WARNING: /var/www/mysite.com/web/core/CliMulti/CliPhp.php(89): Warning - is_executable(): open_basedir restriction in effect. File(/usr/bin/php) is not within the allowed path(s): (/var/www/mysite.com/web:/var/www/mysite.com/tmp) - Matomo 3.13.1 - Please report this message in the Matomo forums: https://forum.matomo.org (please do a search first as it might have been reported already) (Module: Installation, Action: getSystemCheck, In CLI mode: false)
I can confirm this error message, and it disappeared after adding /usr/bin/ at open_basedir in php.ini (which I reverted thinking that it is a bad idea).
Debian Jessie with php5.6-fpm
(This message was shown first time immediately after Matomo update 3.11.x > 3.13.1)
That will keep the warning away, but it generated a new warning in System check:
Errors below may be due to a partial or failed upload of Matomo files. → Try to reupload all the Matomo files in BINARY mode. ←