If you run a single unit test webservice/tests/externallib_test.php it will fail with the error

dml_read_exception: Error reading from database (ERROR: column "version" does not exist
LINE 1: SELECT id, name, version FROM phpu_modules ORDER BY name A...

So I found out that config is set manually in webservice/tests/externallib_test.php :

set_config('version', '2012083100.00');

this causes following condition in lib/classes/plugin_manager.php

if ($CFG->version < 2013092001.02) {
// We did not upgrade the database yet.
$modules = $DB->get_records('modules', array(), 'name ASC', 'id, name, version');

while modules table doesn't have version column

However, if you run core_user_testsuite before this test, then everything passes