install_tidyverse.sh

#!/bin/bash

set -e

## build ARGs
NCPUS=${NCPUS:--1}

# a function to install apt packages only if they are not installed
function apt_install() {
    if ! dpkg -s "$@" >/dev/null 2>&1; then
        if [ "$(find /var/lib/apt/lists/* | wc -l)" = "0" ]; then
            apt-get update
        fi
        apt-get install -y --no-install-recommends "$@"
    fi
}

apt_install \
    libxml2-dev \
    libcairo2-dev \
    libgit2-dev \
    default-libmysqlclient-dev \
    libpq-dev \
    libsasl2-dev \
    libsqlite3-dev \
    libssh2-1-dev \
    libxtst6 \
    libcurl4-openssl-dev \
    libharfbuzz-dev \
    libfribidi-dev \
    libfreetype6-dev \
    libpng-dev \
    libtiff5-dev \
    libjpeg-dev \
    unixodbc-dev \
    libhdf5-serial-dev \
    build-essential \
    gcc \
    cmake

install2.r --error --skipinstalled -n "$NCPUS" \
    tidyverse \
    devtools \
    BiocManager \
    vroom \
    factoextra


## a bridge to far? -- brings in another 60 packages
# install2.r --error --skipinstalled -n "$NCPUS" tidymodels

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

## Strip binary installed lybraries from RSPM
## https://github.com/rocker-org/rocker-versioned2/issues/340
strip /usr/local/lib/R/site-library/*/libs/*.so

# Check the tidyverse core packages' version
echo -e "Check the tidyverse package...\n"

R -q -e "library(tidyverse)"

echo -e "\nInstall tidyverse package, done!"