If you want analyze tables with "mysqlcheck", you need to use the "--analyze" option. The following tutorial exercise shows you how to analyze all tables in "mysql" database:
>cd mysqlbin
>mysqlcheck -u root --analyze mysql
mysql.columns_priv Table is already up to date
mysql.db Table is already up to date
mysql.func Table is already up to date
mysql.help_category Table is already up to date
mysql.help_keyword Table is already up to date
mysql.help_relation Table is already up to date
mysql.help_topic Table is already up to date
mysql.host Table is already up to date
mysql.proc Table is already up to date
mysql.tables_priv Table is already up to date
mysql.time_zone Table is already up to date
mysql.time_zone_leap_second Table is already up to date
mysql.time_zone_name Table is already up to date
mysql.time_zone_transition Table is already up to date
mysql.time_zone_transition_type Table is already up to date
mysql.user Table is already up to date