sys-devel/prelink has been masked for deletion: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c6833772e8bfb5a88b7a2803cf9e7f92da217a4c Portage still contains various prelink-related code. One part of it is prelink-checksums feature (for FEATURES). Another is generation of /etc/prelink.conf.d/portage.conf: https://gitweb.gentoo.org/proj/portage.git/tree/lib/portage/util/env_update.py?id=3812225ace5db8c691cbe027d234a3e223972199#n240 Unfortunately this code never deletes /etc/prelink.conf.d/portage.conf. Regardless of whether other code (including code for generation of /etc/prelink.conf.d/portage.conf) is deleted sooner or later, I suggest that Portage now be changed to delete prelink-related files in /etc: /etc/prelink.conf.d/portage.conf /etc/prelink.cache (this was generated by prelink itself, but ebuild failed to delete it in pkg_postrm()) /etc/prelink.conf Code for deletion of above files can be in 'else:' branch after 'if prelink_capable:' branch if prelink-related code should remain longer in Portage.