localhost:PodTest3 haiwang$ pod install Analyzing dependencies Downloading dependencies Installing MBProgressHUD (0.9.2) Installing Masonry (1.0.2) Generating Pods p
I made it work using Cocoapods 1.1.1 with Xcode 8.1 on macOS 10.12.1 (the one with TouchBar support) by removing generated workspace, running pod deintegrate and running pod install again.
pod deintegrate
pod install