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With reference to http://drupal.org/node/561990#comment-6861664 (see comments #39 to #41), I understand that the code for lock_acquire actually suppresses this error, but Boost does not ignore the following error...
I see it in the /admin/reports/dblog under "boost" type:
There are php errors on this page, preventing boost from caching. ERROR: Array [type] => 512 [message] => Duplicate entry 'variable_cache_regenerate' for key 1 query: INSERT INTO semaphore (name, value, expire) VALUES ('variable_cache_regenerate', '151849102550d2f24540f987.74939510', 1356001891.2661) [file] => /var/www/mysite/includes/database.mysql.inc [line] => 135
Using: Drupal 6, Boost, NGINX, InnoDB tables (most of them)