install-silicon.sh

# Install script for additional packages needed for Apple silicon chips that
# have to rely on rocker/rstudio image built with ARM64
# Adapted from scripts provided by rocker, e.g.
# https://github.com/rocker-org/rocker-versioned2/blob/master/scripts/\
# 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 \
    gdal-bin \
    lbzip2 \
    libfftw3-dev \
    libgdal-dev \
    libgeos-dev \
    libgsl0-dev \
    libgl1-mesa-dev \
    libglu1-mesa-dev \
    libhdf4-alt-dev \
    libhdf5-dev \
    libjq-dev \
    libpq-dev \
    libproj-dev \
    libprotobuf-dev \
    libnetcdf-dev \
    libsqlite3-dev \
    libssl-dev \
    libudunits2-dev \
    netcdf-bin \
    postgis \
    protobuf-compiler \
    sqlite3 \
    tk-dev \
    unixodbc-dev

install2.r --error --skipmissing --skipinstalled -n "$NCPUS" \
    tidyverse \
    devtools \
    rmarkdown \
    RColorBrewer \
    RandomFields \
    RNetCDF \
    classInt \
    deldir \
    gstat \
    hdf5r \
    mapdata \
    maptools \
    mapview \
    ncdf4 \
    proj4 \
    raster \
    rgdal \
    rgeos \
    rlas \
    sf \
    sp \
    spacetime \
    spatstat \
    spatialreg \
    spdep \
    stars \
    terra \
    tidync \
    tmap \
    geoR \
    geosphere \
    rmapshaper \
    patchwork \
    kableExtra \
    prettydoc \
    cowplot \
    here \
    rmdformats


# 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