Similar to what Peter, said. But, I will recommend that if you do a manual Binary Install, then for further subsequent upgrades just use that method to update to the next release, whenever it comes out. And don't touch the apt/Software Center version of it.
Your issue is not related to the binary install at all. So, firstly either fix your source for getdeb by properly adding it to your system by following all the 3 steps specified here:
http://www.getdeb.net/updates/Ubuntu...how_to_install or remove getdeb completely by doing so:
Code:
sudo apt-get remove getdeb-repository
in the commandline. Other things to note is as I said earlier keep only one version of calibre, not both. From what I glean you still have calibre installed from the Software Center. To remove it run:
Code:
sudo apt purge calibre
.