SR1 to SP14 Upgrade - Portal Platform Warning

Hello all,
I am upgrading the recently installed SR1 to SP12. I successfully applied the Patch for WEBAS J2EE server. Now I'm trying to apply Portal Platform patches. During the "Deploy EAR Files" phase (6 of 12), it gave a warning Message box saying "The deloplyment may require manual postprocessing. See output of logfile C:\ProgramFiles\sapinst_instdir\callSdmViaSapinst.log' and in the status Bar it said 'Finished but with Warning'.
When I checked the log file i didnt fine any error or warning. It seems to me fine. Wonder what this message means.
(During the WAS Upgrade i upgraded the Central Instance and I dont have any other dialog instances).
But After I clicked Ok on the message box, the installation continued Normally and it seems to be going fine.
Can anyone help me out in this ?
Thanks.

Eric,
Thank you so much for answering me. It really helps.
One more question before i end this thread. I am new to portals and we are installing Portal on the Test box. To demonstrate the upper authorities how it might help for the company. I have so far installed SR1 and now upgrading to SP14. I have not installed TREX so far but will be installing in future. We are installing everything onto one box. I have installed Oracle database, WEBAS, Portal and KMC on the same drive(D:). The drive capacity is 34GB and i have so far used 11.5 GB and left with like 22.5GB. So my question is if I install TREX on another Drive (E:), will 22.5GB space on D: sufficient for doing the development which includes ESS, MSS import and bit of development?

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