Ubuntu latest removes R from its default installation

[zkamvar]

Instructions for Hub Administrators 2024-12-11

If you have not customized your workflows, use the hubCI package to update your workflows:

library("hubCI")

use_hub_github_action(name = "validate-submission")
use_hub_github_action(name = "validate-config")
use_hub_github_action(name = "cache-hubeval-deps")
use_hub_github_action(name = "hubverse-aws-upload")

Problem

In actions/runner-images#10636, GitHub announced that the ubuntu-latest workflows are removing R.

They are rolling this feature out across runners at the moment:

This change will be rolled out over a period of several weeks beginning December 5th and will complete on January 17th, 2025.

Impact

This means that all validation checks will eventually fail as the update rolls out.

It has already hit the flu sight repo in cdcepi/FluSight-forecast-hub#1251

I made a PR for them to pin their ubuntu runner: cdcepi/FluSight-forecast-hub#1253

Solution

The solution is one of two things:

1. pin the ubuntu runner to 22.04 OR
2. set install-r: true in the setup R step

The benefits of pinning the ubuntu runner to 22.04 is that it will continue to work for another three years (LTS lifecycle). The drawback is that we will eventually have to find a better solution when LTS ends.

The downside of setting install_r: true is that it increases the run time of the validation by about a minute. This is primarily an issue for submission turnover and not of cost since the runner minutes on public repositories do not count against allocated minutes.

[zkamvar]

Note that this does not affect our package repositories because we already install the latest version of R by default.

[annakrystalli]

Noting that this issue (hubverse-org/hubValidations#57) also exists and might be worth bumping up the priority ladder and benchmarking against the above options.

This option is also a potential: https://github.com/eddelbuettel/github-actions/tree/master/r2u-setup

[annakrystalli]

Note that if a hub is using the vanilla workflow, hub admins or team members on forks needing to update their workflow can use hubCI::use_hub_github_action("validate-submission") to update their workflow to the latest version

[zkamvar]

Note that if a hub is using the vanilla workflow, hub admins or team members on forks needing to update their workflow can use hubCI::use_hub_github_action("validate-submission") to update their workflow to the latest version

Oh we should make a release first, no?

[zkamvar]

I'll go ahead and do that.

[annakrystalli]

Oh yeah good call!

[zkamvar]

done!

[zkamvar]

I'm going to close this issue as it has been addressed and communicated.