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Creating spatial indexes returns an error if the data base type is not myisam:
ERROR 1464 (HY000): The used table type doesn’t support SPATIAL indexes
You can change the database type to myisam and this example will work by doing the following:
alter table geom engine=myisam;
For reference, check the documentation here http://dev.mysql.com/doc/refman//5.5/en/creating-spatial-indexes.html
Source:stackexchange.com