Brew update failed: untracked working tree files would be overwritten by merge

Question

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

error: The following untracked working tree files would be overwrittenby me         


        

Answer 1

$ cd $(brew --prefix)
$ git clean -fd
$ git reset --hard
$ sudo chown -R `whoami` `brew --prefix`
$ brew update

Note: steps 2&3 worked for me since I did step 5 before 4 before I got the error. The brew update before changing the owner of the folder caused the whole problem.

Answer 2

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 3

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 4

sudo chown -R USER /usr/local/bin

note - for USER use command whom i.e. your username

sudo brew doctor

Answer 5

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 6

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versions have formulae under its installation prefix and Library/Formula/, so that's where you need to look for those outdated/changed files.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