After running Tools/gtk/install-dependencies script, it didn't install libicu-dev package on ubuntu. This result in harfbuzz being built without icu support when running Tools/Scripts/update-webkitgtk-libs script. Then webkit fails to build because it is missing hb-icu.h at some point.
Actually, sorry for the noise, I didn't see apt-get wasn't happy when running the install-dependencies script. It said: E: Unable to correct problems, you have held broken packages. So that's my system that is broken.