I think it looks like an issue with your composer dependencies not being up to date but it could also be something else (there could be issues with files permissions, etc.).
You can try something like this in your passbolt directory in /var/www:
cd /var/www/passbolt
sudo su -s /bin/bash -c "composer install --no-dev -n" www-data
sudo su -s /bin/bash -c "./bin/cake passbolt migrate --backup" www-data
sudo su -s /bin/bash -c "./bin/cake cache clear_all" www-data
See also: Passbolt Help | Update passbolt source install
The deprecation warnings are ok, they will be removed when we drop support for older PHP versions.
Ps. We strongly encourage people to not use LinuxBabe tutorials. They are one-off installation tutorial disconnected from our release tests and regular support scenarios. You would save yourselves some trouble down the line by switching to one official package.