When you run the setup and choose upgrade you immediately get the message from compatibility report “Windows Server 2008 R2 cannot be upgraded to Windows Server 2012 R2 (With a GUI)”.
You need to have Service Pack 1 installed on Windows 2008 R2 to be able to perform the in-place upgrade. Download SP1 from the link below.
https://www.catalog.update.microsoft.com/Search.aspx?q=kb976932
Note: You also need to use a 2012 R2 setup edition in the same language and bit version (64bit).