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I have a clean install of Ubuntu 16.04 LTS and only installed the necessary packages tobuild the toolchains. The toolchains built successfully without error.
Then I tried building HB from the most recent sources using the following command:
Is cmake present in Ubuntu? If not, try installing cmake in Ubuntu, so Handbrake finds cmake and skips trying to compile its own local copy of cmake (that is failing for you).
sudo apt-get install cmake
You can see the /Handbrake/make/configure.py probing for what tools are present :-
/Handbrake/build/log/config.info.txt and config.verbose.txt
A message like " .. enabling local xxx" indicates Handbrake is compiling its own local copy of tool xxx
Its probably useful to check your Ubuntu also has autoconf, automake, libtool and pkg-config