three packages install /usr/bin/extract sci-chemistry/pdb-extract media-libs/libextractor app-crypt/pkcrack To fix this I would suggest to rename after following scheme app-crypt/pkcrack extract --> pkextract media-libs/libextractor extract --> libextract sci-chemistry/pdb-extract can keep its extract --> Reason: 1. it already contains pdb_extract as binary, so things like pdb-extract aren't good 2. it is often used by other programms and third party scripts
*** This bug has been marked as a duplicate of bug 247394 ***