fix #609
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| on: | |
| workflow_dispatch: | |
| workflow_call: | |
| inputs: | |
| error-on: | |
| description: Input for the 'error_on' parameter in rcmdcheck::rcmdcheck() | |
| required: false | |
| default: note | |
| type: string | |
| push: | |
| branches: | |
| - main | |
| - devel | |
| pull_request: | |
| branches: | |
| - main | |
| - devel | |
| name: R CMD Check | |
| concurrency: | |
| group: r-cmd-check-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| R-CMD-check: | |
| runs-on: ubuntu-latest | |
| container: | |
| image: "ghcr.io/pharmaverse/admiralci-${{ matrix.r_version }}:latest" | |
| name: (${{ matrix.r_version }}) | |
| if: > | |
| !contains(github.event.commits[0].message, '[skip r-cmd-check]') | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| r_version: ['release', 'devel', 'oldrel'] | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| R_KEEP_PKG_SOURCE: true | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| R_REPOS: "https://cran.r-project.org" | |
| DEPS_IGNORE: >- | |
| pharmaversesdtm, | |
| pharmaverseadam, | |
| admiral, | |
| admiraldev, | |
| admiralophtha, | |
| admiralonco, | |
| admiralvaccine, | |
| staged.dependencies | |
| # DEPS_IGNORE: env variable to ignore package when building renv.lock (step Upload dependencies artifact) | |
| # (improvments ideas : get this list of deps to ignore from staged.dependencies yml file) | |
| steps: | |
| ##################### BEGIN boilerplate steps ##################### | |
| - name: Get branch names | |
| id: branch-name | |
| uses: tj-actions/branch-names@v8 | |
| - name: Checkout repo (PR) 🛎 | |
| uses: actions/checkout@v4 | |
| if: | | |
| github.event_name == 'pull_request' | |
| with: | |
| ref: ${{ steps.branch-name.outputs.head_ref_branch }} | |
| repository: ${{ github.event.pull_request.head.repo.full_name }} | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| if: | | |
| github.event_name != 'pull_request' | |
| with: | |
| ref: ${{ steps.branch-name.outputs.head_ref_branch }} | |
| - name: Restore cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: | | |
| ~/.staged.dependencies | |
| key: staged-deps | |
| - name: Run Staged dependencies | |
| uses: insightsengineering/staged-dependencies-action@v1 | |
| if: | | |
| (github.event_name == 'workflow_dispatch' && matrix.r_version == 'devel') || | |
| matrix.r_version != 'devel' | |
| with: | |
| run-system-dependencies: false | |
| renv-restore: false | |
| enable-check: false | |
| cran-repos: "$R_REPOS" | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Install dependencies from DESCRIPTION | |
| if: | | |
| (github.event_name == 'workflow_dispatch' && matrix.r_version == 'devel') || | |
| matrix.r_version != 'devel' | |
| run: | | |
| remotes::install_local(force = TRUE, dependencies = TRUE) | |
| shell: Rscript {0} | |
| ##################### END boilerplate steps ##################### | |
| - name: Upload dependencies artifact | |
| if: | | |
| (github.event_name == 'workflow_dispatch' && matrix.r_version == 'devel') || | |
| matrix.r_version != 'devel' | |
| run: | | |
| dir.create("/workspace/tmp") | |
| library(dplyr) | |
| installed_packages <- as.data.frame(installed.packages()) | |
| packages_to_remove <- Sys.getenv("DEPS_IGNORE", "") | |
| packages_to_remove <- unlist(strsplit(packages_to_remove, ",")) | |
| installed_packages <- installed_packages %>% filter(LibPath != "/usr/local/lib/R/library") %>% # remove pre-built deps | |
| filter(!Package %in% packages_to_remove) | |
| # save deps as csv file | |
| write.csv(installed_packages, "/workspace/tmp/deps-${{ matrix.r_version }}.csv", row.names = FALSE) | |
| # create also renv.lock file | |
| setwd("/workspace/tmp") | |
| renv_lock <- list( | |
| "R" = list( | |
| "Version" = paste(R.version$major, R.version$minor, sep=".") | |
| ), | |
| "Repositories" = list( | |
| list(Name = "CRAN", URL = Sys.getenv("R_REPOS")) | |
| ), | |
| "Packages" = list() | |
| ) | |
| # Populate with information about each package | |
| for (package in installed_packages$Package) { | |
| dep_name <- package | |
| dep_version <- installed_packages[installed_packages$Package == package, "Version"] | |
| version_parts <- strsplit(dep_version, "\\.")[[1]] | |
| if (length(version_parts) == 4) { | |
| print(sprintf("skipping installation of dep %s", dep_name)) | |
| } else { | |
| print(sprintf("append dependency %s - version %s", dep_name, dep_version)) | |
| requirements <- tools::package_dependencies(dep_name, recursive = TRUE) | |
| have_requirements <- length(requirements[[1]]) > 0 | |
| if (have_requirements) { | |
| renv_lock[["Packages"]][[dep_name]] <- list( | |
| "Package" = dep_name, | |
| "Version" = dep_version, | |
| "Source" = "Repository", | |
| "Repository" = "CRAN", | |
| "Requirements" = requirements[[dep_name]] | |
| ) | |
| } else { | |
| renv_lock[["Packages"]][[dep_name]] <- list( | |
| "Package" = dep_name, | |
| "Version" = dep_version, | |
| "Source" = "Repository", | |
| "Repository" = "CRAN" | |
| ) | |
| } | |
| } | |
| } | |
| # Write the list to a JSON file (renv.lock) | |
| writeLines(jsonlite::toJSON(renv_lock, pretty = TRUE, auto_unbox = TRUE), "renv-${{ matrix.r_version }}.lock") | |
| print("generated renv.lock content") | |
| system("cat renv-${{ matrix.r_version }}.lock") | |
| shell: Rscript {0} | |
| - name: Upload deps.csv and renv.lock artifacts | |
| uses: actions/upload-artifact@v2 | |
| if: | | |
| (github.event_name == 'workflow_dispatch' && matrix.r_version == 'devel') || | |
| matrix.r_version != 'devel' | |
| with: | |
| name: deps | |
| path: | | |
| /workspace/tmp/ | |
| - name: Check Version | |
| id: check_version | |
| if: | | |
| (github.event_name == 'workflow_dispatch' && matrix.r_version == 'devel') || | |
| matrix.r_version != 'devel' | |
| run: | | |
| maintenance_version="F" | |
| description_dat <- readLines("DESCRIPTION") | |
| for (i in seq_along(description_dat)) { | |
| if (grepl("^Version:", description_dat[i])) { | |
| current_version <- sub("^Version: ", "", description_dat[i]) | |
| version_parts <- strsplit(current_version, "\\.")[[1]] | |
| # check if maintenance version | |
| if (length(version_parts) == 4) { | |
| print("Maintenance version detected (format X.Y.Z.M with M >= 9000)") | |
| maintenance_version="T" | |
| } | |
| } | |
| } | |
| cat(sprintf("maintenance_version=%s", maintenance_version), file = Sys.getenv("GITHUB_OUTPUT"), append = TRUE) | |
| shell: Rscript {0} | |
| - name: Check | |
| if: | | |
| (github.event_name == 'workflow_dispatch' && matrix.r_version == 'devel') || | |
| matrix.r_version != 'devel' | |
| env: | |
| _R_CHECK_CRAN_INCOMING_REMOTE_: false | |
| _R_CHECK_FORCE_SUGGESTS_: false | |
| run: | | |
| unlink("tmp",recursive=TRUE) | |
| if ("${{steps.check_version.outputs.maintenance_version}}" == "T"){ | |
| Sys.setenv("_R_CHECK_CRAN_INCOMING_SKIP_LARGE_VERSION_" = TRUE) | |
| } | |
| if (!requireNamespace("rcmdcheck", quietly = TRUE)) install.packages("rcmdcheck") | |
| options(crayon.enabled = TRUE) | |
| check_error_on <- "${{ inputs.error-on }}" | |
| if (check_error_on == "") { | |
| check_error_on <- "note" | |
| } | |
| rcmdcheck::rcmdcheck( | |
| args = c("--no-manual", "--as-cran"), | |
| error_on = check_error_on, | |
| check_dir = "check" | |
| ) | |
| shell: Rscript {0} | |
| - name: Upload check results | |
| if: failure() | |
| uses: actions/upload-artifact@main | |
| with: | |
| name: r${{ matrix.r_version }}-results | |
| path: check |