I was trying to build a docker container using Apptainer. I have a long list of R packages to be installed with specific versions. I need to install it from CRAN/BioConductor directly and not from conda. Now, for each package I try to install, I might hit a roadblock due to missing libraries and then have to go back and add it using apt install. This becomes an iterative process and takes a long time. Is there an interactive way to build the container. I was trying using sandbox and fakeroot but it does not get the full capabilities to write while installing the system libraries. What other solution can I integrate?

Bootstrap: docker
From: ubuntu:22.04
%labels
    Author author_name
    version v0.1

%post 
    export DEBIAN_FRONTEND=noninteractive
    
    # Update system and install requirements
    apt-get -qq update
    

    apt -y install build-essential gfortran curl cmake pkg-config zip unzip 
                   libglib2.0-0 libpango-1.0-0 libpangocairo-1.0-0 libpaper-utils 
                   libtcl8.6 libtk8.6 libxt6 lmod 
    
    apt -y install libbz2-dev libicu-dev liblzma-dev libopenblas-dev libpq-dev 
                   libpcre2-dev zlib1g-dev libssl-dev libudunits2-dev libncurses-dev libcairo2-dev 
                   libsodium-dev libmariadb-dev libcurl4-openssl-dev libssh2-1-dev libxml2-dev 
                   libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev libfontconfig1-dev 
                   libharfbuzz-dev libfribidi-dev liblapack-dev libgit2-dev libmagick++-dev 
    
    
    curl -o /tmp/libicu60_60.2-3ubuntu3.2_amd64.deb http://security.ubuntu.com/ubuntu/pool/main/i/icu/libicu60_60.2-3ubuntu3.2_amd64.deb
    dpkg -i /tmp/libicu60_60.2-3ubuntu3.2_amd64.deb

  
    # Install R with all recommended 
    export R_VERSION=4.2.2
    curl -o /tmp/r-${R_VERSION}_1_amd64.deb https://cdn.rstudio.com/r/ubuntu-2204/pkgs/r-${R_VERSION}_1_amd64.deb
    dpkg -i /tmp/r-${R_VERSION}_1_amd64.deb

    ln -s /opt/R/${R_VERSION}/bin/R /usr/local/bin/R
    ln -s /opt/R/${R_VERSION}/bin/Rscript /usr/local/bin/Rscript


    # Install the R packages
    
    R -e 'install.packages("remotes", dependencies = TRUE, repos = c("https://cloud.r-project.org/", "http://rforge.net/"))'
    R -e 'remotes::install_version(package = "BiocManager", version = "1.30.22", dependencies = TRUE, repos = c("https://cloud.r-project.org/", "http://rforge.net/"), upgrade = "never")'

    R -e 'remotes::install_version(package = "dplyr", version = "1.1.4", dependencies = TRUE, repos = c("https://cloud.r-project.org/", "http://rforge.net/"), upgrade = "never")' 
    R -e 'remotes::install_version(package = "ggplot2", version = "3.5.1", dependencies = TRUE, repos = c("https://cloud.r-project.org/", "http://rforge.net/"), upgrade = "never")'  ##### downgraded to 3.4.3
    R -e 'remotes::install_version(package = "ggpubr", version = "0.6.0", dependencies = TRUE, repos = c("https://cloud.r-project.org/", "http://rforge.net/"), upgrade = "never")'