I've never seen this show up as a build problem; it's (typically) a Tomcat warning that appears at webapp startup time. It's not a real problem or error... we don't actually recommend using APR, so every deployment logs this warning. The webapp should run just fine, despite the warning.

If LabKey Server is not responding to requests after startup then likely something else is going on. We'll need to see a full log to help further.

Adam