I've been running sqlite3 on my local dev environment (Ubuntu 10.04 Lucid Lynx, sqlite3 3.6.22) and have seen more than one of these fatal "database is locked" #fails. In each case, a page reload fixes it fine. I'll see if I can do an upgrade of sqlite and see what happens.
Error message
PDOException: SQLSTATE[HY000]: General error: 5 database is locked: INSERT INTO {variable} (name, value) VALUES (?, ?); Array ( [0] => rules_empty_sets [1] => a:55:{s:29:"commerce_cart_product_prepare";i:0;s:33:"commerce_customer_profile_presave";i:1;s:32:"commerce_customer_profile_insert";i:2;s:32:"commerce_customer_profile_update";i:3;s:32:"commerce_customer_profile_delete";i:4;s:26:"commerce_line_item_presave";i:5;s:25:"commerce_line_item_insert";i:6;s:25:"commerce_line_item_update";i:7;s:25:"commerce_line_item_delete";i:8;s:22:"commerce_order_presave";i:9;s:21:"commerce_order_insert";i:10;s:21:"commerce_order_update";i:11;s:21:"commerce_order_delete";i:12;s:36:"commerce_payment_transaction_presave";i:13;s:35:"commerce_payment_transaction_insert";i:14;s:35:"commerce_payment_transaction_update";i:15;s:35:"commerce_payment_transaction_delete";i:16;s:24:"commerce_product_presave";i:17;s:23:"commerce_product_insert";i:18;s:23:"commerce_product_update";i:19;s:23:"commerce_product_delete";i:20;s:19:"rules_config_insert";i:21;s:19:"rules_config_update";i:22;s:20:"rules_config_presave";i:23;s:19:"rules_config_delete";i:24;s:11:"node_insert";i:25;s:11:"node_update";i:26;s:12:"node_presave";i:27;s:9:"node_view";i:28;s:11:"node_delete";i:29;s:4:"init";i:30;s:4:"cron";i:31;s:8:"watchdog";i:32;s:11:"user_insert";i:33;s:11:"user_update";i:34;s:12:"user_presave";i:35;s:9:"user_view";i:36;s:11:"user_delete";i:37;s:10:"user_login";i:38;s:11:"user_logout";i:39;s:14:"comment_insert";i:40;s:14:"comment_update";i:41;s:15:"comment_presave";i:42;s:12:"comment_view";i:43;s:14:"comment_delete";i:44;s:15:"comment_publish";i:45;s:17:"comment_unpublish";i:46;s:20:"taxonomy_term_insert";i:47;s:20:"taxonomy_term_update";i:48;s:21:"taxonomy_term_presave";i:49;s:20:"taxonomy_term_delete";i:50;s:26:"taxonomy_vocabulary_insert";i:51;s:26:"taxonomy_vocabulary_update";i:52;s:27:"taxonomy_vocabulary_presave";i:53;s:26:"taxonomy_vocabulary_delete";i:54;} ) in variable_set() (line 804 of /home/rfay/workspace/d7git/includes/bootstrap.inc).
Problem
The SQLite database does not support row level locks. As a result we have to acquire a reserved lock on the database immediately.
For more information, see: https://bugs.php.net/42766.