I have up graded four Piwik sites and not had any issues with three of them, the last one however generated the following output when running the database upgrade:
A database upgrade is required. Execute update? (y/N) y
Starting the database upgrade process now. This may take a while, so please be patient.
*** Update ***
Database Upgrade Required
Your Piwik database is out-of-date, and must be upgraded before you can continue.
Piwik database will be upgraded from version 2.16.2 to the new version 2.16.3.
The following dimensions will be updated: log_visit.visit_entry_idaction_url.
The database upgrade process may take a while, so please be patient.
WARNING [2016-10-03 10:28:22] /web/stats.transitionnetwork.org/piwik/libs/Zend/Db/Statement/Pdo.php(228): Notice - Array to string conversion - Piwik 2.16.3 - Please report this message in the Piwik forums: http://forum.piwik.org (please do a search first as it might have been reported already)
WARNING [2016-10-03 10:28:22] /web/stats.transitionnetwork.org/piwik/libs/Zend/Db/Statement/Pdo.php(228): Notice - Array to string conversion - Piwik 2.16.3 - Please report this message in the Piwik forums: http://forum.piwik.org (please do a search first as it might have been reported already)
WARNING [2016-10-03 10:28:22] /web/stats.transitionnetwork.org/piwik/libs/Zend/Db/Statement/Pdo.php(228): Notice - Array to string conversion - Piwik 2.16.3 - Please report this message in the Piwik forums: http://forum.piwik.org (please do a search first as it might have been reported already)
WARNING [2016-10-03 10:28:22] /web/stats.transitionnetwork.org/piwik/libs/Zend/Db/Statement/Pdo.php(228): Notice - Array to string conversion - Piwik 2.16.3 - Please report this message in the Piwik forums: http://forum.piwik.org (please do a search first as it might have been reported already)
WARNING [2016-10-03 10:28:22] /web/stats.transitionnetwork.org/piwik/libs/Zend/Db/Statement/Pdo.php(228): Notice - Array to string conversion - Piwik 2.16.3 - Please report this message in the Piwik forums: http://forum.piwik.org (please do a search first as it might have been reported already)
WARNING [2016-10-03 10:28:22] /web/stats.transitionnetwork.org/piwik/libs/Zend/Db/Statement/Pdo.php(228): Notice - Array to string conversion - Piwik 2.16.3 - Please report this message in the Piwik forums: http://forum.piwik.org (please do a search first as it might have been reported already)
WARNING [2016-10-03 10:28:22] /web/stats.transitionnetwork.org/piwik/libs/Zend/Db/Statement/Pdo.php(228): Notice - Array to string conversion - Piwik 2.16.3 - Please report this message in the Piwik forums: http://forum.piwik.org (please do a search first as it might have been reported already)
WARNING [2016-10-03 10:28:22] /web/stats.transitionnetwork.org/piwik/libs/Zend/Db/Statement/Pdo.php(228): Notice - Array to string conversion - Piwik 2.16.3 - Please report this message in the Piwik forums: http://forum.piwik.org (please do a search first as it might have been reported already)
Executing ALTER TABLE `log_visit` MODIFY COLUMN `visit_entry_idaction_url` INTEGER(11) UNSIGNED NULL DEFAULT NULL... Done. [1 / 1]
Piwik has been successfully updated!
It appears you have executed this update with user root:root, while your Piwik files are owned by www-data:www-data.
To ensure that the Piwik files are readable by the correct user, you may need to run the following command (or a similar command depending on your server configuration):
$ chown -R root:root /web/stats.transitionnetwork.org/piwik
So I thought I’d best report it here… the full set of commands I ran are listed here.