You’re getting Undefined index errors because you’re loading the files directly and not rendered through the server. The server typically populates those values and it’s actually more secure to run with less elevated privileges (through an HTTP request).
Throw your manual cron to a curl or wget — whichever you have installed on your server.
curl -s -H "User-Agent: Mozilla/5.0 (Windows NT 6.1; WOW64)" http://YourWebsiteURL.com/wp-cron.php?doing_wp_cron
OR
wget -O /dev/null http://www.YourWebsiteURL.com/wp-cron.php?doing_wp_cron > /dev/null 2>&1
This should trigger your cron and with www privileges instead of server root access.