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Yeah, Gradle is very fragile and constantly complains about weird stuff. Usually it complains after rosjava updates, so if you recently updated your Indigo packages that might have been the cause. I usually remove the ~/.gradle directory (the one in your home) and sometimes also the build and devel in my workspace and recompile everything and that helps. Otherwise, from the information you provided it's hard to say anything else, you'd need to tell us how exactly you're installing KnowRob, your workspace setup etc... Maybe @moritz has a better idea.