The file /etc/cron.daily/mysql-server should not been present. You can safely 
remove the file. It looks like a bug of an old version not having removed it 
during upgrade.
Nowadays, binlog expiry is done by mysql-server and configred in my.cnf.

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/etc/cron.daily/mysql-server is broken
https://bugs.launchpad.net/bugs/49712
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