The problem is in following file 011-HIVE-3649.derby.sql that contains following line:
ALTER TABLE "SDS" ADD "IS_STOREDASSUBDIRECTORIES" CHAR(1) NOT NULL;
This query will however fail if the table SDS have at least one row.
PostgreSQL upgrade scripts are not valid
Oracle metastore update script will fail when upgrading from 0.9.0 to 0.10.0
Mysql metastore upgrade script will end up with different schema than the full schema load