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Common Issues

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Samuel John edited this page Jul 13, 2013 · 22 revisions

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

brew complains about absence of "Command Line Tools"

The "Command Line Tools" package is now installed from within Xcode. ⌘, will get you to preferences. Visit the "Downloads" tab and hit the install button next to "Command Line Tools".

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. Don't do that.

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 OS X provided files and directories to be unmodified since OS X 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 two issues:

  1. You are using iTerm. The solution is to use Terminal.app when interacting with launchctl.
  2. 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.

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://github.com/mxcl/homebrew/wiki/checklist-before-filing-a-new-issue
/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: Segmentation fault: 11 on `import <some_python_module>

A Segmentation fault: 11 is in 95% due to a different Python executable used for building the software vs. the python you use to import the module. Note that e.g. the boost bottle is built against system python and should be brewed from source to make it work with a brewed Python. This can even happen when both python executables are the same version (e.g. 2.7.2). The explanation is that Python packages with C-extensions (those that have .so files) are compiled against a certain python binary/library that may have been built with a different arch (e.g. Apple's python is still not a pure 64bit). Other things can go wrong, too. Welcome to the dirty underworld of C.

To solve this, you should remove the problematic formulae with those python bindings and all of it's dependencies.

  • brew rm $(brew deps <problematic_formula>)
  • brew rm <problematic_formula>
  • Also check the $(brew --prefix)/lib/python2.7/site-packages directory and delete all remains of the corresponding python modules if they were not cleanly removed by the previous steps.
  • Check that which python points to the python you want. Perhaps now is the time to brew install python.
  • Then reinstall brew install <problematic_formula>
  • Now start python and try to import the module installed by the <problematic_formula>

You can basically use any Python (2.x) for the bindings homebrew provides, but you can't mix. Homebrew formulae use a brewed Python if available or, if not so, they use whatever python is in your PATH.

Python: Fatal Python error: PyThreadState_Get: no current thread 

Fatal Python error: PyThreadState_Get: no current thread
Abort trap: 6

This happens for boost, pygtk and/or pygobject and related modules, for the same reason as described above. If the boost is your problem, please brew rm boost, brew install boost --build-from-source. This is needed because the boost bottle is built against system python.

To solve this, follow the steps above.

Python: Python.h not found

The formula needs a depends_on :python, probably.

Python: easy-install.pth cannot be linked

Warning: Could not link <formulaname>. 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 <formulaname>'

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/<formulaname>/<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 of setuptools here but fix by adding --record=installed.txt and --single-version-externally-managed flags to setup.py:

Python: site-packages path in the Cellar not in the PYTHONPATH

Symptom:

system python, "setup.py", "install", "--prefix=#{prefix}"

TEST FAILED: /usr/local/Cellar/mapserver/6.2.1/lib/python2.7/site-packages/ does NOT support .pth files
error: bad install directory or PYTHONPATH

You are attempting to install a package to a directory that is not
on PYTHONPATH and which Python does not read ".pth" files from.  The
installation directory you specified (via --install-dir, --prefix, or
the distutils default setting) was:

    /usr/local/Cellar/mapserver/6.2.1/lib/python2.7/site-packages/

and your PYTHONPATH environment variable currently contains:

    ''

Here are some of your options for correcting the problem:

* You can choose a different installation directory, i.e., one that is
  on PYTHONPATH or supports .pth files

* You can add the installation directory to the PYTHONPATH environment
  variable.  (It must then also be on PYTHONPATH whenever you run
  Python and want to use the package(s) you are installing.)

* You can set up the installation directory to support ".pth" files by
  using one of the approaches described here:

  http://packages.python.org/distribute/easy_install.html#custom-installation-locations

Please make the appropriate changes for your system and try again.

Solution: The failing python command has to be put into a python do ... end block:

def install
  ..
  python do
    system python, "setup.py", "install", "--prefix=#{prefix}"
  end
  ...
end
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