Merge branch 'contents' of https://github.com/Genentech/phase1b into … #7
Workflow file for this run
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| --- | ||
| name: R CMD Check 🧬 | ||
| on: | ||
| push: | ||
| tags: | ||
| - "v*" | ||
| branches: | ||
| - main | ||
| - pre-release | ||
| pull_request: | ||
| types: | ||
| - opened | ||
| - synchronize | ||
| - reopened | ||
| - ready_for_review | ||
| branches: | ||
| - main | ||
| - pre-release | ||
| workflow_dispatch: | ||
| workflow_call: | ||
| secrets: | ||
| GITHUB_TOKEN: | ||
|
Check failure on line 23 in .github/workflows/build-check-install.yaml
|
||
| description: | | ||
| Github token with read access to repositories, required for staged.dependencies installation | ||
| required: false | ||
| inputs: | ||
| install-system-dependencies: | ||
| description: Check for and install system dependencies | ||
| required: false | ||
| default: false | ||
| type: boolean | ||
| enable-staged-dependencies-check: | ||
| description: Enable staged dependencies YAML check | ||
| required: false | ||
| default: true | ||
| type: boolean | ||
| R_CHECK_FORCE_SUGGESTS: | ||
| description: If true, give an error if suggested packages are not available | ||
| required: false | ||
| default: true | ||
| type: boolean | ||
| skip-r-cmd-check: | ||
| description: Skip the R CMD check step in this workflow | ||
| required: false | ||
| default: false | ||
| type: boolean | ||
| skip-r-cmd-install: | ||
| description: Skip the R CMD INSTALL step in this workflow | ||
| required: false | ||
| default: false | ||
| type: boolean | ||
| check-note-blocklist: | ||
| description: Whether to check for NOTEs that should cause the pipeline to fail | ||
| required: false | ||
| default: false | ||
| type: boolean | ||
| note-blocklist: | ||
| description: List of regular expressions appearing in NOTEs that should cause the pipeline to fail | ||
| # Example usage: | ||
| # note-blocklist: | | ||
| # checking package dependencies ... NOTE( )+Depends: includes the non-default packages | ||
| # checking R code for possible problems ... NOTE( )+.*: no visible global function definition for | ||
| # checking for unstated dependencies in vignettes ... NOTE( )+\'.*\' import not declared from | ||
| # checking dependencies in R code ... NOTE( )+Namespace in Imports field not imported from | ||
| # checking installed package size ... NOTE( )+installed size is | ||
| required: false | ||
| default: "" | ||
| type: string | ||
| concurrency: | ||
| group: r-cmd-${{ github.event.pull_request.number || github.ref }} | ||
| cancel-in-progress: true | ||
| jobs: | ||
| build-install-check: | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| config: | ||
| - image: ghcr.io/insightsengineering/rstudio_4.2.1_bioc_3.15 | ||
| tag: latest | ||
| name: ${{ matrix.config.image }}, version ${{ matrix.config.tag }} | ||
| runs-on: ubuntu-latest | ||
| if: > | ||
| !contains(github.event.commits[0].message, '[skip r-cmd]') | ||
| && github.event.pull_request.draft == false | ||
| container: | ||
| image: ${{ matrix.config.image }}:${{ matrix.config.tag }} | ||
| steps: | ||
| - name: Get branch names 🌿 | ||
| id: branch-name | ||
| uses: tj-actions/branch-names@v5 | ||
| - name: Checkout repo 🛎 | ||
| uses: actions/checkout@v3 | ||
| with: | ||
| ref: ${{ steps.branch-name.outputs.head_ref_branch }} | ||
| path: ${{ github.event.repository.name }} | ||
| - name: Run Staged dependencies 🎦 | ||
| uses: insightsengineering/staged-dependencies-action@v1 | ||
| with: | ||
| run-system-dependencies: ${{ inputs.install-system-dependencies }} | ||
| env: | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
| SD_REPO_PATH: ${{ github.event.repository.name }} | ||
| SD_ENABLE_CHECK: ${{ inputs.enable-staged-dependencies-check }} | ||
| - name: Show session info and installed packages ℹ | ||
| run: | | ||
| sessionInfo() | ||
| as.data.frame(installed.packages()[, c("LibPath", "Version")]) | ||
| shell: Rscript {0} | ||
| - name: Build R package 🏗 | ||
| run: | | ||
| R CMD build ${{ github.event.repository.name }} | ||
| echo "PKGBUILD=$(echo *.tar.gz)" >> $GITHUB_ENV | ||
| shell: bash | ||
| - name: Set TESTING_DEPTH ⚙ | ||
| env: | ||
| COMMIT_NEWEST_MESSAGE: ${{ github.event.head_commit.message }} | ||
| COMMIT_OLDEST_MESSAGE: ${{ github.event.commits[0].message }} | ||
| run: | | ||
| cd ${{ github.event.repository.name }} | ||
| # set TESTING_DEPTH for PR | ||
| if [[ ! -z "${GITHUB_HEAD_REF}" ]]; then | ||
| TESTING_DEPTH=3 | ||
| echo "TESTING_DEPTH=3" >> $GITHUB_ENV | ||
| COMMIT_NEWEST_MESSAGE=$(git log --format=%B -n 1 ${{ github.event.after }}) | ||
| fi | ||
| if [[ $COMMIT_NEWEST_MESSAGE == *"[skip tests]"* ]]; then | ||
| echo "NO_TESTS=1" >> $GITHUB_ENV | ||
| fi | ||
| # default TESTING_DEPTH | ||
| if [[ -z "${TESTING_DEPTH}" ]]; then | ||
| echo "TESTING_DEPTH=1" >> $GITHUB_ENV | ||
| fi | ||
| shell: bash | ||
| - name: Run R CMD check 🏁 | ||
| run: | | ||
| if [ "${{ inputs.skip-r-cmd-check }}" == "true" ] | ||
| then { | ||
| echo "Skipping R CMD check as 'skip-r-cmd-check' was set to 'true'" | ||
| exit 0 | ||
| } | ||
| fi | ||
| if [ "${{ inputs.R_CHECK_FORCE_SUGGESTS }}" == "" ] | ||
| then { | ||
| _R_CHECK_FORCE_SUGGESTS_="FALSE" | ||
| } | ||
| fi | ||
| if [[ -z "${{ env.NO_TESTS }}" ]]; then | ||
| R CMD check ${{ env.PKGBUILD }} | ||
| else | ||
| R CMD check --no-tests ${{ env.PKGBUILD }} | ||
| fi | ||
| shell: bash | ||
| continue-on-error: true | ||
| env: | ||
| _R_CHECK_TESTS_NLINES_: 0 | ||
| _R_CHECK_VIGNETTES_NLINES_: 0 | ||
| _R_CHECK_FORCE_SUGGESTS_: ${{ inputs.R_CHECK_FORCE_SUGGESTS }} | ||
| - name: Check whether JUnit XML report exists 🚦 | ||
| id: check-junit-xml | ||
| uses: andstor/file-existence-action@v1 | ||
| with: | ||
| files: "${{ github.event.repository.name }}.Rcheck/tests/testthat/junit-result.xml" | ||
| - name: Publish Unit Test Summary 📑 | ||
| uses: EnricoMi/publish-unit-test-result-action@v1 | ||
| if: steps.check-junit-xml.outputs.files_exists == 'true' && github.event_name == 'pull_request' | ||
| with: | ||
| check_name: Unit Tests Summary | ||
| files: "${{ github.event.repository.name }}.Rcheck/tests/testthat/junit-result.xml" | ||
| - name: Catch warnings in R CMD check output 🗳 | ||
| id: catch-errors | ||
| run: | | ||
| check_log <- "${{ github.event.repository.name }}.Rcheck/00check.log" | ||
| if (file.exists(check_log)) { | ||
| x <- tail(readLines(check_log), 1) | ||
| if (grepl("ERROR", x)) { | ||
| writeLines(readLines(check_log)) | ||
| stop("❌ R CMD check has errors") | ||
| } | ||
| if (grepl("WARNING", x)) { | ||
| writeLines(readLines(check_log)) | ||
| stop("⚠ R CMD check has warnings") | ||
| } | ||
| if ("${{ inputs.check-note-blocklist }}" == "true") { | ||
| print("Checking notes...") | ||
| regexes <- "${{ inputs.note-blocklist }}" | ||
| regexes <- unlist(strsplit(regexes, split = "\n")) | ||
| lines <- paste(readLines(check_log), collapse = " ") | ||
| notes_result <- vapply( | ||
| regexes, | ||
| function(r){ | ||
| if (grepl(r, lines)) { | ||
| print(r) | ||
| return(TRUE) | ||
| } | ||
| return(FALSE) | ||
| }, | ||
| logical(1) | ||
| ) | ||
| if (any(notes_result)) { | ||
| stop("NOTEs on the blocklist were found (see above).") | ||
| } | ||
| } | ||
| } | ||
| shell: Rscript {0} | ||
| - name: Install R package 🚧 | ||
| run: | | ||
| if [ "${{ inputs.skip-r-cmd-install }}" == "true" ] | ||
| then { | ||
| echo "Skipping R CMD INSTALL as 'skip-r-cmd-install' was set to 'true'" | ||
| exit 0 | ||
| } | ||
| fi | ||
| R CMD INSTALL ${{ env.PKGBUILD }} | ||
| shell: bash | ||
| - name: Upload package build ⤴ | ||
| if: startsWith(github.ref, 'refs/tags/v') | ||
| uses: actions/upload-artifact@v3 | ||
| with: | ||
| path: ${{ env.PKGBUILD }} | ||
| name: ${{ env.PKGBUILD }} | ||
| upload-release-assets: | ||
| name: Upload build tar.gz | ||
| needs: build-install-check | ||
| runs-on: ubuntu-latest | ||
| if: > | ||
| startsWith(github.ref, 'refs/tags/v') | ||
| && (!contains(github.event.commits[0].message, '[skip r-cmd]')) | ||
| && github.event.pull_request.draft == false | ||
| steps: | ||
| - name: Checkout repo 🛎 | ||
| uses: actions/checkout@v3 | ||
| - name: Set release version and package build filename 📐 | ||
| run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/v}" >> $GITHUB_ENV | ||
| - name: Get package build filename 📦 | ||
| run: echo "PKGBUILD=${{ github.event.repository.name }}_${{ env.RELEASE_VERSION }}.tar.gz" >> $GITHUB_ENV | ||
| - name: Download artifact ⏬ | ||
| uses: actions/download-artifact@v3 | ||
| with: | ||
| name: ${{ env.PKGBUILD }} | ||
| - name: Upload binaries to release 🔼 | ||
| uses: svenstaro/upload-release-action@v2 | ||
| with: | ||
| repo_token: ${{ secrets.GITHUB_TOKEN }} | ||
| file: ${{ env.PKGBUILD }} | ||
| asset_name: ${{ env.PKGBUILD }} | ||
| tag: ${{ github.ref }} | ||
| overwrite: true | ||
