Symptoms
If Jail Apache Virtual Hosts is enabled in WHM, the Smart Update or Clone feature of WPTK can fail with an error similar to the following:
Unable to perform Smart Update on this website because the site clone is different from the original
Checking the cloned site shows a Database Error.
Description
With Jail Apache Virtual Hosts enabled, connections to the database host localhost will fail. See the following page for more information:
Database connection error (jailed apache vhosts)
WPTK will use the host provided by the WHM API, which will be localhost instead of the required 127.0.0.1. This causes the clone and smart update to fail.
We've opened an internal case for our development team to investigate this further. For reference, the case number is CPANEL-48796. Follow this article to receive an email notification when a solution is published in the product.
Workaround
Disable Jail Apache Virtual Hosts: