Why is my container when starting as root seem to be empty?

When I get into my container nothing seems to have ebeen installed? docker pull brandojazz/iit-term-synthesis:test then

docker run -u root -ti brandojazz/iit-term-synthesis:test_arm bash

see:

(base) root@897a4007076f:/home/bot# opam switch
[WARNING] Running as root is not recommended
[ERROR] Opam has not been initialised, please run `opam init'

it should have been initialized.

FROM continuumio/miniconda3
# FROM --platform=linux/amd64 continuumio/miniconda3

MAINTAINER Brando Miranda "[email protected]"

RUN apt-get update \
  && apt-get install -y --no-install-recommends \
    ssh \
    git \
    m4 \
    libgmp-dev \
    opam \
    wget \
    ca-certificates \
    rsync \
    strace \
    gcc
#    rlwrap \
#    sudo

# https://github.com/giampaolo/psutil/pull/2103

RUN useradd -m bot
# format for chpasswd user_name:password
# RUN echo "bot:bot" | chpasswd
# RUN && adduser docker sudo

WORKDIR /home/bot
USER bot

ADD https://api.github.com/repos/IBM/pycoq/git/refs/heads/main version.json

# -- setup opam like VP's PyCoq
RUN opam init --disable-sandboxing
# compiler + '_' + coq_serapi + '.' + coq_serapi_pin
RUN opam switch create ocaml-variants.4.07.1+flambda_coq-serapi.8.11.0+0.11.1 ocaml-variants.4.07.1+flambda
RUN opam switch ocaml-variants.4.07.1+flambda_coq-serapi.8.11.0+0.11.1
RUN eval $(opam env)

RUN opam repo add coq-released https://coq.inria.fr/opam/released
# RUN opam pin add -y coq 8.11.0
# ['opam', 'repo', '--all-switches', 'add', '--set-default', 'coq-released', 'https://coq.inria.fr/opam/released']
RUN opam repo --all-switches add --set-default coq-released https://coq.inria.fr/opam/released
RUN opam update --all
RUN opam pin add -y coq 8.11.0

#RUN opam install -y --switch ocaml-variants.4.07.1+flambda_coq-serapi_coq-serapi_8.11.0+0.11.1 coq-serapi 8.11.0+0.11.1
RUN opam install -y coq-serapi

#RUN eval $(opam env)
#
## makes sure depedencies for pycoq are installed once already in the docker image
#RUN pip install https://github.com/ddelange/psutil/releases/download/release-5.9.1/psutil-5.9.1-cp36-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
#ENV WANDB_API_KEY="SECRET"
#RUN pip install wandb --upgrade
#
#RUN pip install ultimate-utils
## RUN pip install pycoq  # do not uncomment on arm, unless serlib is removed from setup.py in the pypi pycoq version.
## RUN pip install ~/iit-term-synthesis  # likely won't work cuz we don't have iit or have pused it to pypi
#
## then make sure editable mode is done to be able to use changing pycoq from system
#RUN echo "pip install -e /home/bot/ultimate-utils" >> ~/.bashrc
#RUN echo "pip install -e /home/bot/pycoq" >> ~/.bashrc
#RUN echo "pip install -e /home/bot/iit-term-synthesis" >> ~/.bashrc
#RUN echo "pip install wandb --upgrade" >> ~/.bashrc
#
#RUN echo "eval $(opam env)" >> ~/.bashrc
## - set env variable for bash terminal prompt p1 to be nicely colored
#ENV force_color_prompt=yes
#
#RUN mkdir -p /home/bot/data/

# RUN pytest --pyargs pycoq
#CMD /bin/bash

NB: This may not be your only problem (I have no idea what opam is or how it works), but one thing jumps out:

This...

RUN eval $(opam env)

...doesn't do anything. Each RUN invocation happens in a new subshell; environment variables set in one RUN command aren't going to be visible in a subsequent RUN command.

Rather than a list of single-command RUN commands, chain everything together in a single command:

RUN eval $(opam env) && \
  opam repo add coq-released https://coq.inria.fr/opam/released && \
  opam repo --all-switches add --set-default coq-released https://coq.inria.fr/opam/released && \
  opam update --all && \
  opam pin add -y coq 8.11.0 && \
  opam install -y coq-serapi

Because the above runs in a single shell, the environment set by eval $(opam env) will be available to all the following commands.

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