Open kimsin98 opened 1 year ago
thanks @kimsin98 - this limitation is not intended. could you please give an example of a neurodocker command line where this fails?
This would build fine.
docker run --rm repronim/neurodocker:0.7.0 generate docker \
--base neurodebian:bullseye --pkg-manager apt \
--user=neuro --workdir /home/neuro \
--miniconda create_env=neuro activate=true \
conda_install='jupyter nilearn' \
> Dockerfile
But after 0.8.0
docker run --rm repronim/neurodocker:0.8.0 generate docker \
-b neurodebian:bullseye -p apt \
--user=neuro --workdir /home/neuro \
--miniconda version=latest env_name=neuro env_exists=false \
conda_install='jupyter nilearn' \
> Dockerfile
docker build runs into a permission error because it is not running as root
Step 6/9 : RUN apt-get update -qq && apt-get install -y -q --no-install-recommends bzip2 ca-certificates curl && rm -rf /var/lib/apt/lists/* && export PATH="/opt/miniconda-latest/bin:$PATH" && echo "Downloading Miniconda installer ..." && conda_installer="/tmp/miniconda.sh" && curl -fsSL -o "$conda_installer" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh && bash "$conda_installer" -b -p /opt/miniconda-latest && rm -f "$conda_installer" && conda update -yq -nbase conda && conda config --system --prepend channels conda-forge && conda config --set channel_priority strict && conda config --system --set auto_update_conda false && conda config --system --set show_channel_urls true && conda init bash && conda create -y --name neuro && conda install -y --name neuro "jupyter" "nilearn" && sync && conda clean --all --yes && sync && rm -rf ~/.cache/pip/*
---> Running in 2a0cd57132ca
E: List directory /var/lib/apt/lists/partial is missing. - Acquire (13: Permission denied)
The command '/bin/sh -c apt-get update -qq && apt-get install -y -q --no-install-recommends bzip2 ca-certificates curl && rm -rf /var/lib/apt/lists/* && export PATH="/opt/miniconda-latest/bin:$PATH" && echo "Downloading Miniconda installer ..." && conda_installer="/tmp/miniconda.sh" && curl -fsSL -o "$conda_installer" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh && bash "$conda_installer" -b -p /opt/miniconda-latest && rm -f "$conda_installer" && conda update -yq -nbase conda && conda config --system --prepend channels conda-forge && conda config --set channel_priority strict && conda config --system --set auto_update_conda false && conda config --system --set show_channel_urls true && conda init bash && conda create -y --name neuro && conda install -y --name neuro "jupyter" "nilearn" && sync && conda clean --all --yes && sync && rm -rf ~/.cache/pip/*' returned a non-zero code: 100
This issue is stale because it has been open for 30 days with no activity.
Currently, due to the apt/yum dependency check,
--miniconda
has to run as root. This can lead to some surprises and inconveniences like https://github.com/ReproNim/neurodocker/issues/506#issuecomment-1397386258 becauseconda init
only runs as root.If this limitation is not intended, a possible fix is temporarily switching to root for the dependency check.