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Try to use the latest version of OpenCV (master branch). There were some fixes related to ffmpeg/libav support made after 3.1 release.

~~Try to use the latest version of OpenCV (~~Install masterpkg-config ~~branch). There were some fixes related~~ package. I was able to ~~ffmpeg/libav support made after 3.1 release.~~build OpenCV with ffmpeg in Ubuntu 16.04 using the following Docker config:

FROM ubuntu:16.04

RUN apt-get update -y

RUN apt-get install \
    libtiff-dev \
    gcc \
    g++ \
    cmake \
    ninja-build \
    -y

RUN apt-get install \
    libavutil-dev \
    libavcodec-dev \
    libavfilter-dev \
    libavformat-dev \
    libavdevice-dev \
    pkg-config \
    -y

RUN mkdir -p /build
VOLUME /opencv

CMD cd /build && rm -rf * && cmake -GNinja ../opencv && ninja