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My version (2.41) has stopped working as well. I have El Capitan too. It hangs on the "Initializing user interface..." screen--never loads. I have to force quit the app. Even after uninstalling it, I have to power off the computer by the switch because the computer hangs at shut-down. Once I restart the computer is normal and fine unless I try to start Calibre. I have downloaded it twice and installed it three times all to no avail. Although I have a large (4,500) library, it is not that because on the reinstalls I have created new libraries it different locations. I am anxiously awaiting a new version of Calibre which I hope will work for me.
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