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Same thing happens going to 3.2.0

Upgrade CiviCRM to Version 3.2.0
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DB Error: already exists
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Error Details:

Array
(
    [callback] => Array
        (
           

• => CRM_Core_Error
[1] => handle
        )

   

=> -5
    [message] => DB Error: already exists
    [mode] => 16
    [debug_info] => CREATE TABLE `civicrm_entity_financial_trxn` (
  `id` int(10) unsigned NOT NULL AUTO_INCREMENT COMMENT 'ID',
  `entity_table` varchar(64) COLLATE utf8_unicode_ci NOT NULL,
  `entity_id` int(10) unsigned NOT NULL,
  `financial_trxn_id` int(10) unsigned DEFAULT NULL,
  `amount` decimal(20,2) NOT NULL COMMENT 'allocated amount of transaction to this entity',
  PRIMARY KEY (`id`),
  KEY `FK_civicrm_entity_financial_trxn_financial_trxn_id` (`financial_trxn_id`)
) ENGINE=InnoDB  DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci [nativecode=1050 ** Table 'civicrm_entity_financial_trxn' already exists]
    [type] => DB_Error
    [user_info] => CREATE TABLE `civicrm_entity_financial_trxn` (
  `id` int(10) unsigned NOT NULL AUTO_INCREMENT COMMENT 'ID',
  `entity_table` varchar(64) COLLATE utf8_unicode_ci NOT NULL,
  `entity_id` int(10) unsigned NOT NULL,
  `financial_trxn_id` int(10) unsigned DEFAULT NULL,
  `amount` decimal(20,2) NOT NULL COMMENT 'allocated amount of transaction to this entity',
  PRIMARY KEY (`id`),
  KEY `FK_civicrm_entity_financial_trxn_financial_trxn_id` (`financial_trxn_id`)
) ENGINE=InnoDB  DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci [nativecode=1050 ** Table 'civicrm_entity_financial_trxn' already exists]
    [to_string] => [db_error: message="DB Error: already exists" code=-5 mode=callback callback=CRM_Core_Error::handle prefix="" info="CREATE TABLE `civicrm_entity_financial_trxn` (
  `id` int(10) unsigned NOT NULL AUTO_INCREMENT COMMENT 'ID',
  `entity_table` varchar(64) COLLATE utf8_unicode_ci NOT NULL,
  `entity_id` int(10) unsigned NOT NULL,
  `financial_trxn_id` int(10) unsigned DEFAULT NULL,
  `amount` decimal(20,2) NOT NULL COMMENT 'allocated amount of transaction to this entity',
  PRIMARY KEY (`id`),
  KEY `FK_civicrm_entity_financial_trxn_financial_trxn_id` (`financial_trxn_id`)
) ENGINE=InnoDB  DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci [nativecode=1050 ** Table 'civicrm_entity_financial_trxn' already exists]"]
)

As mentioned on irc, this seems like a failed upgrade that hasn't been backed out properly. The civicrm_entity_financial_trxn table was only added in 3.2, so the code to do the upgrade to 3.2 isn't expecting it to be there and is failing. Finding a backup is the best approach. Failing that, manually executing:
DROP TABLE civicrm_entity_financial_trxn;

should help. If the same error appears for other tables (fairly likely to my mind) I'd check to see if they are also ones that were added after 3.1 (http://svn.civicrm.org/civicrm/trunk/xml/schema/) and if necessary drop them too.

HTH,
Joe

Next it complained about civicrm_financial_account (an empty table), then about civicrm_website (a table with one entry) and now it is complaining about civicrm_address_format (also empty). After deleting these tables, it worked.