There are many things going on wrong after I upgraded to OSX 10.12. For example, the Latex issue logged here.
Here I plan to log stuff that went wrong and how to fix them. As I kept updating, it could be long.
Brew errors
After OSX is updated, brew no longer has the write permission to /usr/local/. And I need to fix it by:
sudo chown -R $(whoami) /usr/local
Solution from here. After I did this, another error pops up:
$ brew update /usr/local/Library/Homebrew/cmd/update.sh: line 6: /usr/local/Library/ENV/scm/git: No such file or directory
The fix is to run the following (according to this):
cd "$(brew --repository)" && git fetch && git reset --hard origin/master
Tada! Problem fixed.