Unknown option '--no-beep'
The no-beep option causes the mysql command line client not to beep when errors occur.  

If that's an option you want, it should be in the [mysql] section of your my.cnf.  This error suggests that it's in the [client] section of your my.cnf, which causes mysql_upgrade to throw the error since the option isn't recognized.

Check your my.cnf and either remove the line or place it in the [mysql] section instead of [client] and you should be good.


  The [client] option group is read by all client programs (but not by
  mysqld). This enables you to specify options that apply to all
  clients. For example, [client] is the perfect group to use to specify
  the password that you use to connect to the server. (But make sure
  that the option file is readable and writable only by yourself, so
  that other people cannot find out your password.) Be sure not to put
  an option in the [client] group unless it is recognized by all client
  programs that you use. Programs that do not understand the option quit
  after displaying an error message if you try to run them.


-- http://dev.mysql.com/doc/refman/5.5/en/option-files.html