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You are correct, there are patches that can take an hour to process (like .NET) and service packs that could take multiple hours. The Deployment Tracker is our primary method for customers to track the status of deployments. (Tracker can be opened from Main menu > View > Deployment Tracker, or F3 when in Protect.) As you pointed out, some patches may take longer than expected to process and it may seem like they are hung. The Tracker status for these slow processing patches should be set to 'Executing' and in most cases you should wait and allow the process to continue.
We don’t have a great mechanism to determine if a patch install is hung or if it is just taking a long time to install. The actual patch installs are mostly controlled by the vendor's patch installer and the OS/Product. The Tracker waits for statuses from the client but a hung patch will never send new statuses. Patch installs that are hung will never make it past the status of Executed. The most that the client side logs will give you is if the patch process for a specific patch started. The logs cannot track the progress of the patch install. The only viable way to see if the patch is hung or not is to look in the Task Manager of the client machine and verify if the patch install or trusted-installer is using CPU\RAM. Killing the patch install process will often allow the remainder of the deployment to complete. This isn't 100% since a patch install can use no CPU for long periods depending on what is happening on the client at the time.
I hope this information proves useful.
It's very useful and that's what I'm doing now so I'm glad that I wasn't missing something obvious.
Thanks for the quick response!