The up-to-date checks using the cache are not currently reliable. In particular, a clean does not always trigger a rebuild.

Here is a sequence that can reproduce the problem with the java quickstart sample:

Go to the quickstart sample and run 'gradle build'. - this makes sure you have the output classes

Then delete the .gradle cache directory. (This simulates changing to a new version of gradle where a new subdirectory is used underneath the .gradle dir).

Now do 'gradle build' - this will create the caches (and seems to cache that the output files are there).

Now do 'gradle clean build' - the build will fail because it thinks compileJava is UP-TO-DATE.

It is now stuck in a state where it always thinks it is up to date.

Deleting the cache manually (or using -C rebuild option) can get around the problem for that run, but you can run into similar issues later. Currently it seems you have to do -C rebuild every time to consistently avoid this.