pre-commit.ci does not work with our hooks

[lorenzwalthert]

https://pre-commit.ci is an upcoming CI/CD service by the creator of pre-commit that lets you run your pre-commit hooks via GitHub (and more to come). It does not work for script, system or local hooks as discussed in pre-commit-ci/issues#13 because the Rscript executable is not installed in the standard Docker image. For pre-commit to work with our R hooks on CI/CD, we must add support for R / renv as a language in pre-commit.

Alternative: https://github.com/openproblems-bio/openproblems/blob/main/.github/workflows/pre-commit.yml

[PelzKo]

Is the current status still to use the alternative or is R support in pre-commit.ci in sight?
Because when I tried to implement pre-commit.ci (free open source version), I got the error message "Executable Rscript not found"
Or is there just something specific to consider?

[lorenzwalthert]

Yes, I suggest to use this GitHub Action.

There is a pending issue (pre-commit-ci/runner-image#59) to support R out of the box. This will be through the language:r and will require {precommit} to also change the config from language: script to language: r.

[lorenzwalthert]

Now, R is supported as a language (pre-commit-ci/runner-image#80 (comment)). However, there are multiple problems:

• Because in our source installation, we chose to strip away the recommended packages, {Matrix} (which is a recursive dependency of {precommit}) can't be build because build-time-dependencies are not there at runtime. This needs a new image build that does contain the recommended packages.
• All packages that have system dependencies like {gert} won't work. System dependencies that are shipped with the package (like {git2r}) are possible if they are installed in /opt/r.
• We can get rid or the {usethis} -> {git2r} dependency for most of {precommit}, but not the roxygenize hook but using {cli} as we do for {touchstone}.
• the roxygen hook requires the ability to load the package, so all packages that have recursive system dependencies won't run.
• to install system dependencies, we could use pak::local_system_dependencies() or similar, but probably they won't be persistent with /opt/r.

[lorenzwalthert]

@PelzKo I opened #291 to maybe document the use of GitHub Actions + {precommit} to save everyone from trial and error. In #291, there is also a link to a very elaborated Github Action workflow file that you could probably adapt.

[lorenzwalthert]

@PelzKo I am happy to say that with release v0.2.0, pre-commit.ci is working for all hooks except roxygenize if your package has dependencies that have system dependencies. Please see NEWS.md for details. TLDR; use_ci(ci = "native") for migrating existing, use_precommit() for new ones after you updated {precommit}. There is also a vignette on CI.

[luchaoqi]

Hello, I am having a similar problem:

[INFO] This may take a few minutes...
An unexpected error has occurred: CalledProcessError: command: ('Rscript', '--vanilla', '-e', '            prefix_dir <- \'/home/lqi/.cache/pre-commit/repowt1wkajq\'\n            options(\n                repos = c(CRAN = "https://cran.rstudio.com"),\n                renv.consent = TRUE\n            )\n            source("renv/activate.R")\n            renv::restore()\n            activate_statement <- paste0(\n              \'suppressWarnings({\',\n              \'old <- setwd("\', getwd(), \'"); \',\n              \'source("renv/activate.R"); \',\n              \'setwd(old); \',\n              \'renv::load("\', getwd(), \'");})\'\n            )\n            writeLines(activate_statement, \'activate.R\')\n            is_package <- tryCatch(\n              {\n                  path_desc <- file.path(prefix_dir, \'DESCRIPTION\')\n                  suppressWarnings(desc <- read.dcf(path_desc))\n                  "Package" %in% colnames(desc)\n              },\n              error = function(...) FALSE\n            )\n            if (is_package) {\n                renv::install(prefix_dir)\n            }\n            ')
return code: 1
expected return code: 0
stdout:
    Executable `Rscript` not found
stderr: (none)
Check the log at /home/lqi/.cache/pre-commit/pre-commit.log

My config

-   repo: https://github.com/lorenzwalthert/precommit
    rev: v0.2.2.9013
    hooks:
    -   id: style-files
        language: r
    -   id: parsable-R
        language: r
    -   id: no-browser-statement
        language: r
    -   id: readme-rmd-rendered
        language: r
    -   id: roxygenize
        language: r
    -   id: use-tidy-description
        language: r
    -   id: lintr
        args: [--warn_only]
        language: r

and pre-commit was installed using pip.
Did I miss something above or should I install any extra system-level dependencies in my local environment (it doesn't have R installed but I remember pre-commit should cover it)?

[luchaoqi]

Ah, I think I got the answer: https://pre-commit.com/#r
So to make pre-commit happy, I still have to install R locally?

[lorenzwalthert]

You need an R installation @luchaoqi yes. R itself is not boostrapped, only the packges.