I upgraded my atom 2.2.1 to 2.3.1 on an Ubuntu 14.04 VPS with apache, php7.1 and mysql 5.6, following the instructions from
https://www.accesstomemory.org/en/docs/2.3/admin-manual/installation/upgrading/
There are several calls to function modify($query, $parameters) of /lib/QubitPdo.class.php, using only 1 argument ($query) and omitting the second argument. This causes a php error that stops the upgrade-sql tool execution.
I managed to run it by making the second argument of the function optional ie function modify($query, $parameters='')
The tool execution concluded without any errors and it looks like it added a few records in the databse, without modifying its structure but I cannot be sure that everything worked as intended.
Although I searched the forum for this problem, I couldn't find anything related.
Please let me know if my fix was correct.