PhyInit: Change to InnoDB tables causes ALTER TABLE errors

Changing the table types to InnoDB now causes problems with using ALTER TABLE to create foreign keys.
For example:

ALTER TABLE tree ADD CONSTRAINT FKNode
FOREIGN KEY (node_id) REFERENCES node (node_id);

is giving the error:

DBD::mysql::db do failed: Can't create table './biosql/#sql-cc7_bba.frm' (errno: 150) at ./PhyInit.pl line 363, <> line 1.

Typing the SQL code directly in the MySQL Command line gives:

ERROR 1005: Can't create table './biosql/#sql-cc7_ba6.frm' (errno: 150)

It looks there may be some help in an online discussion of this issue. It is odd that it flags this as a "Can't create table error" when this is really an ALTER TABLE problem.

Info on Foreign Key constraints is also in the MySQL manual. The conditions for foreign key definitions that are listed in the MySQL manual are:

• Both tables must be InnoDB tables and they must not be TEMPORARY tables.
  All of my tables are now InnoDB tables so this is not the problem.

• Corresponding columns in the foreign key and the referenced key must have similar internal data types inside InnoDB so that they can be compared without a type conversion. The size and sign of integer types must be the same. The length of string types need not be the same. For non-binary (character) string columns, the character set and collation must be the same.
  Both columns in the broken SQL are INT(11) so this is probably not the problem.
  

• In the referencing table, there must be an index where the foreign key columns are listed as the first columns in the same order. Such an index is created on the referencing table automatically if it does not exist.
  This is it, adding indexes to the tables fixed the problem.
  

• In the referenced table, there must be an index where the referenced columns are listed as the first columns in the same order.
  This is it, adding indexes to the tables fixed the problem.
  

• Index prefixes on foreign key columns are not supported. One consequence of this is that BLOB and TEXT columns cannot be included in a foreign key, because indexes on those columns must always include a prefix length.
  This is not the problem since the columns are INT(11).
  

• If the CONSTRAINT symbol clause is given, the symbol value must be unique in the database. If the clause is not given, InnoDB creates the name automatically.
  This is not the problem since FKnode is a unique value in the database. As a test, I ran the SQL without specifying the symbol, and I still have the error.
  

I am crossing these off the list as I can ..