This has happened to me during every OS X upgrade/reinstallation I can remember. The first time, I also assumed that it just wasn't working. I've since learned that the 99% is deceiving in terms of the expectations it might give you. You just have to be patient and it'll eventually work.

It would have finished eventually. This only happens if you have a lot of stuff in /usr/local (e.g. Homebrew).

https://jimlindley.com/blog/yosemite-upgrade-homebrew-tips/