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:

```r
# Restart your R session so it is clear (Ctrl-Shift-F10 in Rstudio)
userRlib = "~/tempRPackages/4.1" # important to specify version here ... things may not work as expected below if omitted
if (!dir.exists(userRlib)) dir.create(userRlib, recursive = TRUE)
.libPaths(userRlib)
if (!require("Require")) {install.packages("Require"); library(Require)}
Require("PredictiveEcology/SpaDES.install (>= 0.0.5.9002)", dependencies = FALSE) # install/load this package
installSpaDES()
modulePath = "modules"
makeSureAllPackagesInstalled(modulePath)
```