If the java overlay is installed, "pmerge -avDuN world" will fail citing a malformed atom. Reproducible: Always Steps to Reproduce: 1. emerge layman pkgcore 2. Configure layman to install the java-overlay on your system. 3. pmerge -avDuN world Actual Results: # pmerge -avDuN world Error in configuration: Instantiating default domain 'livefs domain': Caught exception "ProfileError: profile '/var/lib/layman/java-overlay/profiles', file 'package.mask', error atom '-=dev-java/sun-jdk-1.5*' is malformed: error -=dev-java/sun-jdk-1.5*" instantiating pkgcore.ebuild.domain.domain Expected Results: It should not fail. I think that this might be an issue in the overlay, rather than an issue in pkgcore. It depends on whether or not the atom "-=dev-java/sun-jdk-1.5*" is valid.
Due to bug #336524, the problematic atom was removed. However, I guess it is necessary to treat them a little less faily.
This was resolved in pkgcore a while back; it didn't help that profile format versioning didn't exist back then (does now).
