Using source(functions.R) in R Script with Docker
Introduction
In this article, we will explore a common issue faced by many R users who are building Docker images for their R scripts. The problem is related to the way source() function handles file paths and working directories within a Docker container.
Understanding the Source() Function
The source() function in R is used to execute a specified file as R code. It takes two main arguments: the filename and an optional encoding parameter. When called, source() reads the specified file line by line and executes each line of code.
However, one key detail that makes source() behave unexpectedly within a Docker container is its reliance on the current working directory (CWD). In a local R session, the CWD defaults to the directory from which the script was run. But in a Docker container, this behavior changes due to the way Linux file systems work.
How Docker Containers Work
Docker containers are isolated environments that run applications within their own virtualized space. Each container has its own CWD and file system hierarchy, which is separate from the host machine’s file system.
When we copy files into a Docker image using the COPY instruction, they are placed in the root directory of the container (i.e., /). This means that any relative paths specified within those files will be interpreted based on this new root directory.
The Problem
In our example, we have an R script named analysis.R that uses custom functions from another file named functions.R. Within the functions.R file, there is a source() call to execute the analysis.R script.
However, when we run the Docker image containing these files, the CWD defaults to / (the root directory), not the /home directory where our scripts are located. This means that the relative path ./functions.R used within analysis.R does not point to the correct location of functions.R.
Solving the Problem
The problem can be solved by setting the working directory within the Docker image to the desired location using the WORKDIR instruction.
Here is an updated version of our Dockerfile:
FROM rocker/r-ver:3.6.2
WORKDIR /home
COPY analysis.R analysis.R
COPY functions.R functions.R
In this updated Dockerfile, we set the working directory to /home before copying our scripts into it. This ensures that any relative paths within those files are correctly interpreted.
Best Practices for Working with R in Docker
Here are some additional best practices for using R with Docker:
- Set the working directory explicitly within your Docker image using the WORKDIR instruction.
- Use absolute file paths whenever possible to avoid issues with relative paths and CWDs.
- Make sure that any required dependencies, such as packages or data files, are included in the container image using COPY instructions.
- Test your Docker image thoroughly before running it in production by creating a test script that reproduces the problematic behavior.
Conclusion
In this article, we have explored a common issue faced by many R users who build Docker images for their scripts. By understanding how source() works and how Docker containers operate, we can take steps to solve issues like this one.
By following best practices such as setting the working directory explicitly and using absolute file paths, you can write reliable and robust Dockerfiles for your R projects.
Last modified on 2025-02-09