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The log_bin_trust_routine_creators system variable (use log_bin_trust_function_creators).
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The myisam_max_extra_sort_file_size system variable.
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The record_buffer system variable (use read_buffer_size).
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The sql_log_update system variable.
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The table_type system variable (use storage_engine).
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The FRAC_SECOND modifier for the TIMESTAMPADD() function.
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The TYPE table option to specify the storage engine for CREATE TABLE or ALTER TABLE (use ENGINE).
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The SHOW TABLE TYPES SQL statement (use SHOW ENGINES).
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The SHOW INNODB STATUS and SHOW MUTEX STATUS SQL statements (use SHOW ENGINE INNODB STATUS SHOW ENGINE INNODB MUTEX).
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The SHOW PLUGIN SQL statement (use SHOW PLUGINS).
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The LOAD TABLE ... FROM MASTER and LOAD DATA FROM MASTER SQL statements (use mysqldump or mysqlhotcopy to dump tables and mysql to reload dump files).
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The BACKUP TABLE and RESTORE TABLE SQL statements (use mysqldump or mysqlhotcopy to dump tables and mysql to reload dump files).
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TIMESTAMP(N) data type: The ability to specify a display width of N (use without N).
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The --default-character-set and --default-collation server options (use --character-set-server and --collation-server).
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The --delay-key-write-for-all-tables server option (use --delay-key-write=ALL).
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The --enable-locking and --skip-locking server options (use --external-locking and --skip-external-locking).
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The --log-bin-trust-routine-creators server option (use --log-bin-trust-function-creators).
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The --log-long-format server option.
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The --log-update server option.
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The --master-xxx server options to set replication parameters (use the CHANGE MASTER TO statement instead): --master-host, --master-user, --master-password, --master-port, --master-connect-retry, --master-ssl, --master-ssl-ca, --master-ssl-capath, --master-ssl-cert, --master-ssl-cipher, --master-ssl-key.
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The --safe-show-database server option.
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The --skip-symlink and --use-symbolic-links server options (use --skip-symbolic-links and --symbolic-links).
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The --sql-bin-update-same server option.
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The --warnings server option (use --log-warnings).
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The --no-named-commands option for mysql (use --skip-named-commands
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The --no-pager option for mysql (use --skip-pager).
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The --no-tee option for mysql (use --skip-tee).
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The --position option for mysqlbinlog (use --start-position).
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The --all option for mysqldump (use --create-options).
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The --first-slave option for mysqldump (use --lock-all-tables).
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The --config-file option for mysqld_multi (use --defaults-extra-file).
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The --set-variable=var_name=value and -O var_name=value general-purpose options for setting program variables (use --var_name=value).
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The --with-pstack option for configure and the --enable-pstack option for mysqld.