Update strategies on R min deps check workflow #960
Workflow file for this run
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| name: Audit Dependencies 🕵️♀️ | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| types: | |
| - opened | |
| - synchronize | |
| - reopened | |
| - ready_for_review | |
| branches: | |
| - main | |
| workflow_dispatch: | |
| workflow_call: | |
| inputs: | |
| package-subdirectory: | |
| description: Subdirectory in the repository, where the R package is located. | |
| required: false | |
| type: string | |
| default: "." | |
| allow-failure: | |
| description: Allow workflow to fail if one or more vulnerabilities are found. | |
| required: false | |
| type: boolean | |
| default: false | |
| jobs: | |
| audit: | |
| runs-on: ubuntu-latest | |
| container: | |
| image: ghcr.io/insightsengineering/rstudio_4.3.1_bioc_3.17:latest | |
| name: oysteR scan 🦪 | |
| if: > | |
| !contains(github.event.commits[0].message, '[skip audit]') | |
| && github.event.pull_request.draft == false | |
| steps: | |
| - name: Checkout repo 🛎 | |
| uses: actions/checkout@v3 | |
| - name: Normalize inputs 🛠️ | |
| id: normalizer | |
| run: | | |
| ALLOW_FAILURE="${{ inputs.allow-failure }}" | |
| if [ "$ALLOW_FAILURE" == "" ] | |
| then { | |
| ALLOW_FAILURE=false | |
| } | |
| fi | |
| echo "allow-failure=$ALLOW_FAILURE" >> "$GITHUB_ENV" | |
| shell: bash | |
| - name: Run oysteR scan on dependencies 🔍 | |
| run: | | |
| tryCatch( | |
| expr = { | |
| dependencies_scan = oysteR::audit_description( | |
| dir = ".", | |
| fields = c("Depends", "Imports", "Suggests"), | |
| verbose = TRUE | |
| ) | |
| print(as.data.frame( | |
| dependencies_scan[c( | |
| "package", | |
| "version", | |
| "vulnerabilities", | |
| "no_of_vulnerabilities" | |
| )] | |
| )) | |
| Sys.sleep(1) | |
| deps_with_vulnerabilities = subset(dependencies_scan, no_of_vulnerabilities > 0) | |
| if(nrow(deps_with_vulnerabilities) > 0) { | |
| message("❗ Vulnerabilities found in the following dependencies:") | |
| message(deps_with_vulnerabilities["package"]) | |
| if ("${{ env.allow-failure }}" == "true") quit(status=1) | |
| } | |
| }, | |
| error = function(e) { | |
| message('🚨 Caught an error!') | |
| print(e) | |
| } | |
| ) | |
| shell: Rscript {0} | |
| working-directory: ${{ inputs.package-subdirectory }} | |
| - name: Run oysteR scan on renv.lock 🔒 | |
| run: | | |
| tryCatch( | |
| expr = { | |
| if (file.exists("renv.lock")) { | |
| renv_lock_scan = oysteR::audit_renv_lock(dir = ".", verbose = TRUE) | |
| print(as.data.frame( | |
| renv_lock_scan[c( | |
| "package", | |
| "version", | |
| "vulnerabilities", | |
| "no_of_vulnerabilities" | |
| )] | |
| )) | |
| Sys.sleep(1) | |
| deps_with_vulnerabilities = subset(renv_lock_scan, no_of_vulnerabilities > 0) | |
| if(nrow(deps_with_vulnerabilities) > 0) { | |
| message("❗ Vulnerabilities found in the following dependencies:") | |
| message(deps_with_vulnerabilities["package"]) | |
| if ("${{ env.allow-failure }}" == "true") quit(status=1) | |
| } | |
| } else { | |
| print("No renv.lock file, not scanning.") | |
| } | |
| }, | |
| error = function(e) { | |
| message('🚨 Caught an error!') | |
| print(e) | |
| } | |
| ) | |
| shell: Rscript {0} |