I don't think you can upgrade directly from 2003 to 2012 R2, but 2012 R2 is fully supported on the 2900, so there should be no issue running it on there. I would strongly suggest you update the system firmware (BIOS, ESM/BMC, PERC (driver first)) before moving to 2012 R2.
I'm going to migrate a Power Edge 2900 from Server 2003 to Server 2012 R2. Any known pitfalls?  Will I have a problem with the SAS6/iR Raid controller? I've done a couple new installs on other machines with Server 2012 R2, bur never an upgrade. Just a little nervous, I have the week end to work on this. Thanks
Any Pitfalls Migrating from Server 2003 to 2012 R2 on Power Edge 2900