localhost:PodTest3 haiwang$ pod install
Analyzing dependencies
Downloading dependencies
Installing MBProgressHUD (0.9.2)
Installing Masonry (1.0.2)
Generating Pods p
I'm having the same issue with Cocoapods 1.1.1 on rvm ruby (tried 2.2.4p230, and 2.0.0p648 which is the equal to system ruby version), with Xcode 8.1 (8B62), macOS 10.12.1 (16B2657), and only thing that helps me is updating to Cocoapods 1.2.0.beta.1, or using system ruby:
$ rvm system do pod install
and of course if you don't have cocoapods installed in system gemset:
$ sudo rvm system do gem install cocoapods