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As for MySQL, deprecated alerts are usually considered as warnings and not errors.
It is recommended for developers to not use deprecated features in new software, and update existing software.
A deprecated feature might be removed in the future, but will usually remain for quite some time.
Hence, this alert should be none of your business.
If you have issues or do not want to use a deprecated feature, you should try a more recent MySQL version (current and stable should be 5.6, most recent is 5.7).
MySQL 5.6 has been running in production and development with my last (Metin2) projects without any issues.
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