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

1. Update package versions and install the SpaDES package via CRAN:

   # Restart your R session so it is clear (Ctrl-Shift-F10 in Rstudio)
   
   # If you have any of our packages or their dependencies, please update them first
   # Get latest versions of key SpaDES packages from CRAN
   deps <- tools::package_dependencies("SpaDES", recursive = TRUE)
   update.packages(oldPkgs = unlist(deps), ask = FALSE) 
   
   # install the latest version of the SpaDES packages, including "Suggested"
   install.packages("SpaDES", dependencies = TRUE) 

   The development branch on GitHub may contain useful bug fixes that are not in the CRAN version. To install this development version:

   library("devtools")
   install_github("PredictiveEcology/SpaDES@development")
   install_github("PredictiveEcology/SpaDES.shiny@development") ## optional

2. Using the instructions above, devtools::install_github() will automatically try to install the optional fastshp package. This additional package requires OS development tools (e.g., Rtools for Windows). If the above installation doesn't work for you, be sure to install the necessary development tools before reinstalling the package.

   install.packages("fastshp", repos = "https://rforge.net", type = "source")