For me, the fix was to point to the actual mysql directory in the basement, as shown on the installation page.
eg:
During mysql installation (using brew install mysql56 ) this path was shown to me: /usr/local/Cellar/mysql56/5.6.27/bin/mysql_install_db...
I used this to define basedir like this:
mysql_install_db --verbose --user=`whoami` --basedir="/usr/local/Cellar/mysql56/5.6.27" --datadir=/usr/local/var/mysql --tmpdir=/tmp
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