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I suspect this https://github.com/shogun-toolbox/shogun/issues/2626 has something to do with the issue I was facing.
sudo apt-get install libhdf5-openmpi-dev
solved my immediate issues. However: here I got new problems about not finding libvtkproj4-6.2.so. I think there were some bugs around that as well, but the issues differ slightly: https://github.com/PointCloudLibrary/pcl/issues/1594 https://bugs.launchpad.net/ubuntu/+source/vtk6/+bug/1573234
This issue could be fixed by
sudo apt-get install libvtkproj-dev
But I knew I was on the wrong path trying to fix the symptoms of a problem instead of the source. The new issue that appeared was that catkin could not find costmap_2d anymore.
So: I fixed all my problems with
sudo apt-get update
sudo apt-get install ros-kinetic-navigation
I don't know if the first 2 calls are completely overwritten by the apt-get update and reinstall of the navigation package (don't know if they had an effect in solving my problem). All I know is: it works now.
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