Brew update failed: untracked working tree files w

Question

Trying to update Homebrew with brew update I got the following error

error: The following untracked working tree files would be overwrittenby merge:     
 Library/Formula/argp-standalone.rb
 Library/Formula/cocot.rb 
Please move or remove them before you can merge. 
Aborting 
Updating e088818..5909e2c 
Error: Failed while executing git pull  origin refs/heads/master:refs/remotes/origin/master

I found a blog post by someone who experienced a similar problem after having installed Mountain Lion (which I did this week too). He explains how he removed the files referred to in the error message

I removed these files:
$ cd $(brew --prefix)
$ rm cocot.rb
However, removing these files didn't help with the brew update. Instead I had to manually update brew through git:
$ cd $(brew --prefix)
$ git fetch origin
$ git reset --hard origin/master
$ brew update
Already up-to-date.

Assuming those instructions are correct (which I maybe shouldn't assume), I tried to follow these instructions and do

    $ cd $(brew --prefix)
    $ rm cocot.rb

However, it said 'file doesn't exist' when I tried to rm cocot.rb

One thing I'm not sure about is the cd $(brew --prefix) Are those the exact words I type or do I have to replace prefix with something? the cd was successful, so I'm assuming it was correct -- it moved me into /usr/local, but there was no file to remove. Contents of /usr/local are

Cellar              clamXav             git             mysql               var Library             doc             heroku              mysql-5.5.15-osx10.6-x86_64 README.md           etc             include             rvm bin             foreman             lib             share

At any rate, do you know how I can fix the 'brew update'

Update: After removing the files according to favoretti's instructions and trying chown -R <your_username> $(brew --prefix)/.git, I got the following error running brew update

error: The following untracked working tree files would be overwritten by merge:
    Library/Aliases/gperftools
    Library/Aliases/hashdeep
    Library/Aliases/htop
    Library/Aliases/nodejs
    Library/Aliases/ocio
    Library/Aliases/oiio
    Library/Aliases/pgrep
    Library/Aliases/pkill
    Library/Aliases/qt4
    Library/Aliases/twolame
    Library/Aliases/wxwidgets
    Library/Contributions/cmds/brew-aspell-dictionaries
    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-ls-taps.rb
    Library/Contributions/cmds/brew-man
    Library/Contributions/cmds/brew-md5-to-sha1
    Library/Contributions/cmds/brew-mirror-check.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.rb
    Library/Contributions/cmds/brew-tests.rb
    Library/Contributions/cmds/brew-unpack.rb
    Library/Contributions/cmds/brew-which.rb
    Library/Contributions/cmds/git
    Library/Contributions/cmds/svn
    Library/ENV/4.3/apr-1-config
    Library/ENV/4.3/bsdmake
    Library/ENV/4.3/c++
    Library/ENV/4.3/c89
    Library/ENV/4.3/c99
    Library/ENV/4.3/cc
    Library/ENV/4.3/clang
    Library/ENV/4.3/clang++
    Library/ENV/4.3/cpp
    Library/ENV/4.3/g++
    Library/ENV/4.3/gcc
    Library/ENV/4.3/git
    Library/ENV/4.3/i686-apple-darwin11-llvm-g++-4.2
    Library/ENV/4.3/i686-apple-darwin11-llvm-gcc-4.2
    Library/ENV/4.3/ld
    Library/ENV/4.3/llvm-g++
    Library/ENV/4.3/llvm-g++-4.2
    Library/ENV/4.3/llvm-gcc
    Library/ENV/4.3/llvm-gcc-4.2
    Library/ENV/4.3/make
    Library/ENV/4.3/mig
    Library/ENV/4.3/sed
    Library/ENV/4.3/svn
    Library/ENV/4.3/xcrun
    Library/ENV/libsuperenv.rb
    Library/ENV/pkgconfig/leopard/libcrypto.pc
    Library/ENV/pkgconfig/leopard/libcurl.pc
    Library/ENV/pkgconfig/mountain_lion/libcurl.pc
    Library/ENV/pkgconfig/mountain_lion/libexslt.pc
    Library/ENV/pkgconfig/mountain_lion/libxml-2.0.pc
    Library/ENV/pkgconfig/mountain_lion/libxslt.pc
    Library/Formula/abcl.rb
    Library/Formula/abcmidi.rb
    Library/Formula/aiccu.rb
    Library/Formula/akka.rb
    Library/Formula/alac.rb
    Library/Formula/alure.rb
    Library/Formula/appledoc.rb
    Library/Formula/arangodb.rb
    Library/Formula/argp-standalone.rb
    Library/Formula/argtable.rb
    Library/Formula/autopano-sift-c.rb
    Library/Formula/avian.rb
    Library/Formula/avidemux.rb
    Library/Formula/avro-cpp.rb
    Library/Formula/aws-cloudsearch.rb
    Library/Formula/aws-sns-cli.rb
    Library/Formula/backupninja.rb
    Library/Formula/bact.rb
    Library/Formula/bam.rb
    Library/Formula/basex.rb
    Library/Formula/berkeley-db4.rb
    Library/Formula/bind.rb
    Library/Formula/blazeblogger.rb
    Library/Formula/bochs.rb
    Library/Formula/boost149.rb
    Library/Formula/bsdconv.rb
    Library/Formula/bsdmake.rb
    Library/Formula/buildapp.rb
    Library/Formula/bup.rb
    Library/Formula/byacc.rb
    Library/Formula/cadubi.rb
    Library/Formula/camellia.rb
    Library/Formula/casperjs.rb
    Library/Formula/ccextractor.rb
    Library/Formula/cconv.rb
    Library/Formula/cdo.rb
    Library/Formula/cdpr.rb
    Library/Formula/cgvg.rb
    Library/Formula/checkstyle.rb
    Library/Formula/chordii.rb
    Library/Formula/chruby.rb
    Library/Formula/cifer.rb
    Library/Formula/clhep.rb
    Library/Formula/cntlm.rb
    Library/Formula/cocot.rb
    Library/Formula/cogl.rb
    Library/Formula/collada-dom.rb
    Library/Formula/crash.rb
    Library/Formula/crossroads.rb
    Library/Formula/crosstool-ng.rb
    Library/Formula/css-crush.rb
    Library/Formula/csync.rb
    Library/Formula/ctemplate.rb
    Library/Formula/curlftpfs.rb
    Library/Formula/cutter.rb
    Library/Formula/cvsutils.rb
    Library/Formula/darkstat.rb
    Library/Formula/darner.rb
    Library/Formula/dart.rb
    Library/Formula/dasm.rb
    Library/Formula/debianutils.rb
    Library/Formula/dfc.rb
    Library/Formula/dgtal.rb
    Library/Formula/dhcping.rb
    Library/Formula/di.rb
    Library/Formula/dmtx-utils.rb
    Library/Formula/drip.rb
    Library/Formula/dsniff.rb
    Library/Fo
Aborting
Updating e088818..c1fbc29
Error: Failed while executing git pull  origin refs/heads/master:refs/remotes/origin/master

Answer 1

This is caused by an old bug in the update code that has long since been fixed. However, the nature of the bug requires that you do the following:

cd $(brew --repository)
git reset --hard FETCH_HEAD

If brew doctor still complains about uncommitted modifications, also run this command:

cd $(brew --repository)    
git clean -fd

Answer 2

This post helped me after updating to El Capitan. In my case, chown wasn't working ("zsh: command not found: chown"), so step 1 was adding this line to my .zshrc:

export PATH="$PATH:/usr/sbin"

I'd already tried several of the more popular answers above, so I'm pretty sure that git status was coming up clean by the time I pasted in the critical command from the blog post:

sudo chown $(whoami):admin /usr/local && sudo chown -R $(whoami):admin /usr/local

Answer 3

You need to do the following:

cd $(brew --prefix)
rm Library/Formula/argp-standalone.rb
rm Library/Formula/cocot.rb

And then do the

git fetch origin
git reset --hard origin/master
brew update

Basically, to explain a bit more:

cd $(brew --prefix)

tells cd to change the directory to whatever brew --prefix will output. If you try executing brew --prefix command you should see something in lines of:

brew --prefix
/usr/local

So the command would be in this case an equivalent of cd /usr/local. Newer brew versions have formulae under its installation prefix and Library/Formula/, so that's where you need to look for those outdated/changed files.

Note, that if you changed those formulae yourself for a particular reason (like pinning a version) this action will revert them back to default ones and may produce unwanted effects.

@TedPennings noted in comments that this worked for him, but his sequence was:

1. chown everything to my_username:admin, ie, sudo chown -R ted:admin $(brew --prefix)
2. run the two git commands above,git fetch origin and git reset --hard origin/master

Answer 4

Resetting the brew repository should be the most efficient way if you don't mind to discard potential modifications on formulas you might have been applied:

$ cd `brew --prefix`
$ git fetch origin
$ git reset --hard origin/master
$ brew cleanup --force
$ brew update

Answer 5

I had a similar issue where my brew package library got downloaded as a root user and then I was not able to run brew update as git would complain about not able to merge the file.

Solution was to do :-

sudo chown -R <user> /usr/local/Library

Answer 6

Another option is to just use git stash.

The brew update command performs a git pull, so if there are any changed files (or even file attributes, which happened to me when I changed permissions in the directory recursively) you have to somehow fix the conflicts. Using git stash is one way; it takes any changes and puts them aside so you effectively revert to the last updated repo version. The Homebrew 'location' is by default /usr/local and it installs as a git repository. You can look for a .git folder to see for yourself. I'm writing a homebrew uninstall script to be posted on my GitHub profile soon with more info.