[Bioc-devel] Support for Linux ARM64

[Hervé Pagès]

Hi Martin,

Linux runs on many architectures, ARM64 is just one of them.

Our daily builds have traditionally focused on 3 platforms: Intel-based 
Linux (Ubuntu 22.04), Windows, and Intel-based Mac. Note that we 
recently added ARM64-based Mac to our daily builds.

One big difference between Linux and the other platforms is that we only 
produce binary packages for the latter. More precisely:

- on the Linux builders: the daily builds only run 'R CMD INSTALL', 'R 
CMD build', and 'R CMD check', on each Bioconductor package,

- on the Windows and Mac builders: the daily builds run all the above 
plus an additional step that we call the BUILD BIN step that produces a 
binary for each Bioconductor package.

This means that on Linux, as well as on any other Unix-like OS that is 
not macOS (e.g. FreeBSD, OpenBSD, Solaris, HP-UX, etc...), users will 
install all their packages (Bioconductor and CRAN) **from source**. This 
should work as long as they are on a platform where R is supported and 
have the required compilers (C, C++, and Fortran).

Note that if officially supporting a given platform means running the 
daily builds on that particular platform, then there's no way for us to 
do that because platform == OS + architecture, and the list of 
combinations of Unix-like OS's (Linux, FreeBSD, Solaris, etc...) + 
architectures (Intel, ARM64, Sparc, powerpc) is endless. Even if we 
narrow this list to Intel-based Linux, there are hundreds of Linux 
distributions around that use different kernel, compilers, package 
managers, etc...

All this to say that, as far as the daily builds are concerned, we had 
to make choices, and those choices are based on the most commonly used 
platforms. Since all Bioconductor packages are tested daily on 
Intel-based Linux (Ubuntu 22.04), Windows, Intel-based Mac, and 
ARM64-based Mac, we have some reasonable confidence that they will work 
properly on these 4 platforms (still not a 100% guarantee of course, 
there's nothing like that).

My understanding is that ARM64-based Linux is still a marginally used 
platform so probably not worth for us to allocate resources on adding it 
to our daily builds at the moment. If it ever becomes more mainstream in 
the future, then we will certainly reconsider. That does not mean that 
you can't use Bioconductor on a ARM64-based Linux machine **now**. I see 
no reason a priori why you couldn't install (from source) Bioconductor 
packages on this platform, and use them, as long as:

- R is supported on your ARM64-based Linux machine

- you have compilers that are supported by R

- you have the external libraries that are required by some CRAN and/or 
Bioconductor packages.

Hope this helps,

H.

On 05/01/2023 02:01, Martin Grigorov wrote:
> Dear community,
>
> Happy and successful new year!
>
> Appologies if this has been discussed before but
> https://stat.ethz.ch/pipermail/bioc-devel/ does not provide search
> facilities and my googling didn't help much!
>
> I'd like to ask whether Linux ARM64 is officially supported ?
> I know that Mac ARM64 is supported since 3.16 [1] [2].
> I cannot find such test results for Linux ARM64 and the site search [3]
> also mentions "arm64" only in context of "macOS".
> In addition the Docker images are also single-platform [4] (linux/amd64).
>
> How can we help to add support for Linux ARM64 ?
> My employer is willing to donate VMs and man power if the community is
> interested in adding support for Linux ARM64!
>
>
> Regards,
> Martin
>
> 1. https://bioconductor.org/news/bioc_3_16_release/
> 2. https://bioconductor.org/checkResults/3.17/bioc-mac-arm64-LATEST/
> 3. https://bioconductor.org/help/search/index.html?q=arm64/
> 4. https://hub.docker.com/r/bioconductor/bioconductor_docker/tags
>
> 	[[alternative HTML version deleted]]
>
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-- 
Hervé Pagès

Bioconductor Core Team
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