R-hub v2 - R-hub blog (2024)

After eight years, we are retiring the current version of R-hub, in favor of a better, faster, modern system. We call the new system R-hub v2. R-hub v2 runs R package checks on GitHub Actions. R-hub v2 works best if your R package is in a GitHub repository. This post helps you transition to R-hub v2 from the previous version.

Is your package on GitHub?

1. Install or update the rhub package.
2. Run rhub::rhub_setup() to set up R-hub v2 for your package.
3. Run rhub::rhub_check() to run R-hub checks.

You don’t want to put your package on GitHub?

1. Install or update the rhub package.
2. Run rhub::rc_submit() to run R-hub checks.

Do you want to know more? Read on.

R-hub v2 is a completely new check system. To use it you’ll need at least version 2.0.0 of the rhub package.

There are two ways to use R-hub v2. Our recommendation is to store your R package in a GitHub repository and use the rhub::rhub_*() functions to start checks on GitHub Actions, using your own GitHub account.

Alternatively, if you don’t want to store your R package at GitHub, you can use the rhub::rc_*() functions to run checks in a shared GitHub organization at https://github.com/r-hub2, using the R Consortium runners.

In this section we assume that your R package is in a GitHub repository. See “The R Consortium Runners” section below for a different way of using R-hub v2.

Differences from R-hub v1

• The check picks up the package from GitHub, so it does not use changes in your local git clone. You need to push the changes to GitHub first. You can use a non-default branch, with the branch argument of rhub_check().
• You’ll not get an email about the check results. But you’ll receive regular GitHub notifications about check failures, unless you opt out. Github can also turn these into emails if you like.
• There is no live output from the check at the R console. See the ‘Actions’ tab of your repository on GitHub for a live check log.
• Many more specialized platforms are available.
• Most platforms use binary packages, so checks and in particular installing dependencies is much faster.

Private repositories

GitHub Actions is free for public repositories. For private repositories you also get some minutes for free, depending on the GitHub subscription you have. See About billing for GitHub Actions for pricing and more details.

Branches

You can run checks on any branch that you push to GitHub, but the R-hub workflow file (.github/workflows/rhub.yaml within your repo) must be present in both your default branch (usually main) and also in the branch you want to run the check on.

Requirements

• First, you need a GitHub account.

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• Second, you need to have your R package in a GitHub repository. Make sure that upstream git remote is set to the GitHub repository in your local git clone. Run git branch -vv to see your local branches and the upstream branches they are tracking. Example output:

  ❯ git branch -vv ...* main 87a2066 [origin/main] Avoid fancy quotes in test snapshots ...❯ git remote -vorigin git@github.com:r-hub/rhub.git (fetch)origin git@github.com:r-hub/rhub.git (push)

  which means that the main branch is tracking origin/main, and from the second command we can see that origin indeed refers to GitHub.

• Third, you need a GitHub Personal Access Token (PAT) and you need to store it in the git credential store on your machine. You can use gitcreds::gitcreds_set() to add the token to the git credential store. If you cannot use the git credential store for some reason (e.g.you are on Linux, and there is no good credential helper available for you), you can also set the GITHUB_PAT environment variable to your GitHub PAT in the ~/.Renviron file.

Set up R-hub v2

Once you took care of all these requirements, setting up R-hub v2 for your package goes like this.

STEP 1: install the rhub package

Install the rhub package:

install.packages("rhub")

STEP 2: add the R-hub v2 workflow

In your local git clone, switch to your default git branch and call rhub::rhub_setup(). This adds a GitHub Actions workflow to your local repository. Push this change to GitHub, into your default git branch.

rhub::rhub_setup() guides you through the process:

rhub::rhub_setup()

Setting up R-hub v2. ✔ Found R package at /private/tmp/cli. ✔ Found git repository at /private/tmp/cli. ✔ Created workflow file /private/tmp/cli/.github/workflows/rhub.yaml. Notes: • The workflow file must be added to the default branch of the GitHub repository. • GitHub actions must be enabled for the repository. They are disabled for forked repositories by default. Next steps: • Add the workflow file to git using `git add <filename>`. • Commit it to git using `git commit`. • Push the commit to GitHub using `git push`. • Call `rhub::rhub_doctor()` to check that you have set up R-hub correctly. • Call `rhub::rhub_check()` to check your package. 

(If you want to run checks on another branch, you need to add this workflow to that branch as well, manually or with rhub::rhub_setup().)

STEP 3: check your setup

Call rhub::rhub_doctor() to check that everything is set up correctly:

rhub::rhub_doctor()

✔ Found R package at /private/tmp/cli. ✔ Found git repository at /private/tmp/cli. ✔ Found GitHub PAT. ✔ Found repository on GitHub at <https://github.com/r-lib/cli>. ✔ GitHub PAT has the right scopes. ✔ Found R-hub workflow in default branch, and it is active. → WOOT! You are ready to run `rhub::rhub_check()` on this package. 

STEP 4: run checks

If rhub::rhub_doctor() did not find any issue, then you are ready to run checks with rhub::rhub_check(). It goes like this:

rhub::rhub_check()

✔ Found git repository at /private/tmp/cli. ✔ Found GitHub PAT. Available platforms (see `rhub::rhub_platforms()` for details): 1 [VM] linux R-* (any version) ubuntu-latest on GitHub 2 [VM] macos R-* (any version) macos-latest on GitHub 3 [VM] macos-arm64 R-* (any version) macos-14 on GitHub 4 [VM] windows R-* (any version) windows-latest on GitHu 5 [CT] atlas R-devel (2024-04-10 r86396) Fedora Linux 38 (Contai… 6 [CT] clang-asan R-devel (2024-04-10 r86396) Ubuntu 22.04.4 LTS 7 [CT] clang16 R-devel (2024-04-09 r86391) Ubuntu 22.04.4 LTS 8 [CT] clang17 R-devel (2024-04-09 r86391) Ubuntu 22.04.4 LTS 9 [CT] clang18 R-devel (2024-04-09 r86391) Ubuntu 22.04.4 LTS 10 [CT] donttest R-devel (2024-04-09 r86391) Ubuntu 22.04.4 LTS 11 [CT] gcc13 R-devel (2024-04-10 r86396) Fedora Linux 38 (Contai…12 [CT] intel R-devel (2024-04-10 r86396) Fedora Linux 38 (Contai…13 [CT] mkl R-devel (2024-04-10 r86396) Fedora Linux 38 (Contai…14 [CT] nold R-devel (2024-04-10 r86396) Ubuntu 22.04.4 LTS 15 [CT] nosuggests R-devel (2024-04-10 r86396) Fedora Linux 38 (Contai…16 [CT] ubuntu-clang R-devel (2024-04-10 r86396) Ubuntu 22.04.4 LTS 17 [CT] ubuntu-gcc12 R-devel (2024-04-10 r86396) Ubuntu 22.04.4 LTS 18 [CT] ubuntu-next R-4.4.0 beta (2024-04-09 r86391) Ubuntu 22.04.4 LTS 19 [CT] ubuntu-release R-4.3.3 (2024-02-29) Ubuntu 22.04.4 LTS 20 [CT] valgrind R-devel (2024-04-10 r86396) Fedora Linux 38 (Contai… Selection (comma separated numbers, 0 to cancel): 1, 5 ✔ Check started: linux, atlas (disillusive-gibbon). See <https://github.com/r-lib/cli/actions> for live output! 

If you don’t want to put your package on GitHub, you can still use the rhub package to run package checks on any supported platform using a shared pool of runners in the https://github.com/r-hub2 GitHub organization, that belong to the R Consortium.

Set up the RC runners

The process is similar to R-hub v1:

STEP 1: install the rhub package

install.packages("rhub")

STEP 2: get an R-hub token

Obtain a token from R-hub, to verify your email address:

rc_new_token()

You do not need to do this, if you already submitted packages to a previous version of R-hub from the same machine, using the same email address. Call rc_list_local_tokens() to see the email addresses that you you already have tokens for on this machine.

STEP 3: submit a check

Submit a check with

rc_submit()

Select the platforms you want to use, and follow the instructions and the link provided to see your check results.

Limitations of the RC runners

Using the R Consortium runners comes with some limitations.

• You package will be public for the world, and will be stored in the https://github.com/r-hub2 organization. Your check output and results will be public for anyone with a GitHub account. If you want to keep your package private, you can put it in a private GitHub repository, and use the rhub_setup() and rhub_check() functions instead of the RC runners.
• The R Consortium runners are shared among all users, so you might need to wait for your builds to start.
• You have to wait at least five minutes between submissions with rc_submit().
• Currently you need to create a GitHub account to see the check logs of your package. You don’t need a GitHub account to submit the checks.

To avoid these limitations (except for the need for a GitHub account), put your package in a GitHub repository, and use the rhub_setup() and rhub_check() functions instead of rc_submit() and the R Consortium runners.

We believe that R-hub v2 is already working better than the previous version of R-hub, but you might still run into edge cases.

If you have question about R-hub, please use our discussions forum on GitHub.

If you found a bug, then please open an issue at our issue tracker.

We hope that this resource will be useful for your R work!