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Messages - Jake Shackelford (Patch My PC)

I would suggest adding an exclusion to that particular EXE to start. You may need to explore allowing exclusions on other folders related to content distribution within ConfigMgr but I would start solely with the ScriptRunner.exe. Depending on the security tool it can detect as a false positive just do to the nature of the exe running in the system context.
This was caused when Adobe changed the actual display name for the application, it caused detections to fail or only show as half compliant. With this in mind we adjusted the rules and added a (Rev 1) tag so that no one would have to republish the update manually and be in a broken state.
We're going to run this through some tests quick and assuming everything comes back great we'll have this change in place hopefully in the next catalog release! Thank you!
We don't have a direct way to do it in the publisher today, however if you do set them in Intune you can navigate to our Publisher and on the Intune Apps or Intune Updates Tab select Options, There will be an option to carry over Application Dependencies moving forward. 
Passing this along to the devs as a request. It also helps if you could make this request on our ideas page, found here: https://ideas.patchmypc.com/
Would you be able to grab the following logs from an affected client device and email them to [email protected]?

%WinDir%\CCM\Logs\PatchMyPC-ScriptRunner.log (If exist)
This may be found in the %ProgramData%\PatchMyPC\ if the Install was initiated by the user from Software Center.
You need to run Get-WindowsUpdateLog on Windows 8.1 and newer in PowerShell.
Fantastic! If you need any help along the way please let us know!
It will work both ways. You essentially skip the first initial install documentation pieces for Intune and move onto the next steps. So yes you can use the Intune Only documentation for SCCM+Intune.

Ultimately it's going to depend on how you have Co-Management enabled on how things function. The application slider for co-management works differently than all the other sliders. You can move that slider over to Intune and still get applications from ConfigMgr with the added benefit of being able to push them from intune as well.

If you'd like you can schedule a setup call on our website and we can help you get this going as well. https://patchmypc.com/schedule-setup-call
Were these the original configurations or did they get changed? Would you be able to send a copy of your patchmypc.log to [email protected]
Currently that version of R For Windows isn't signed by the developer. Once it is signed we will add that version to the catalog.
Keep us posted! Sometimes the issue can just appear at odd times, the reason behind it is the ConfigMgr Client sometimes isn't fast enough to deploy out the certificate when it gets installed.
We do have a KB article about this found here: https://patchmypc.com/applications-fail-to-install-during-osd-in-sccm-with-error-authorizationmanager-check-failed-0x87d00327

If you reach out to us via email [email protected] we can request some logs and dig into what might be happening.
We are actively looking at fixing this in the next release! We apologize for the inconvenience.
If you'd like by all means, we can dig in and see if we can reproduce.