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fatal error: Eigen: No such file or directory #include <Eigen>

The problem seems to be with the linking, somehow. When I call catkin_make_isolated there is no problem finding FindEigen3.config, but the source files themselves don't see #include <Eigen>

CMakeLists.txt has the following references to Eigen3:

 find_package(Eigen3 REQUIRED)

 include_directories(
    ${catkin_INCLUDE_DIRS}
    ${Eigen3_INCLUDE_DIRS}
  )

  catkin_package(CATKIN_DEPENDS message_runtime
    DEPENDS Eigen3
  )

and package.xml has

  <build_depend>roscpp</build_depend>
  <run_depend>roscpp</run_depend>
  <build_depend>cmake_modules</build_depend>
  <run_depend>cmake_modules</run_depend>

I've gone back and forth with this problem for hours, but I'm at my wits end. I'd be really grateful if you could shed a light on this.

Tell me if you need to see other file contents. I really appreciate it!

I'm running catkin_make_isolated and some packages, which seem to be the one I got with git clone trigger a message like

The dependency target "geometry_msgs_gencpp" of target "tf_conversions"
  does not exist.
This warning is for project developers.  Use -Wno-dev to suppress it.

or

The dependency target "tf2_msgs_gencpp" of target "tf2_ros_buffer_server"
  does not exist.
This warning is for project developers.  Use -Wno-dev to suppress it.

I'm not sure what I'm missing here. I googled and browsed the git's but I didn't find any clues. Do I need to take care of these messages?

First link.

I did run the setup from that installation page. Roscore does actually run, but specifically there's a problem downloading packages.

Yes. I did it, but no luck.

I've tried running sudo apt-get install ros-indigo-ros-tutorials ros-indigo-geometry-tutorials ros-indigo-rviz ros-indigo-rosbash ros-indigo-rqt-tf-tree but it outputs:

Reading package lists... Done
Building dependency tree       
Reading state information... Done
E: Unable to locate package ros-indigo-ros-tutorials
E: Unable to locate package ros-indigo-geometry-tutorials
E: Unable to locate package ros-indigo-rviz
E: Unable to locate package ros-indigo-rosbash
E: Unable to locate package ros-indigo-rqt-tf-tree

apt-get seems to be able to download other things such as nmap but the ROS packages simply are un-locatable. Any ideas? I'm pretty new to Raspbian (I'm on a RPi) and feel a bit at a loss.

Thanks!