Pharmaverse and containers | R bloggers

Streamlining our Pharmaverse blog: reducing publishing time with containers

As an active contributor to the pharmaverse blog, I have always appreciated the opportunity to share new insights and tools with our community. The Pharmaverse blog has some interesting publishing options. While the blog publishing process was effective, I wondered if there was a way to optimize our workflows. Currently, it typically took about 17 minutes to put a new post into the CI/CD blog publishing pipeline. Containers are always used as a solution. Unfortunately I wasn’t sure how to create a new container/image to meet my needs and relied on a few simple steps install.packages() in the CI/CD pipeline. Luckily, I came across the fantastic Maciej Nasinski and we built a specific container for the publishing process for the pharmaverse blog, which allowed for a remarkable reduction in publishing time.

Below I discuss how the Pharmaverse container image improved our blog’s publishing workflow, reducing our implementation time to about 5 minutes. We’re also interested in feedback on possible other uses for this container (such as devcontainers) or building additional containers for certain purposes. For those interested, we would be happy to provide a tutorial on containers or contact you if you have any ideas or would like to get involved!

The previous approach: Package installation overhead

Our previous CI/CD (GitHub Actions) workflow for building and deploying the Pharmaverse blog, while extensive, also included a time-consuming step. It used the direct “Install Dependencies” step from the r-lib actions, which required installing a series of Pharmaverse-specific R packages during each run. As we added more packages to the Pharmaverse to the blog, this became very cumbersome!

The relevant part of our old construction implementation task highlighted this:

  build-deploy:
    # ... other configurations ...
    steps:
      # ... checkout and setup Quarto ...
      - name: Setup R
        uses: r-lib/actions/setup-r@v2
        with:
          use-public-rspm: true

      - name: Install dependencies
        uses: r-lib/actions/setup-r-dependencies@v2
        with:
          packages: |
            jsonlite
            tidyverse
            spelling
            janitor
            diffdf
            admiral
            admiralonco
            # ... and many, many more packages ...
            haven
      # ... other steps like install tinytex and publish ...

This “Install Dependencies” step, which involved a substantial list of Pharmaverse packages, was a major contributor to the 17 minute execution time. Each workflow run required these packages to be downloaded and configured, extending the overall deployment time.

Adopting the Pharmaverse container image: an efficient alternative

The solution to this challenge came with the introduction of the Pharmaverse container image: ghcr.io/pharmaverse/docker_pharmaverse:4.5.1. This container image is specifically designed for pharmaceutical data analysis and includes more than 40 essential Pharmaverse packages pre-installed. These packages include various functionalities, including CDISC ADaM/SDTM, clinical trial reporting and regulatory submissions. Built on the rocker/tidyverse image, it includes R 4.5.1 and provides a preconfigured environment.

By integrating this image into our CI/CD pipeline (GitHub Actions), we were able to bypass the extensive package installation phase.

Here’s an overview of our updated build deployment task:

  build-deploy:
    needs: Update-post-dates
    runs-on: ubuntu-latest
    container:
      image: "ghcr.io/pharmaverse/docker_pharmaverse:4.5.1"
    permissions:
      contents: write
    steps:
      - name: Check out repository
        uses: actions/checkout@v4

      - name: Configure Git safe directory
        run: git config --global --add safe.directory /__w/blog/blog

      - name: Set up Quarto
        uses: quarto-dev/quarto-actions/setup@v2
        with:
            version: 1.9.12

      # NOTE: Explicit R package installation is no longer required here.

      - name: Install tinytex
        run: quarto install tool tinytex

      - name: Mark repo directory as safe
        run: git config --global --add safe.directory /__w/blog/blog

      - name: Publish
        uses: quarto-dev/quarto-actions/publish@v2
        with:
          path: . # Path to your .qmd file
          target: gh-pages  # Target branch for GitHub Pages
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

The result of this change is a consistent reduction in publication time. Our blog will now be published in about 5 minutes. Yes!

Broader applications of the Pharmaverse Container Image

While this update directly benefits the publication of our blog, the Pharmaverse container image provides broader utility. It is a valuable resource for:

• Pharmaceutical data analysis: supporting tasks related to ADaM, SDTM and TLFs.
• Clinical Trial Programming: Assist with regulatory submissions.
• Reproducible research: providing a consistent and verifiable environment.
• Training & education: Offering a ready-made setup for educational purposes.
• CI/CD Pipelines: Improving automated testing and reporting as observed in our own workflow.
• Collaborative development: Facilitating consistent environments across teams.