago trying to update an old homebrew install. Doing this:

git reset --hard origin/master 

in /usr/local fixed it for me.

It seems like other folks have had this issue too. Have you looked over any of the proposed workarounds here?