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Not sure what causes this. genmsg should be a ROS package that you have from source in your catkin workspace.
Maybe try to wipe your build, devel and install space and start the build anew.
What version of Python are you using? Years back I remember issue with using python from homebrew instead of the system supplied one, but I have no idea what the current state is there (http://answers.ros.org/question/110671/recommended-python-version-on-os-x-with-homebrew/). Actually, I notice that both the install instructions and Mike Purvis' script (https://github.com/mikepurvis/ros-install-osx) install brewed python, so that seems to be the way to go currently.
Which ROS distribution are you trying to install? Kinetic? How did you populate your workspace? Which packages are there?
Maybe check the issue for "Sierra" and "Kinetic" in https://github.com/mikepurvis/ros-install-osx for additional tips.
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