The mysql_install_db script is used to create a new empty MySQL data directory and create the grant tables. In dev-db/mysql-5.6.21-r1, the script fails because it contains a --loose-skip-innodb option when starting up MySQL to create the tables, but the --skip-innodb option is deprecated/unsupported. The relevant command is at line 395 in the script: mysqld_install_cmd_line="$mysqld_bootstrap $defaults $mysqld_opt --bootstrap \ --basedir=$basedir --datadir=$ldata --log-warnings=0 --loose-skip-innodb \ --loose-skip-ndbcluster $args --max_allowed_packet=8M \ --default-storage-engine=myisam \ --net_buffer_length=16K" Removing --loose-skip-innodb from this command will fix the problem. Reproducible: Always
Please do not run the mysql_install_db script yourself. As the post-install instructions state, you should run `emerge --config =dev-db/mysql-5.6.21-r1` in order for the correct options to be set. This will create the base system tables, fill timezone data and help tables and set the administrative password.
