There has been a recent change in the rosdistro system, and tools such as rosdep have been updated. I would recommend the following two things:
1. Make sure rosdep is up to date:
`sudo apt-get update`
`sudo apt-get install python-rosdep`
2. Run `sudo rosdep init` to reinitialize your /etc/ros/rosdep/sources.list.d, then `rosdep update` to update your local cache
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