Trying to install an in-place upgrade for Windows 2008 R2 -> 2012 R2 -> 2016 Server, it might come to a compatibility check issue which you cannot skip or accept by default.
With version 2016, some features like Unix Identity management features were removed. In some cases Windows Setup sees those components as installed even if they are not.
First make sure you run the DISM / ServerManagerCmd commands to uninstall the Unix identity features.
Then if you are absolutely sure they are not enabled any more and the compatibility check fails again, copy your Windows Server 2016 setup ISO/DVD content to a place where you have write permissions, e.g. your local HDD.
Edit sources\compliance.ini: Remove or comment the line which contains “IDMUUpgradeComplianceCheck”.
Save it and restart setup.