I hit this speedbump last week but forgot to mention it.
[rosbuild] Building package gazebo
Failed to invoke /opt/ros/fuerte/bin/rospack deps-manifests gazebo
[rospack] Error: package/stack gazebo depends on non-existent package
protobuf
Adding protobuf as below to .rosinstall fixes it...
- tar: {local-name: protobuf, uri:
'https://code.ros.org/svn/release/download/stacks/protobuf/protobuf-0.1.0/protobuf-0.1.0.tar.bz2',
version: protobuf-0.1.0}
protobuf wiki says it's needed on some distros but not others but I
don't understand how to tell rospack that my distro has version > 2.3
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