GenCode.php fails when another civicrm installation exists in modules/

Using svn civicrm-3.3:

• checkout svn code into an arbitrary directory
• create settings_location.php to define where CIVICRM_CONFDIR is
• set up xml/schema/... so that we can generate our new DAO's
• php GenCode.php schema/Schema.xml

Fails with these errors related to require_once:
PHP Notice: Constant PEAR_LOG_EMERG already defined in /home/www-data/compasspoint.awight/sites/all/modules/civicrm/packages/Log.php on line 10
PHP Notice: Constant PEAR_LOG_ALERT already defined in /home/www-data/compasspoint.awight/sites/all/modules/civicrm/packages/Log.php on line 11
PHP Notice: Constant PEAR_LOG_CRIT already defined in /home/www-data/compasspoint.awight/sites/all/modules/civicrm/packages/Log.php on line 12
PHP Notice: Constant PEAR_LOG_ERR already defined in /home/www-data/compasspoint.awight/sites/all/modules/civicrm/packages/Log.php on line 13
PHP Notice: Constant PEAR_LOG_WARNING already defined in /home/www-data/compasspoint.awight/sites/all/modules/civicrm/packages/Log.php on line 14
PHP Notice: Constant PEAR_LOG_NOTICE already defined in /home/www-data/compasspoint.awight/sites/all/modules/civicrm/packages/Log.php on line 15
PHP Notice: Constant PEAR_LOG_INFO already defined in /home/www-data/compasspoint.awight/sites/all/modules/civicrm/packages/Log.php on line 16
PHP Notice: Constant PEAR_LOG_DEBUG already defined in /home/www-data/compasspoint.awight/sites/all/modules/civicrm/packages/Log.php on line 17
PHP Notice: Constant PEAR_LOG_ALL already defined in /home/www-data/compasspoint.awight/sites/all/modules/civicrm/packages/Log.php on line 19
PHP Notice: Constant PEAR_LOG_NONE already defined in /home/www-data/compasspoint.awight/sites/all/modules/civicrm/packages/Log.php on line 20
PHP Notice: Constant PEAR_LOG_TYPE_SYSTEM already defined in /home/www-data/compasspoint.awight/sites/all/modules/civicrm/packages/Log.php on line 23
PHP Notice: Constant PEAR_LOG_TYPE_MAIL already defined in /home/www-data/compasspoint.awight/sites/all/modules/civicrm/packages/Log.php on line 24
PHP Notice: Constant PEAR_LOG_TYPE_DEBUG already defined in /home/www-data/compasspoint.awight/sites/all/modules/civicrm/packages/Log.php on line 25
PHP Notice: Constant PEAR_LOG_TYPE_FILE already defined in /home/www-data/compasspoint.awight/sites/all/modules/civicrm/packages/Log.php on line 26
PHP Fatal error: Cannot redeclare class Log in /home/www-data/compasspoint.awight/sites/all/modules/civicrm/packages/Log.php on line 38

Workaround is to temporarily replace the sites/all/modules/civicrm directory with the one we checked out of svn.