Upgrading from Yosemite to El Capitan seem to have wiped out the already installed CocoaPods. When I pod install Alamofire/SwiftyJson, it says \'Pod command not found\'
I faced the same problem and it was fixed by using the following command
$ sudo gem install cocoapods --source http://rubygems.org
I struggled with same issue 1 week, finally this works for me
Disable IPv6 and try again with sudo gem install cocoapods --source http://rubygems.org
Issues seems with network
Few more details give on rugby gems forum - https://help.rubygems.org/discussions/problems/31074-timeout-error