Skip to contents

ARTEMIS Installation Guide

Strahinja Stevanovic, Svetozar Nesic

2026-05-11

InstallationGuide.Rmd

Introduction

This vignette describes how you need to install the Observational Health Data Science and Informatics (OHDSI) ARTEMIS package under Windows, Mac, and Linux.

Software Prerequisites

Before installing ARTEMIS, ensure that Python (version ≥ 3.12) is installed on your system.
You can check which Python version R detects using:

system("python --version", intern = TRUE)

If you want ARTEMIS to use a specific Python interpreter, set the ARTEMIS_PYTHON environment variable before installation:

Sys.setenv(ARTEMIS_PYTHON = "/path/to/your/python")

ARTEMIS can be installed directly from GitHub:

# Install devtools if it is not already installed
if (!requireNamespace("devtools", quietly = TRUE)) {
  install.packages("devtools")
}

# Install ARTEMIS from GitHub
devtools::install_github("OHDSI/ARTEMIS")

If you are unsure how to install Python or set ARTEMIS_PYTHON, refer to the OS-specific setup instructions below.

On Windows

Install Python 3.12 or above from the Microsoft Store or from: https://www.python.org/downloads/windows/

Then open cmd or PowerShell and set the environment variable:

set ARTEMIS_PYTHON=<ABS\\PATH\\TO\\python.exe (v3.12+)>

Other requirements checklist:

  • R, Rtools, and devtools installed

  • Microsoft Visual C++ 14.0 or greater (required by Python packages like numpy)

  • Visual Studio Build Tools (for faster Cython-compiled alignment)

On Linux or macOS

Install Python 3.12+ using your preferred package manager (e.g., Homebrew, apt, pacman) or download it from: https://www.python.org/

Then from the terminal, set the Python version environment variable:

export ARTEMIS_PYTHON="/absolute/path/to/python3.12"

Other dependencies you might need installed:

base-devel, r, git, libgit2, zlib, libxml2, openssl, curl, pkgconf, 
pandoc, glpk, gmp, libtool, graphviz, make, cmake, tzdata, 
jdk-openjdk, libcurl-compat, gcc-fortran, openblas, lapack

Reticulate

💡 You do NOT need to manually set up reticulate — ARTEMIS takes care of it automatically during setup. This section is for informational purposes only.

ARTEMIS relies on a python back-end via reticulate and depending on your reticulate settings, system and environment, you may need to run the following commands before loading the package:

reticulate::py_install("numpy")
reticulate::py_install("pandas")

**Other python dependencies for the build**
reticulate::py_install("setuptools")
reticulate::py_install("wheel")
reticulate::py_install("Cython")
reticulate::py_install("tqdm")

If you do not presently have reticulate or python3.12 installed you may first need to run the following commands to ensure that reticulate can access a valid python install on your system:

install.packages("reticulate")
library(reticulate)

This will prompt reticulate to install python, create a local virtualenv called “r-reticulate” and, finally, set this virtual environment as the local environment for use when running python via R through reticulate.