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Installer fails to detect InnoDB on MySQL 5.6+ #202
app/code/core/Mage/Install/Model/Installer/Db/Mysql4.php tries to use have_innodb to check for the presence of InnoDB support. It should instead (or perhaps, also) check using SHOW ENGINES - have_innodb has been deprecated since MySQL 5.1 and removed in 5.6.
Currently, both for Magento 1.x and 2.x, we have to modify Mage_Install_Model_Installer_Db_Mysql4::supportEngine to return true (since we know we have InnoDB) on our MySQL 5.6 installations to work around this.