Common Issues

This is a list of commonly encountered problems, known issues, and their solutions.

brew complains about absence of “Command Line Tools”

You need to have the Xcode Command Line Utilities installed (and updated): run xcode-select --install in the terminal.

Ruby: bad interpreter: /usr/bin/ruby^M: no such file or directory

You cloned with git, and your Git configuration is set to use Windows line endings. See this page: https://help.github.com/articles/dealing-with-line-endings

Ruby: bad interpreter: /usr/bin/ruby

You don’t have a /usr/bin/ruby or it is not executable. It’s not recommended to let this persist; you’d be surprised how many .apps, tools and scripts expect your macOS-provided files and directories to be unmodified since macOS was installed.

brew update complains about untracked working tree files

After running brew update, you receive a Git error warning about untracked files or local changes that would be overwritten by a checkout or merge, followed by a list of files inside your Homebrew installation.

This is caused by an old bug in 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)/Library
git clean -fd

launchctl refuses to load launchd plist files

When trying to load a plist file into launchctl, you receive an error that resembles

Bug: launchctl.c:2325 (23930):13: (dbfd = open(g_job_overrides_db_path, [...]
launch_msg(): Socket is not connected

or

Could not open job overrides database at: /private/var/db/launchd.db/com.apple.launchd/overrides.plist: 13: Permission denied
launch_msg(): Socket is not connected

These are likely due to one of four issues:

1. You are using iTerm. The solution is to use Terminal.app when interacting with launchctl.
2. You are using a terminal multiplexer such as tmux or screen. You should interact with launchctl from a separate Terminal.app shell.
3. You are attempting to run launchctl while logged in remotely. You should enable screen sharing on the remote machine and issue the command using Terminal.app running on that machine.
4. You are su‘ed as a different user.

brew upgrade errors out

When running brew upgrade, you see something like this:

$ brew upgrade
Error: undefined method `include?' for nil:NilClass
Please report this bug:
    https://docs.brew.sh/Troubleshooting
/usr/local/Library/Homebrew/formula.rb:393:in `canonical_name'
/usr/local/Library/Homebrew/formula.rb:425:in `factory'
/usr/local/Library/Contributions/examples/brew-upgrade.rb:7
/usr/local/Library/Contributions/examples/brew-upgrade.rb:7:in `map'
/usr/local/Library/Contributions/examples/brew-upgrade.rb:7
/usr/local/bin/brew:46:in `require'
/usr/local/bin/brew:46:in `require?'
/usr/local/bin/brew:79

This happens because an old version of the upgrade command is hanging around for some reason. The fix:

cd $(brew --repository)/Library/Contributions/examples
git clean -n # if this doesn't list anything that you want to keep, then
git clean -f # this will remove untracked files

Python: easy-install.pth cannot be linked

Warning: Could not link <formula>. Unlinking...
Error: The `brew link` step did not complete successfully
The formula built, but is not symlinked into /usr/local
You can try again using `brew link <formula>'

Possible conflicting files are:
/usr/local/lib/python2.7/site-packages/site.py
/usr/local/lib/python2.7/site-packages/easy-install.pth
==> Could not symlink file: /homebrew/Cellar/<formula>/<version>/lib/python2.7/site-packages/site.py
Target /usr/local/lib/python2.7/site-packages/site.py already exists. You may need to delete it.
To force the link and overwrite all other conflicting files, do:
  brew link --overwrite formula_name

To list all files that would be deleted:
  brew link --overwrite --dry-run formula_name

Don’t follow the advice here but fix by using Language::Python.setup_install_args in the formula as described in Python for Formula Authors.

Upgrading macOS

Upgrading macOS can cause errors like the following:

• dyld: Library not loaded: /usr/local/opt/icu4c/lib/libicui18n.54.dylib
• configure: error: Cannot find libz

Following a macOS upgrade it may be necessary to reinstall the Xcode Command Line Tools and brew upgrade all installed formula:

xcode-select --install
brew upgrade