The checked out libodb/odb/version-build2.hxx and libodb-sqlite/odb/sqlite/version-build2.hxx will be overwritten during the build process but these changes should be ignored. To do this automatically, run: git update-index --assume-unchanged libodb/odb/version-build2.hxx git update-index --assume-unchanged libodb-sqlite/odb/sqlite/version-build2.hxx