Emulated build and test of Bioconductor packages for Linux ARM64

Build and test for Linux ARM64 with Docker on x86_64 host

tech-notes
ARM64
Author

Martin Grigorov

Published

June 9, 2023

Bioconductor on Linux ARM64

ARM64, also known as aarch64, architecture is used in almost all mobile devices because of its lower electricity consumption compared to x86_64. In the last few years it is also being introduced more and more in server/cloud environments for the same reason.

Since June 8th 2023 the Bioconductor project has added a Linux ARM64 builder to the daily builds

Build on Linux ARM64

If you have access to a Linux ARM64 [virtual] machine (e.g. AWS Graviton, OracleCloud A1 Compute, etc.) then you can easily setup R 4.3.0 and start working on your Bioconductor package.

In this article I am going to explain the steps needed in case you work on x86_64 host machine by using the Bioconductor Docker Linux ARM64 image, i.e. using emulation.

Fetch the image:

$ docker pull --platform linux/arm64 ghcr.io/bioconductor/bioconductor:devel-r-latest

Note the --platform argument! It tells the Docker client to pull the arm64 flavor of the image. If omitted it will download the amd64 flavor that matches the architecture of the host.

Run the image (unsuccessful)

If you try to run this image you will see an error about the wrong binary format:

$ docker run -it --rm ghcr.io/bioconductor/bioconductor:devel-r-latest bash
WARNING: The requested image’s platform (linux/arm64) does not match the detected host platform (linux/amd64/v4) and no specific platform was requested
exec /usr/bin/bash: exec format error

Run the image (successful)

To make it possible to run arm64 Docker images on x86_64 host we will need to install QEMU (qemu-user-static):

$ docker run --rm --privileged aptman/qus -s -- -p aarch64
cat ./qemu-binfmt-conf.sh | sh -s -- --path=/qus/bin -p aarch64 --suffix -static
Setting /qus/bin/qemu-aarch64-static as binfmt interpreter for aarch64

Now it is possible to run the image:

$ docker run -it --rm ghcr.io/bioconductor/bioconductor:devel-r-latest bash
WARNING: The requested image’s platform (linux/arm64) does not match the detected host platform (linux/amd64/v4) and no specific platform was requested
root@b40c553def79:/# uname -a
Linux b40c553def79 6.2.0 #5 SMP PREEMPT_DYNAMIC Wed Mar 22 12:42:40 UTC 2023 aarch64 aarch64 aarch64 GNU/Linux

Build Bioconductor packages

The Docker image comes with R pre-installed:

root@b40c553def79:/# R --version
R version 4.3.0 (2023–04–21) — “Already Tomorrow”

To build and test a Bioconductor package you will need to git clone it locally:

root@b40c553def79:/# mkdir bioc && cd bioc
root@b40c553def79:/# git clone https://git.bioconductor.org/packages/xyz
root@b40c553def79:/# R CMD build xyz
root@b40c553def79:/# R CMD check xyz_VERSION.tar.gz

That’s it!

Optimization

For easier and faster development it would be better to clone the package on your x86_64 host and mount the folder:

$ docker run -it --rm -v /path/to/package:/dev ghcr.io/bioconductor/bioconductor:devel-r-latest bash

This way it will be easier to edit the source files with your preferred text editor on your workstation.