Well now, this is interesting. The agent mentione previously ran flawlessly for a couple of weeks. The day I left for Christmas vacation, I started getting the lock wait timeout error. The difference? I altered the table to include a foreign key constraint. Not sure how this could possibly be the issue but when I dropped the foreign key constraint, the agent worked perfectly. I'm still at a loss as to why this problem happened. I'm using INNODB tables in MySQL 4.0.16. It looks like the one record which timed out was being updated and the referenced record and field values existed. In addition, I had already updated 26,000 records so I can't figure out what's wrong with this one particular record. Any thoughts appreciated.
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