I always forget that major software upgrades in OS X reset permissions in /usr/local. When I checked my brew install, I saw that message. I played around with write permissions only, but in the end, did what brew recommended and reset the permissions as described. That allowed me to update brew and move on to the next task: updating Python3.
I was not as far back as I expected. I was sitting on Python 3.4. The upgrades went smoothly and I’m back to Python 3.5.1. I thought I had modules installed, but I’m not getting any list of local modules installed. It’s very possible, since I never did much with on the desktop. That will be the next task.