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I finally found the solution:

I had to add source /opt/ros/kinetic/setup.bash directly in the subshell, the indirect sourcing through the ~./bashrc did not work for some reason. Is that a bug?

Working solution:

build_output=$( source /opt/ros/kinetic/setup.bash && catkin_make )

Thanks @gvdhoorn for your support.

I finally found the solution:

I had to add source /opt/ros/kinetic/setup.bash directly in the subshell, the indirect sourcing through the ~./bashrc did not work for some reason. Is that a bug?

Working solution:

build_output=$( source /opt/ros/kinetic/setup.bash && catkin_make )

Thanks @gvdhoorn for your support.

EDIT: This is why it didn't work:

This was the output of git invoking the githook script: /opt/ros/kinetic/setup.sh: line 47: TMPDIR: unbound variable. Which is usually not a problem, but the strict script rules enforced by set -euo pipefail caused it to crash.