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You can do wither in place upgrade (not recommended) or migration, this depends on what are the roles you will migrate AD, DNS, File...
Step required to migrate from from2008 R2 to2012 Datecenter, depends on the roles of the server (AD, DHCP, IIS, or any other application). You have to first explore the steps required for migrating the roles.
As such there are no challenges in upgrading2008 R2 installed with OS only to Server2012. However you should note that presence of certain roles may not let you to upgrade to2012. One role I am aware of is, Cluster service.
Hope this helps.
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