WordPress Toolkit Quarantine Error and Quick Resolution

If you have received within the past 48 hrs a notification such as this:

Updates were not installed for the following items: Website "/home/$username/public_html" (https://$domain.com): Failed to reset cache for the instance #1: WordPress Toolkit was not able to finish running an operation on this site in 60 seconds, so the operation was terminated. This could mean that your WordPress installation might be infected with malware. Check the wp-config.php file of the installation for potential malware code or run an anti-virus scan. If you cannot find any traces of malware, try running the operation again later.

it is likely because of an existing issue with WordPress Toolkit.


By default, the cPanel WordPress Toolkit plugin automatically checks your WordPress website daily for malware infection.

It turned out that as presently coded, WordPress Toolkit creates a false match if it could not verify WordPress file checksums via api.wordpress.org or if api.wordpress.org is unavailable or inaccessible.


For now, the workaround is as follows:

Log in to your cPanel.

Visit WordPress Toolkit.

You will see something like this:

Click on Check WordPress Integrity


Click the "Verify Checksum"


WordPress Toolkit Check Integrity


Once the checksum check is completed, you will see this:


Close the pop-up.

Now click on "Refresh".

You will notice that the issue has gone away.

If you are unable to do this by yourself, please contact our technical support team at https://dashboard.webhostingmagic.com/submitticket.php

It is also worth noting that you can install WordPress using other methods including

  • Softaculous WordPress Manager
  • WP-CLI
  • or manual WordPress installation

If you wish to use either of these instead of WordPress Toolkit and are not sure where to start, please do visit and create a technical support request and create request.

The cPanel WordPress Toolkit development team is aware of this problem and working on a permanent fix.

We are also following the issue.

Customers will receive an email notification when a solution is published in the product