R_installer_debian_ubuntu.sh

#!/usr/bin/env bash

set -e
set +x

# This bash script:
#   1. adds the CRAN repository
#   2. installs R
#   3. installs R packages for AFNI
#
# Should work on most Debian-based Linux distributions.
# Based heavily on
# https://github.com/Shotgunosine/afni_add_rcran_ubuntu/blob/master/%40add_rcran_ubuntu.tcsh

echo "++ Attempting to install R ..."

apt-get update -qq
apt-get install -yq --no-install-recommends curl dirmngr gnupg

source /etc/os-release

# Get OS name (e.g., 'debian', 'ubuntu').
OS_NAME="$(echo $NAME | sed 's/ .*//' | tr '[:upper:]' '[:lower:]')"
echo "++ OS name is ${OS_NAME}"

# Get codename and remove non-alpha characters (but keep spaces).
OS_CODENAME="$(echo $VERSION | sed 's/[^A-Z a-z]//g')"
# Remove everything except first word, and make lowercase.
OS_CODENAME="$(echo $OS_CODENAME | sed 's/ .*//' | tr '[:upper:]' '[:lower:]')"
echo "++ OS codename is ${OS_CODENAME}"

# Get key. The gpg keys are fetched from DropBox and then updated from the
# keyservers. The keyservers can be unreliable for some reason.
echo "++ Adding key for CRAN repository ..."
if [ "$OS_NAME" == "debian" ]; then
    CRAN_SUBDIR="${OS_CODENAME}-cran34"
    apt-key adv --fetch-keys https://dl.dropbox.com/s/28b2hl1mds4ggqx/r-cran-debian.gpg
    # Syntax from https://github.com/poldracklab/fmriprep/blob/master/Dockerfile#L21
    (apt-key adv --refresh-keys --keyserver hkp://pool.sks-keyservers.net E19F5F87128899B192B1A2C2AD5F960A256A04AF || true)
elif [ "$OS_NAME" == "ubuntu" ]; then
    CRAN_SUBDIR="${OS_CODENAME}"
    apt-key adv --fetch-keys https://dl.dropbox.com/s/i1psi8vbhvvmj97/r-cran-ubuntu.gpg
    (apt-key adv --refresh-keys --keyserver keyserver.ubuntu.com E084DAB9 || true)
fi

# Add CRAN sources to sources.list.
echo "deb http://cloud.r-project.org/bin/linux/${OS_NAME}/ ${CRAN_SUBDIR}/" | tee --append /etc/apt/sources.list

apt-get update -qq
echo "++ Removing previously installed R ..."
apt-get remove -y r-base r-base-core r-base-dev
echo "++ Installing R ..."
apt-get install -yq --no-install-recommends r-base-dev

# r-cran-rmpi is not available (yet?) on debian stretch.
# https://packages.debian.org/jessie/r-cran-rmpi
echo "++ Installing the R package Rmpi ..."
{
  apt-get install -yq --no-install-recommends r-cran-rmpi
} || {
  echo "++ r-cran-rmpi could not be installed with apt-get. Trying a different installation method ..."
  apt-get install -yq --no-install-recommends mpi-default-bin &&
  curl -sSL -o /tmp/rcranrmpi.deb http://ftp.us.debian.org/debian/pool/main/r/rmpi/r-cran-rmpi_0.6-6-4_amd64.deb &&
  dpkg -i /tmp/rcranrmpi.deb &&
  rm -f /tmp/rcranrmpi.deb
}

apt-get clean
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

echo "++ Finished installing R."