Singularity definition file for R

r.def

BootStrap: docker
From: ubuntu:18.04

%labels
  Maintainer Dan Fitch
  R_Version 3.6.3

%apprun R
  exec R "${@}"

%apprun Rscript
  exec Rscript "${@}"

%apprun Rstudio
  exec Rstudio "${@}"

%runscript
  exec R "${@}"

%post
  # Software versions
  export R_VERSION=3.6.3

  # Get dependencies
  # gnupg is new as of 18.04, required to add apt keys
  apt-get update
  apt-get install -y --no-install-recommends \
    locales \
    gnupg

  # Run tzdata and force noninteractive
  DEBIAN_FRONTEND=noninteractive apt install -y tzdata

  # Configure default locale
  echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen
  locale-gen en_US.utf8
  /usr/sbin/update-locale LANG=en_US.UTF-8
  export LC_ALL=en_US.UTF-8
  export LANG=en_US.UTF-8
  
  # Install R
  echo "deb http://cran.r-project.org/bin/linux/ubuntu bionic-cran35/" > /etc/apt/sources.list.d/r.list
  apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
  apt-get update
  apt-get install -y \
    r-base=${R_VERSION}* \
    r-base-core=${R_VERSION}* \
    r-base-dev=${R_VERSION}* \
    r-recommended=${R_VERSION}* \
    r-base-html=${R_VERSION}* \
    r-doc-html=${R_VERSION}* \
    libcurl4-openssl-dev \
    libssl-dev \
    libxml2-dev \
    libcairo2-dev \
    libxt-dev \
    sqlite3 \
    libsqlite3-dev

  # Add a default CRAN mirror
  echo "options(repos = c(CRAN = 'https://cran.rstudio.com/'), download.file.method = 'libcurl')" >> /usr/lib/R/etc/Rprofile.site

  # Add a directory for host R libraries
  mkdir -p /library
  echo "R_LIBS_SITE=/library:\${R_LIBS_SITE}" >> /usr/lib/R/etc/Renviron.site

  # Install packages
  R --slave -e 'install.packages("pacman", repos="https://cloud.r-project.org/")'
  R --slave -e 'install.packages("tidyverse", repos="https://cloud.r-project.org/")'
  R --slave -e 'install.packages("psych", repos="https://cloud.r-project.org/")'
  # MORE PACKAGES CAN GO HERE WHEEEEE

  # Clean up
  rm -rf /var/lib/apt/lists/*