Been using Brew for as long as i can remember.
Most of the message usually require a `brew doctor` or `brew update` command which completely fixes the issue.
And i cant even remember the last time i had to do that..
When they brought in brew cask i was completely blown away and i use brew exclusively for installing almost everything on my mac.
I tried macports at first, but bailed out of that after i shot myself in the foot inside the hour. Switched to brew and have never looked back since.