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JAGS and JAGS-WIENER Installation Guide for macOS

This guide provides step-by-step instructions for installing JAGS and the JAGS-WIENER module on macOS systems.

Check and Install Homebrew

First, check if Homebrew is installed:

which brew

If Homebrew is not installed (no output from the above command), install it:

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

After installation, if you're using an Apple Silicon Mac (M1/M2/M3), add Homebrew to your PATH:

echo 'eval "$(/opt/homebrew/bin/brew shellenv)"' >> ~/.zprofile
eval "$(/opt/homebrew/bin/brew shellenv)"

Verify Homebrew installation:

brew --version

Prerequisites

Now install the required build tools:

brew install autoconf automake libtool

1. Install JAGS

Install JAGS using Homebrew:

brew install jags

2. Install R Packages

Open R and install the required packages:

install.packages(c("rjags", "R2jags"))

If you encounter any package installation errors, try reinstalling with:

install.packages("rjags", type="source", INSTALL_opts = "--no-compress-data")

3. Install JAGS-WIENER

Clone the Repository

cd ~
git clone https://github.com/yeagle/jags-wiener.git
cd jags-wiener

Check and Create JAGS Modules Directory

# Check if modules directory exists
if [ ! -d "/opt/homebrew/lib/JAGS/modules-4" ]; then
    echo "Creating JAGS modules directory..."
    sudo mkdir -p /opt/homebrew/lib/JAGS/modules-4
else
    echo "JAGS modules directory already exists"
fi

# Verify JAGS installation location
brew list jags

# Verify JAGS include files
ls /opt/homebrew/Cellar/jags/4.3.2/include/JAGS/distribution/

# If ScalarDist.h is not found, locate it:
find $(brew --prefix) -name "ScalarDist.h"

Configure and Install

# Clean any previous attempts
make clean

# Create auxiliary files
autoreconf -fvi

# Configure with correct paths (adjust version if needed based on your JAGS installation)
./configure \
  CPPFLAGS="-I/opt/homebrew/Cellar/jags/4.3.2/include/JAGS" \
  LDFLAGS="-L/opt/homebrew/Cellar/jags/4.3.2/lib" \
  --prefix=/opt/homebrew \
  --with-jags-module=/opt/homebrew/lib/JAGS/modules-4

# Build and install
make
sudo make install

4. Verify Installation

Check Module Location and Permissions

# Check if module was installed
ls -l /opt/homebrew/lib/JAGS/modules-4/wiener.so

# If not found, search for it
find /opt/homebrew -name "wiener.so"

# Check permissions
ls -l /opt/homebrew/lib/JAGS/modules-4/

Test in R

Open R and run:

library(R2jags)
load.module("wiener")
load.module("dic")
list.modules()

A successful installation should show:

  • "basemod"
  • "bugs"
  • "dic"
  • "wiener"

Troubleshooting

If Module Not Found

If you get the error "File not found: /opt/homebrew/lib/JAGS/modules-4/wiener.so":

  1. Check module directory structure:
ls -la /opt/homebrew/lib/JAGS/
ls -la /opt/homebrew/lib/JAGS/modules-4/
  1. Locate the built module:
find /opt/homebrew -name "wiener.so"
  1. If found in a different location, create a symbolic link:
sudo ln -s /path/to/found/wiener.so /opt/homebrew/lib/JAGS/modules-4/wiener.so
  1. Check file permissions:
sudo chmod 755 /opt/homebrew/lib/JAGS/modules-4/wiener.so

If Build Fails

If you encounter build errors, try completely removing and reinstalling both JAGS and JAGS-WIENER:

# Remove current installations
brew uninstall jags
cd jags-wiener
sudo make uninstall

# Clean up any remaining files
sudo rm -rf /opt/homebrew/lib/JAGS/modules-4/wiener.so

# Reinstall JAGS
brew install jags

# Then follow the JAGS-WIENER installation steps again