Docker File Non-Zero Code 100 Error When Building

Question

Here is my Docker File:

 FROM ubuntu:16.04
MAINTAINER Alexandre Savio <[email protected]>
RUN ln -snf /bin/bash /bin/sh
ARG DEBIAN_FRONTEND=noninteractive
ENV PETPVC_VERSION v1.2.1
ENV PETPVC_GIT https://github.com/UCL/PETPVC.git
ENV ITK_VERSION v4.12.2
ENV ITK_GIT http://itk.org/ITK.git
ENV VTK_VERSION v6.3.0
ENV VTK_GIT https://gitlab.kitware.com/vtk/vtk.git
ENV SIMPLEITK_VERSION v1.0.1
ENV SIMPLEITK_GIT http://itk.org/SimpleITK.git
ENV ANTS_VERSION v2.2.0
ENV ANTS_GIT https://github.com/stnava/ANTs.gi
ENV NEURODEBIAN_URL http://neuro.debian.net/lists/xenial.de-m.full
ENV NEURODEBIAN_PGP hkp://pool.sks-keyservers.net:80 0xA5D32F012649A5A9
ENV LIBXP_URL http://mirrors.kernel.org/ubuntu/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb
ENV AFNI_URL https://afni.nimh.nih.gov/pub/dist/bin/linux_fedora_21_64/@update.afni.binaries
ENV CAMINO_GIT git://git.code.sf.net/p/camino/code
ENV SPM12_URL http://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/dev/spm12_latest_Linux_R2017b.zip
ENV MLAB_URL http://ssd.mathworks.com/supportfiles/downloads/R2017b/deployment_files/R2017b/installers/glnxa64/MCR_R2017b_glnxa64_installer.zip
ENV MCR_VERSION_DIR v93
ENV PYENV_NAME pyenv
ENV N_CPUS 2
RUN apt-get update && \
    apt-get -y install apt-utils locales && \
    echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen && \
    locale-gen en_US.utf8 && \
    /usr/sbin/update-locale LANG=en_US.UTF-8
ENV LC_ALL en_US.UTF-8
ENV LANG en_US.UTF-8
ENV LANGUAGE en_US.UTF-8
ENV TERM xterm
ENV HOME /work
ENV SOFT $HOME/soft
ENV BASHRC $HOME/.bashrc
ENV BASICUSER basicuser
ENV BASICUSER_UID 1000
RUN useradd -m -d $HOME -s /bin/bash -N -u $BASICUSER_UID $BASICUSER && \
    mkdir $SOFT && \
    mkdir $HOME/.scripts && \
    mkdir $HOME/.nipype
USER $BASICUSER
WORKDIR $HOME
COPY root/.* $HOME/
COPY root/* $HOME/
COPY root/.scripts/* $HOME/.scripts/
COPY root/.nipype/* $HOME/.nipype/
USER root
RUN \
    chown -R $BASICUSER $HOME && \
    echo "export SOFT=\$HOME/soft" >> $BASHRC && \
    echo "source /etc/fsl/5.0/fsl.sh" >> $BASHRC && \
    echo "export FSLPARALLEL=condor"  >> $BASHRC && \
    apt-get update && \
    apt-get install -y wget bzip2 unzip htop curl git && \
    wget -O- $NEURODEBIAN_URL | tee /etc/apt/sources.list.d/neurodebian.sources.list && \
    apt-key adv --recv-keys --keyserver hkp://pool.sks-keyservers.net:80 0xA5D32F012649A5A9 && \
    sed -i "s/# \(.*multiverse$\)/\1/g" /etc/apt/sources.list && \
    echo 'deb-src http://archive.ubuntu.com/ubuntu xenial main restricted' | tee /etc/apt/sources.list && \
    apt-get update && \
    apt-get -y upgrade && \
    apt-get install -y \
apt-utils \
locales \
cmake \
gcc-4.9 \
g++-4.9 \
gfortran-4.9 \
gcc-5 \
g++-5 \
gfortran-5 \
tcsh \
libjpeg62 \
libxml2-dev \
libxslt1-dev \
dicomnifti \
dcm2niix \
xdot \
fsl-5.0-eddy-nonfree \
fsl-5.0-core && \
rm -rf /var/lib/apt/lists/* && \
update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-5   90 --slave /usr/bin/g++ g++ /usr/bin/g++-5 && \
update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.9 80 --slave /usr/bin/g++ g++ /usr/bin/g++-4.9 && \
  apt-get build-dep vtk6

 && ln -s /usr/lib/x86_64-linux-gnu/libgsl.so /usr/lib/libgsl.so.0 && \ </code>

I'm specifically getting the error here

Error: The command returned a nonzero code 100

RUN \
    chown -R $BASICUSER $HOME && \
    echo "export SOFT=\$HOME/soft" >> $BASHRC && \
    echo "source /etc/fsl/5.0/fsl.sh" >> $BASHRC && \
    echo "export FSLPARALLEL=condor"  >> $BASHRC && \
    apt-get update && \
    apt-get install -y wget bzip2 unzip htop curl git && \
    wget -O- $NEURODEBIAN_URL | tee /etc/apt/sources.list.d/neurodebian.sources.list && \
    apt-key adv --recv-keys --keyserver hkp://pool.sks-keyservers.net:80 0xA5D32F012649A5A9 && \
    sed -i "s/# (.multiverse$)/\1/g" /etc/apt/sources.list && \
    echo 'deb-src http://archive.ubuntu.com/ubuntu xenial main restricted' | tee /etc/apt/sources.list && \
    apt-get update && \
    apt-get -y upgrade && \
    apt-get install -y \

This is a prebuilt docker file from a repository for neuroimaging, so I would figure that it would work. Is this something wrong on my end?

I'm not entirely sure how to go about debugging and solving this problem.

Answer 1

On your apt-get install line, add -y... what is happening is that your build cannot complete as it is waiting for user confirmation to allow the install, something which will never happen because the Docker build process is non-interactive.

That should fix you up!