After automatically updating to 3.9.0, I receive a number of similar error messages on the “All Websites” screen, for example:
WARNING: / ... www.example.com/core/Plugin/Manager.php(451): Warning - is_dir(): open_basedir restriction in effect. File(/ ... www.example.complugins/CustomAlerts) is not within the allowed path(s): (/ ... www.example.com/:/tmp/) - Matomo 3.9.0 - Please report this message in the Matomo forums: https://forum.matomo.org (please do a search first as it might have been reported already)
Please note that “plugins” in the path is attached to the domain name without any slash.
I solved the problem in core/plugin/Manager.php on line 450 by changing
$corePluginsDir = PIWIK_INCLUDE_PATH . 'plugins/' . $pluginName;
$corePluginsDir = self::getPluginsDirectory() . $pluginName;
This automatically seems to add the slash.