Installation

Prerequisites

To run development modules etc., users will need to have installed R, Rstudio and SpaDES.

Install R

Windows

1. Download and run the R installer (as administrator!) from https://cran.r-project.org/bin/windows/base.
2. Download and install the latest Rtools (as administrator!) from http://cran.r-project.org/bin/windows/Rtools/. Be sure to check the "add rtools to PATH" option during installation.

macOS

1. Download and run the R installer from https://cran.r-project.org/bin/macosx.

2. Install Xcode commandline tools from the terminal:

   xcode-select --install

3. Install homebrew from the terminal (instructions at https://brew.sh/)

4. Install GDAL and other spatial packages (instructions at https://www.alexchubaty.com/post/2020-01-08-using-latest-gdal-macos-redux/)

5. Install OpenMP support for data.table:

   brew update && brew install llvm

6. Install GLPK (needed for full igraph functionality; used with SpaDES.core::moduleGraph):

   brew install glpk

   Then, reinstall igraph from source so it is compiled with GLPK:

   install.packages("igraph", type = "source")

Linux

Install via apt or yum depending on your distribution. Instructions for Ubuntu 18.04 LTS are shown below.

1. Install R and its development libraries:

   sudo apt install r-base r-base-dev

2. Install java and configure R to use it:

   sudo apt build-dep -y r-cran-rjava
   sudo R CMD javareconf

3. Install dependencies for spatial and other packages:

   sudo apt build-dep -y r-cran-tkrplot
   
   sudo apt-get install -y \
     ccache \
     gdal-bin \
     git \
     libcairo2-dev \
     libcurl4-gnutls-dev \
     libgdal-dev \
     libgeos-dev \
     libgit2-dev \
     libgmp-dev \
     libjq-dev \
     libmagick++-dev \
     libproj-dev \
     libprotobuf-dev \
     libprotoc-dev \
     libssh2-1-dev \
     libssl-dev \
     libudunits2-dev \
     libv8-dev \
     libxml2-dev \
     libxt-dev \
     pandoc \
     pandoc-citeproc \
     protobuf-compiler \
     python-gdal \
     python3-gdal \
     curl \
     r-cran-littler

Install Rstudio

Download and run the installer for your operating system from https://www.rstudio.com/products/rstudio/download/#download.

Install SpaDES and other packages

Use the SpaDES.install package. Copied here, without instructions:

if (!require("Require", quietly = TRUE)) {
  # install.packages("Require")

  ## use development version from GitHub
  install.packages("remotes")
  remotes::install_github("PredictiveEcology/Require@development")
  library(Require)
}

Require("PredictiveEcology/SpaDES.install@development")

installSpaDES() ## will install to your default librayr path; see .libPaths()
## adjust this as needed
modulePath <- "modules"
makeSureAllPackagesInstalled(modulePath)