We had small issue with Cron not working on one of freshly installed Magento 2 store last days. First of all, it’s often to forgot that M2 cron setup requires more than one entry, for not only php /bin/magento cron:run but also php update/cron.php to get rid of that annoying “Cron not working” message readiness check in Component Manager.
Later, checking it manually I’ve found out that php update/cron.php call throws out:
PHP Fatal error: require_once(): Failed opening required '/home/www-data/magento2/update/vendor/autoload.php' (include_path='.:/usr/share/php') in /home/www-data/magento2/update/app/bootstrap.php on line 13
The repository cloned didn’t have the update packages installed and to solve it it was necessary to run composer install not only in the Magento2 root directory but also update subfolder.