As you can see, it's identical with the pip2.log. Could it be then, that there is even more programs that don't realize that their requirements have already being met?

As in, program not registering correctly for some reason, even when there is no visible errors during the installation? Ghost in the shell?

That happens sometimes, if you have some stuff installed via pip and some via apt-get and have both vanilla (non-debug) and debug versions of python. That's because of different versions of python requires related versions of packages.
Hmm, tried to check if I had any debug version of those, but didn't have those - just the normal ones. Could pytools conflict with setuptools? As installing pyopencl installs both pytools and numpy by default, it seems

At least when done through the software center.