Phan needs php-ast
to run, unfortunately this does not come included in the MediaWiki-Vagrant installation. To install it follow these instructions (largely influenced by Mainframe98). You can also try to run the associated shell script to automate this part.
From the vagrant home directory run vagrant up
to spin up vagrant then run vagrant ssh
to enter your vagrant shell.
Run the following and accept any prompts
wget http://pear.php.net/go-pear.phar
php go-pear.phar