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calibre does not touch *any* system components, it installs *nothing* to system areas except shortcuts and a few registry keys. If your computer is asking you to reboot because of a calibre installation then windows installer is being flakey.
IIRC, windows installer is very easily confused on this subject. For example if you click a link in calibre which opens in your browser and then you update calibre with that browser still running, windows installer thinks it needs to reboot, for some reason known only to microsoft.
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