Singularity.myR_4-0-2_rstudio_1.3

Bootstrap: docker
From: rocker/rstudio:4.0.2 #rocker/tidyverse:4.0.3 #or: rocker/tidyverse:latest

%environment
  R_VERSION=4.0.2
  export R_VERSION
  export PATH=$PATH

%labels
  Author Sebastien Cunnac
  Version v0.0.1
  R_Version 4.0.2
  build_date March 2021
  R_bioconductor True

%post
  apt-get update
#  apt-get install -y apt-transport-https apt-utils software-properties-common
#  add-apt-repository main
#  add-apt-repository universe
#  add-apt-repository multiverse

  # General Utilities
  apt-get install -y wget rsync git-lfs openssh-client build-essential

  # Specific libs for R packages to run
  apt-get install -y texinfo texlive-latex-extra libmagick++-dev \
      libcairo2-dev libxt-dev \
      libglu1-mesa-dev libgmp-dev libmpfr-dev libv8-dev \
      libudunits2-dev gdal-bin libgdal-dev libglpk-dev libpoppler-cpp-dev

  # cleaning up
  apt-get autoremove --purge --yes
  apt-get clean

  # installing packages from cran
  install2.r --error \
      --deps FALSE --skipinstalled \
      Cairo \
      svglite \
      nloptr \
      rgl \
      fs \
      BiocManager

  # installing Bioconductor
  R --slave -e 'BiocManager::install(ask = FALSE)'

  # disable session timeout
  echo "session-timeout-minutes=0" >> /etc/rstudio/rsession.conf
  echo "auth-timeout-minutes=0" >> /etc/rstudio/rserver.conf
  rstudio-server restart

  # Display versions
  echo '############################################'
  echo "## Build Date: $(date)"
  echo "## R sessionInfo:\n"
  R --slave -e 'sessionInfo()'