I got a pop up that my adobe flash player needs to be updated. I have automatic updates turned on. I also keep getting a popup that my mac is infected with a virus; the last one said three viruses--2 malware and 1 phishing/spyware. I ran malwareby

It sounds like what you saw was a scam website trying to trick you into believing that your computer is infected, and not actual malware. The site would have reappeared after a restart if 1) you had the computer re-open apps that were previously open, and 2) your web browser was set to re-load pages that were previously open.

If this is happening in Safari, quit Safari. (If necessary, force quit Safari.) Then hold down the shift key while re-opening Safari. Then, don't go back to the site you were on when that pop-up appeared, as it's either malicious or has been compromised.

The extension might help.

Safari – Popup takes over

Safari – Popup takes over (2)

Popup remover – Scam Zapper

If the pop-up reloads, force quit Safari (command - option/alt - esc) and reopen with the shift key held down. If that doesn't work, disconnect from the Internet, go to Safari/History and delete the website. Quit and reopen with the shift key held down. Then reconnect to the Internet.

Safari -Tech support scam pop-ups