When dockerizing an R Shiny application hosted via Shiny Server (built from shiny server docker image https://hub.docker.com/r/rocker/shiny), a common issue developers face is that environment variables set via ENV instructions in the Dockerfile (or passed at runtime via docker run -e) are completely missing inside the R Shiny app.

For example, if you set the following environment variable in your Dockerfile:

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ENV SHOULD_IN_SHINY="From dockerfile"

When your app launches and runs Sys.getenv("SHOULD_IN_SHINY"), it returns an empty string "" instead of "From dockerfile". This is not a problem with Docker itself, but rather a consequence of how Shiny Server spawns R worker processes.

In this post, we will look into the root cause behind this behavior in Shiny Server and demonstrate the two recommended solutions to correctly expose environment variables to your R Shiny workers.

The Root Cause: How Shiny Server Spawns R Processes

The reason environment variables do not carry over to your R session lies in how Shiny Server executes R worker processes inside the container.

Shiny Server runs as a system service (typically as root or shiny). When launching an app instance, it re-executes R as the shiny unprivileged user using su. Specifically, the execution call combines two mutually exclusive flags:

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su shiny --login --preserve-environment -c "... R ..."

Let’s break down what these flags request from su:

1. --login (-l): Starts a login shell. This intentionally resets the environment to a minimal whitelist (HOME, PATH, USER, TERM, etc.) and sources system startup profiles (/etc/profile, ~/.profile).
2. --preserve-environment (-p): Explicitly asks su to keep the current environment inherited from the caller (which includes Docker’s ENV variables).

Because Linux’s su utility cannot honor both conflicting behaviors, it chooses --login and prints a warning:

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su: ignoring --preserve-environment, it's mutually exclusive with --login

Note: This warning is emitted by Shiny Server’s underlying process execution call, not by the R app itself. Attempting to suppress or patch it requires modifying and rebuilding Shiny Server C++ code, which is rarely practical.

Because the login shell wins, all custom environment variables passed to the container via ENV or docker run are wiped before R ever starts.

Solutions

Since patching Shiny Server is unnecessary, we can utilize the natural extension points provided by the login shell or R itself.

Solution 1: Use ~/.profile (Recommended for User-Level Shell Vars)

Since --login causes the shell to source ~/.profile for the shiny user, we can write our environment variables to /home/shiny/.profile during the Docker build phase.

In your Dockerfile:

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# Append environment variable to the shiny user's profile
RUN echo 'export SHOULD_IN_SHINY="From dockerfile"' >> /home/shiny/.profile

When Shiny Server executes su shiny --login ..., the login shell will read /home/shiny/.profile and load SHOULD_IN_SHINY into the environment right before starting the R process.

Solution 2: Use ~/.Renviron (Recommended for R-Specific Configs)

Alternatively, R automatically inspects and loads ~/.Renviron on startup, right after the shell environment is initialized.

~/.Renviron is purpose-built for R:

• Scoped strictly to R processes.
• Does not use shell export keywords or $ variable expansions.
• Uses simple KEY=value key-value pairs.

In your Dockerfile, set up /home/shiny/.Renviron:

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# Set up .Renviron for the shiny user
RUN echo 'SHOULD_IN_SHINY="From dockerfile"' >> /home/shiny/.Renviron \
    && chown shiny:shiny /home/shiny/.Renviron

In your Shiny app (app.R or server.R), you can access it reliably:

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should_in_shiny <- Sys.getenv("SHOULD_IN_SHINY")
# Returns: "From dockerfile"

Summary

• The Problem: Shiny Server calls su shiny --login --preserve-environment, causing su to discard inherited environment variables (such as Docker ENV) in favor of a clean login shell.
• Solution 1 (~/.profile): Append export KEY="value" to /home/shiny/.profile in your Dockerfile.
• Solution 2 (~/.Renviron): Append KEY="value" to /home/shiny/.Renviron in your Dockerfile.

Both approaches integrate seamlessly with Docker builds and ensure your Shiny application receives all required configuration variables cleanly.