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Installation instructions

install.Rmd
  1. Clone and cd into this git repo
  2. Make build_install.sh executable by running chmod +x build_install.sh in bash terminal
  3. In terminal, run ./build_install.sh to build and install the package
  4. To ensure a clean start, run:
rm -f src/*.o src/*.so
rm -rf wispack.Rcheck
rm -f wispack_*.tar.gz
./build_install.sh

Note that additional system dependencies are required before the building process. Below are instructions for Mac and Linux (Ubuntu/Debian). Installation on Windows should be possible, but is not currently tested or supported.

Mac

First, ensure your Mac has the necessary backend dependencies:

  1. Xcode developer tools: In terminal, run xcode-select --install and follow the instructions
  2. GNU Fortran compiler: Go to https://mac.r-project.org/tools/, then download and run the relevant gfortran-[version]-universal.pkg
  3. Follow the instructions at this same website to install LaTeX for R

Ensure pkg-config and nlopt are installed, e.g., using Homebrew in a terminal:

brew install pkg-config
brew install nlopt
export PKG_CONFIG_PATH="/opt/homebrew/lib/pkgconfig:$PKG_CONFIG_PATH"

Install Homebrew if needed:

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
echo >> /Users/[name]/.zprofile
echo 'eval "$(/opt/homebrew/bin/brew shellenv zsh)"' >> /Users/[name]/.zprofile
eval "$(/opt/homebrew/bin/brew shellenv zsh)"

Rebuild and cleanly install Rcpp and Stan, in R: install.packages(c("Rcpp", "RcppEigen", "RcppParallel", "StanHeaders"))

Linux

Need to install the following system dependencies: - libxml2 for roxygen2 - r-base-dev, libnlopt-dev (or libnlopt-cxx-dev) for Rcpp, RcppEigen, and StanHeaders

For PDF documentation generation, pdflatex should also be installed

sudo apt install \
    libxml2 \
    r-base-dev \
    libnlopt-dev \
    libnlopt-cxx-dev \
    texlive-latex-base \
    texlive-fonts-recommended \
    texlive-fonts-extra \
    texlive-latex-extra

Build documentation

In R, run:

devtools::document()
pkgdown::build_site()
pkgdown::build_article("<article name>")

System requirements

Wispack is computationally intense. Fitting all but the smallest models can easily use four or five Gb of RAM. We strongly recommend a modern multi-core Unix system (Apple Silicon or Linux) with at least 24 Gb of RAM, although realistically a workstation or compute cluster with 100+ Gb of available RAM and 20 or more cores are needed for realistic run times of complex models.