Add the following to your instrumented app's JVM arguments: -Dclover.logging.level=debug -Dclover.logging.adapter=log4j
Ensure log4j.properties is on your JVM's classpath, here's an example (note the "clover." prefixed class names).
Log4j support get broken at some point in the 2.x development stream. Clover 3.1.1 and greater fixes this.