This endless attempt to pin a problem on a user is tiring...
Quote from Apple Forum:
The System Integrity Protection is designed to block changes to System owned locations including /Applications
You are simply
WRONG you
CANNOT adjust permissions on these system owned directories while SIP is enabled period.
This will be my last
ON TOPIC post since ignoring your faulty assumptions resolved the issue.
See above steps for repairing.
As to why or what caused this on a new machine I have no idea nor do I care. What I can tell you is others have experienced the same issue.
What I do know based on various posts on the Apple Forum as well as issues posted related to VirtualBox and El Capitan users have clearly encountered some snafus here and there.
If applications, computers and the like worked perfectly and there were never install/update issues most that visit this forum wouldn't have jobs.
Quit defaulting to "it's your fault" mentality. It helps no one.