15  Reproducible Environments

An analysis can fail after a package, R, or a system library changes, even when the code is unchanged. Recording software versions and preserving the environment helps colleagues rerun the analysis and diagnose differences.

This chapter covers two levels of environment management:

• Package-level with renv, which records and restores R package versions
• System-level with Docker and the Rocker project, which captures the entire computing environment including R itself, system libraries, and non-R tools
• Bridging both with pracpac, which containerizes R packages by combining renv dependency capture with Docker image generation

These tools exist on a spectrum of complexity and completeness. A good rule of thumb: start with renv for any analysis project involving collaborators, and use Docker when you need to share system dependencies as well as R packages.

Both tools pin whatever your project already depends on. Neither one asks whether a dependency was a good idea, and the answer matters most here, because system dependencies can make installation slower or harder on a server. Chapter 13 covers choosing and vetting packages before they reach the lockfile.

15.1 Package Environments with renv

The renv package gives each R project its own private library. Instead of every project sharing a single system-wide package library (where upgrading a package for one project might break another), renv isolates dependencies per project and records the exact versions in a lockfile.

15.1.1 How renv Works

renv maintains three things:

1. A project-private library at renv/library/: packages installed here don’t affect other projects
2. A lockfile (renv.lock): a plain-text record of every package version used in the project
3. An activation script (renv/activate.R): auto-loaded by .Rprofile to activate the project library when R starts in that directory

The lockfile is what makes sharing and restoring the environment possible. It records the package name, version, source (CRAN, Bioconductor, GitHub), and a hash for verification:

{
  "R": {
    "Version": "4.4.1",
    "Repositories": [
      {
        "Name": "CRAN",
        "URL": "https://packagemanager.posit.co/cran/latest"
      }
    ]
  },
  "Packages": {
    "dplyr": {
      "Package": "dplyr",
      "Version": "1.1.4",
      "Source": "Repository",
      "Repository": "CRAN",
      "Hash": "fedd9d00c2944ff00a0e2696ccf048ec"
    }
  }
}

This file should be committed to version control (see Chapter 1). It’s how collaborators and future you restore the same environment.

15.1.2 Core Workflow

Starting a new project:

renv::init()

This initializes renv in the current project: creates the private library, scans your scripts for library() and require() calls to discover dependencies, installs those packages, and writes the initial renv.lock.

After installing or updating packages:

# Install packages as usual
install.packages("ggplot2")

# or use renv's wrapper -- preferred
renv::install("tidyr")

# Then snapshot to record the new state
renv::snapshot()

renv::snapshot() updates renv.lock to reflect the current state of your project library. Run it whenever you add or update packages, then commit the updated lockfile.

Restoring an environment (e.g., on a new machine or after cloning a repo):

renv::restore()

This reads renv.lock and installs exactly the recorded versions. Collaborators can use it to install the recorded R package versions, provided those versions and their system dependencies remain available.

Tip

When you open a project with an existing renv.lock, renv will notice if your local library is out of sync with the lockfile and suggest running renv::restore(). You can also check status explicitly:

renv::status()

This reports any discrepancies between your installed packages and renv.lock.

Checking for package updates:

renv::update()      # update all packages to latest versions
renv::snapshot()    # then re-record the new state

15.1.3 Working as a Team

When collaborating on a project with renv:

1. One person initializes renv and commits renv.lock, renv/activate.R, and .Rprofile to the repository
2. Everyone else clones the repo and runs renv::restore() to set up their local environment
3. When anyone installs or updates a package, they run renv::snapshot() and commit the updated renv.lock

Commit these files; do not commit the renv/library/ folder itself (add it to .gitignore; renv does this automatically). The library can be rebuilt from the lockfile; committing it would add thousands of binary files to your repository.

Note

renv uses a global package cache on each machine, so packages are only downloaded and installed once even if you use them in multiple projects. Restoring an environment the second time is nearly instant if the packages are already cached.

15.1.4 What renv Does Not Solve

renv restores R package versions, but you must also manage:

• The R installation itself (renv records its version but does not install it): if collaborator A runs R 4.3 and collaborator B runs R 4.4, results may differ even with identical packages
• System libraries: packages that depend on compiled system libraries (e.g., sf needs GDAL, xml2 needs libxml2) can still break if system libraries differ
• Non-R software: any external tools called from R (Python, command-line tools, etc.)
• Namespace conflicts: when multiple packages export functions with the same name, renv does not determine which one your script uses; that depends on load order. See Chapter 12 for how to manage this.

For version and system-level concerns, Docker provides a more complete solution.

15.2 Containers with Docker

Docker is a tool for packaging an entire computing environment (the operating system, system libraries, R, R packages, and any other software) into a portable, self-contained unit called a container. Containers reduce differences between machines, but results can still depend on architecture, external inputs, and runtime settings.

15.2.1 Key Concepts

Image: A read-only template that defines the environment. It contains the files and settings used to start a container.

Container: A running instance of an image. You can run multiple containers from the same image.

Dockerfile: A text file containing the instructions for building an image. It specifies the base image, software to install, files to copy, and startup command.

Registry: A place to store and share images. Docker Hub is the public default; organizations may run private registries.

15.2.2 Why Docker for R?

The limitations of renv described above (R version, system libraries, non-R software) are exactly what Docker addresses. Preserving the image retains the R version and system libraries for later runs. Test it on the deployment platform and preserve required data and external dependencies too.

Docker is especially useful for:

• Deploying analyses to servers: the same image that works locally runs in production (see Chapter 25 for working with IT on institutional deployment)
• Sharing complete analyses: collaborators with a compatible container runtime can run the image
• Pipelines that mix R with other tools: Python, command-line tools, databases, and R all coexist in one image
• Shiny apps: containerized apps can be deployed anywhere without managing a server environment

15.2.3 The Rocker Project

Setting up Docker for R from scratch requires some Linux knowledge and installing R and its dependencies. The Rocker project solves this by providing a curated set of R Docker images that are well-maintained, regularly updated, and designed specifically for data science workflows.

15.2.3.1 The Versioned Stack

The Rocker versioned stack is built around pinned R versions, making it the right choice for reproducible work:

Image	Built on	Contents
rocker/r-ver	Ubuntu LTS	Base R at a specific version
rocker/rstudio	r-ver	Adds RStudio Server
rocker/tidyverse	rstudio	Adds tidyverse, devtools, remotes
rocker/verse	tidyverse	Adds TeX, Pandoc, Quarto
rocker/geospatial	verse	Adds spatial libraries (sf, terra, GDAL)

The versioned images accept an R version tag, which pins both R and the package repository snapshot to that time period:

# R 4.4.1 with RStudio Server
docker pull rocker/rstudio:4.4.1

# R 4.3.0 with tidyverse
docker pull rocker/tidyverse:4.3.0

Tip

Use a specific version tag in production work; use an image digest when you need to identify an exact build. rocker/rstudio:latest will point to different R versions as new releases come out; rocker/rstudio:4.4.1 always means exactly that version.

15.2.3.2 Running Rocker Containers

To start an RStudio Server session in your browser with R 4.4.1:

docker run --rm \
  -p 8787:8787 \
  -e PASSWORD=yourpassword \
  -v "$(pwd)":/home/rstudio/project \
  rocker/rstudio:4.4.1

Then open http://localhost:8787 in a browser and log in with username rstudio and the password you set. The -v flag mounts your current directory into the container so you can access your local files.

Key flags: - --rm: remove the container when it exits (avoids accumulating stopped containers) - -p 8787:8787: map host port 8787 to container port 8787 - -e PASSWORD=...: set the RStudio login password - -v host_path:container_path: mount a local directory into the container

15.2.3.3 Writing a Dockerfile

For projects that need packages beyond what the base Rocker images provide, you write a Dockerfile that extends a Rocker image:

FROM rocker/tidyverse:4.4.1

# Install system dependencies (if needed)
RUN apt-get update && apt-get install -y \
    libssl-dev \
    && rm -rf /var/lib/apt/lists/*

# Install additional R packages
RUN R -e "install.packages(c('janitor', 'gt', 'gtsummary'))"

# Copy project files
COPY . /home/rstudio/project

Build and run the image:

docker build -t my-analysis:latest .
docker run --rm -p 8787:8787 -e PASSWORD=pass my-analysis:latest

Note

Docker and renv together. For the most complete reproducibility, use both: a Dockerfile that pins the R version (via a versioned Rocker base) and renv inside the container to pin package versions. The renv.lock file is copied into the image at build time, and renv::restore() installs the exact package versions during the build. This combination captures the full stack: OS, R, and packages.

15.3 pracpac: R Packaging with Docker

pracpac (Practical R Packaging with Docker) (Nagraj and Turner 2023) bridges the R package development workflow and Docker. It provides a usethis-style interface that automates the generation of Docker configuration for R packages under development, using renv to capture dependencies.

While renv and basic Rocker Dockerfiles cover many use cases, pracpac is aimed at teams that have structured their analysis code as an R package and want to containerize that package, along with all its dependencies, for deployment or sharing.

15.3.1 What pracpac Does

pracpac automates a four-step process that would otherwise require manual effort:

1. Dependency capture: uses renv to snapshot all package dependencies matching the developer’s current environment.
2. Package building: creates a source tarball (.tar.gz) of the R package.
3. Dockerfile generation: writes a Dockerfile that installs the captured dependencies and the package from source.
4. Image building: optionally builds the Docker image with version tags drawn from the package DESCRIPTION file.

The generated Dockerfile uses a Rocker base image, installs renv and BiocManager, restores dependencies from the renv.lock, and installs the package, mirroring the developer’s environment inside the container.

15.3.2 Installation

install.packages("pracpac")

15.3.3 Workflow

15.3.3.1 Step 1: Set up your R package with renv

pracpac assumes your analysis is structured as an R package (with a DESCRIPTION file) and that renv is initialized:

renv::init()
# ... develop your package, install dependencies ...
renv::snapshot()

15.3.3.2 Step 2: Generate Docker configuration

From inside your R package project:

library(pracpac)
use_docker()

This creates a docker/ subdirectory containing three artifacts:

your-package/
├── DESCRIPTION
├── R/
├── renv.lock
└── docker/
    ├── Dockerfile
    ├── renv.lock       # copy of the project lockfile
    └── your-package_1.0.0.tar.gz   # built source package

15.3.3.3 Step 3: Build the Docker image

Either pass build = TRUE to use_docker() to do everything in one step, or build separately:

# One-step: generate and build
use_docker(build = TRUE)

# Two-step: generate first, inspect/customize, then build
use_docker()
# ... optionally edit docker/Dockerfile ...
build_image()

The two-step approach is useful when you want to customize the generated Dockerfile before building, for example to add system library dependencies or additional non-R tools.

15.3.3.4 Step 4: Run and share the image

# Run the container
docker run --rm -it your-package:1.0.0

# Share via Docker Hub or a private registry
docker push your-org/your-package:1.0.0

The image tag is derived from the package version in DESCRIPTION, so image versions stay in sync with package versions automatically.

Tip

pracpac is particularly useful for deploying R-based pipelines alongside non-R tools. After use_docker() generates the initial Dockerfile, you can extend it to install Python, command-line bioinformatics tools, or any other software your pipeline needs. The R dependencies are already handled by renv; you just add the additional layers on top.

15.3.4 Use Cases

Analysis pipelines. Structure your analysis as an R package, containerize with pracpac, and deploy to a server or cloud environment with the package dependencies recorded at build time.

Shiny applications. An R package that contains a Shiny app can be containerized with pracpac, then deployed to any Docker-capable hosting environment.

Reproducible publications. Sharing a Docker image alongside a paper or report means reviewers and readers can rerun the analysis in the supplied environment.

Mixed-language pipelines. If your R package calls Python scripts or command-line tools, customize the generated Dockerfile to add those dependencies. The result is a single container that runs the complete pipeline.

15.4 Choosing Your Approach

You can combine these tools. The right level of environment management depends on how much isolation and portability you need:

Scenario	Recommended approach
Solo project, short duration	renv only
Team collaboration on analysis code	renv + commit renv.lock to git
Need consistent R and system dependencies across machines	renv + Docker (Rocker base)
Deploying an analysis or app to a server	Docker (Rocker base)
Analysis structured as an R package	pracpac
Pipeline mixing R with other tools	pracpac with customized Dockerfile

The most common entry point for DSTT teams is renv: add it to any collaborative project, commit the lockfile, and let teammates restore the environment with renv::restore(). This alone eliminates most “it doesn’t work on my machine” problems. Docker and pracpac become relevant when you need to share a fully self-contained environment or move an analysis into production.

15.5 Further Reading

The tools covered in this chapter (renv, Docker/Rocker, and pracpac) are the most practical starting points for most teams. Nix and rix offer another way to manage reproducible environments.

Nix is a package manager built around the principle of fully reproducible, declarative builds. Unlike renv (which captures R package versions) or Docker (which captures a container image), Nix works at the level of the entire software supply chain: every package, system library, compiler, and tool is described by a precise specification and built from source in an isolated environment. The result is a level of reproducibility that is difficult to achieve any other way.

For R users, Nix’s power is most accessible through rix, an rOpenSci package developed by Bruno Rodrigues and Philipp Baumann. rix provides an R-native interface for generating Nix environments: you specify the R version, packages, and system dependencies in R code, and rix writes the default.nix file that Nix uses to build the environment:

library(rix)

rix(
  r_ver = "4.4.1",
  r_pkgs = c("dplyr", "ggplot2", "tidyr"),
  system_pkgs = NULL,
  git_pkgs = NULL,
  ide = "rstudio",
  project_path = "."
)

This generates a default.nix file that, when built with Nix, produces an environment with exactly that R version and those packages, down to the system library level, without Docker, and with dependencies specified by the generated Nix configuration.

rix is a compelling option if your team is willing to install Nix and invest in learning its model. The payoff is reproducibility that is more rigorous than renv alone and less operationally complex than Docker for day-to-day development. Bruno Rodrigues’s book Building Reproducible Analytical Pipelines with R covers this approach in depth.

Nagraj, V. P., and Stephen D. Turner. 2023. Pracpac: Practical R Packaging with Docker. arXiv:2303.07876. arXiv. https://doi.org/10.48550/arXiv.2303.07876.