Anyhow, I sat determined today to do it myself. Started to analyze the output that I was getting when I was trying to run the setup.py scritpt. It was giving me an import error flask.ext.fas_openid module not found. I researched and found some reference to it in github on python-fedora and saw the same guys who manage pkgdb1 and 2 discussing something about that module there.
I uninstalled python-fedora and rebuilt it, but this time I got the source from github because I thought they have the most update version and I was right. I installed python-fedora from there and I stopped getting that error and my beloved pkgdb2 built successfully. Here is a screenshot of the new deployment. Notice that it is running on the IP address with the proper alias this time and not a random port number. Actually I configured the alias to be pkgdb, I can change it to pkgdb2 or anything else according to our requirements.

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