The queries generated by XHProf aren't (always) very tidy. Depending on your RDBMS settings, this can result in a very unintuitive error on startup. This can be "fixed" by using a lame sql-mode. The easiest way is to pass it as initial command when constructing the PDO object, like so:
new PDO('mysql:dbname=xhprof;host=localhost;charset=utf8', 'username', 'password', array(PDO::MYSQL_ATTR_INIT_COMMAND => 'SET sql_mode = ""'))
This makes MySQL and friends, not trip on the queries doing an ambiguous group-by.