In PredictiveEcology/SpaDES.project: Project Templates Using 'SpaDES'

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  echo = TRUE,
  eval = FALSE
)

Installing R

Traditional installation

Windows

1. Download and run the R installer (as administrator!) from https://cran.r-project.org/bin/windows/base.

2. (Optional) To build and compile packages, download and install the latest Rtools (as administrator!) from https://cran.r-project.org/bin/windows/Rtools/. Be sure to check the "add rtools to PATH" option during installation.

3. (Optional) Install GIS tools by downloading OSGeo4W from http://download.osgeo.org/osgeo4w/osgeo4w-setup-x86_64.exe and running the installer (select 'Express Install').

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 (more info at https://brew.sh/):

   /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

4. Install GDAL and other spatial packages:

   brew install pkg-config brew install gdal

   Then, install spatial R packages from source to pick up the new GDAL and PROJ libraries:

   ```r

   (re)install spatial packages from source

   install.packages("sf", type = "source", configure.args = "--with-proj-lib=$(brew --prefix)/lib/")

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

   legacy spatial packages may still be required until fully retired Oct 2023

   install.packages("rgdal", type = "source", configure.args = c("--with-proj-lib=$(brew --prefix)/lib/", "--with-proj-include=$(brew --prefix)/include/"))

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

   confirm the GDAL, GEOS, PROJ versions being used

   library(sf) library(rgdal) ```

5. Install GLPK (needed for full igraph functionality):

   brew install glpk

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

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

Linux

Install via apt or yum depending on your distribution. Instructions for Ubuntu 20.04 LTS are shown below.

1. Install R and its development libraries following instructions based on https://cran.r-project.org/bin/linux/ubuntu:

   ```

   update indices

   sudo apt update -qq

   install two helper packages we need

   sudo apt install --no-install-recommends software-properties-common dirmngr

   add the signing key (by Michael Rutter) for these repos

   To verify key, run gpg --show-keys /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc

   Fingerprint: E298A3A825C0D65DFD57CBB651716619E084DAB9

   wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc

   add the R 4.0 repo from CRAN

   sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"

   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 \ curl \ gdal-bin \ git \ libcairo2-dev \ libcurl4-openssl-dev \ libgdal-dev \ libgeos-dev \ libgit2-dev \ libglpk-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 \ python3-gdal \ tcl-dev \ tk-dev ```

Alternate installation

For users who require multiple versions of R concurrently, rig (https://github.com/r-lib/rig) provides the simplest mechanism for managing and running multiple installations.

1. Install rig for your system following instructions here: https://github.com/r-lib/rig#id-installation

2. Install the versions of R you need:

   bash rig add 4.3 rig add 4.2 rig add 4.1

   You can see the installed versions (and the default, starred) by using rig list.

   Set the default version using the names from rig list:

   bash rig default 4.3.1 3. Setup symlinks to allow easy launch of versioned R sessions:

   bash rig system make-links

   E.g., to launch R 4.2 on macOS, use R-4.2-arm64

3. On macOS, restrict access to system package directories:

   bash rig system fix-permissions

4. On macOS can also use the menu bar app (https://github.com/r-lib/rig#id-macos-menu-bar-app) to manage their R versions:

   bash open -a Rig

   Be sure to open the Rig app preferences to allow launch at startup.

Launching Rstudio using a specific version of R

## e.g., on macOS:
rig rstudio 4.2-arm64

## e.g., for a project using renv on ubuntu:
cd ~/path/to/project
rig rstudio renv.lock

Installing Rstudio

Recommended.

Download and run the installer for your operating system from https://posit.co/download/rstudio-desktop/.

PredictiveEcology/SpaDES.project documentation built on Dec. 23, 2024, 7:33 a.m.