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‎.github/CI_WORKFLOW.md‎

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# GitHub Actions CI Workflow
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This document describes the continuous integration (CI) workflow for the evaluomeR package.
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## Overview
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The `.github/workflows/test.yaml` workflow automatically runs your R package tests whenever code is pushed or a pull request is created. This ensures code quality and prevents regressions before merging to main branches.
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## Workflow Triggers
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The workflow runs on the following events:
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- **Push**: Any push to `main`, `master`, or `develop` branches
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- **Pull Request**: Any pull request targeting `main`, `master`, or `develop` branches
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- **Manual**: Manually triggered via GitHub Actions UI (workflow_dispatch)
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## Test Matrix
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Tests run across multiple R versions to ensure compatibility:
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- **R 4.3** - Latest stable release from that series
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- **Latest R** - Most current R version available
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All testing occurs on **Ubuntu Latest** runner.
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## Workflow Steps
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### 1. Checkout
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Clones your repository code.
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### 2. Set up R
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Installs the specified R version using the official r-lib setup action.
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### 3. Install System Dependencies
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Installs required system libraries:
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- `libcurl4-openssl-dev` - For HTTP communication
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- `libssl-dev` - For SSL/TLS support
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- `libxml2-dev` - For XML parsing
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### 4. Install R Dependencies
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Automatically installs all package dependencies declared in `DESCRIPTION`:
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- **Depends**: SummarizedExperiment, MultiAssayExperiment, dplyr, cluster, fpc, randomForest, flexmix, RSKC, sparcl
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- **Imports**: All packages listed in the Imports field
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- **Extra packages**: devtools (for package installation)
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### 5. Install Package
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Builds and installs your package locally using `devtools::install_local()`.
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### 6. Run Tests
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Executes all test scripts in the `tests/` directory matching the pattern `test*.R`:
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- testARI.R
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- testATSC.R
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- testATSC_GoldStandard.R
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- testATSC_parallel.R
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- testAll.R
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- testAlpha_parallel.R
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- testAnalysis.R
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- testCBI.R
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- testCH_index.R
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- testDataPreprocessing.R
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- testK_optimo_parallel.R
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- testL1_clustering.R
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- testMetricsRelevancy.R
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- testPCA.R
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- testQuality.R
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- testQuality_parallel.R
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- testStability.R
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- testStability_parallel.R
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Each test is sourced in sequence, with detailed output showing which test is running. If any test fails, the workflow exits with status 1 and reports the error.
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### 7. Upload Artifacts
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Test results and scripts are uploaded as workflow artifacts for 30 days, allowing you to review test output even after the workflow completes.
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## Viewing Results
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### On GitHub
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1. Navigate to your repository
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2. Click the **Actions** tab
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3. Click on the workflow run to see detailed output
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4. Expand any step to see its console output
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5. Download artifacts from the "Artifacts" section
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### Badges
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You can add a status badge to your README:
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```markdown
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[![R Package Tests](https://github.com/neobernad/evaluomeR/actions/workflows/test.yaml/badge.svg)](https://github.com/neobernad/evaluomeR/actions/workflows/test.yaml)
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```
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## Troubleshooting
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### Tests Fail in CI but Pass Locally
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- Ensure your local R version matches one of the CI versions (R 4.3 or latest)
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- Check for platform-specific issues (paths, environment variables)
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- Verify all dependencies are correctly listed in DESCRIPTION
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### Missing Dependencies
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- Add missing packages to DESCRIPTION under either `Depends` or `Imports`
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- For system packages, add them to the "Install system dependencies" step
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- Re-run the workflow after updating DESCRIPTION
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### Long Test Execution Times
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- Consider splitting large parallel tests into separate workflows if needed
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- Optimize test code to reduce runtime
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- Check if tests are downloading large data files
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## Future Enhancements
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Possible improvements to the CI workflow:
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1. **Code Coverage**: Add code coverage reports using `covr` package
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2. **R CMD Check**: Add `R CMD check` for comprehensive package validation
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3. **Platform Matrix**: Extend to include macOS and Windows runners
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4. **Documentation Builds**: Generate and validate vignettes/documentation
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5. **Performance Benchmarks**: Track test execution times over time
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## Related Files
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- `.github/workflows/test.yaml` - The main workflow definition
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- `DESCRIPTION` - Package metadata and dependencies
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- `tests/` - Directory containing all test scripts

‎.github/workflows/pkgdown.yaml‎

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name: pkgdown
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on:
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push:
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branches: [main, master]
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workflow_dispatch:
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permissions:
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contents: read
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pages: write
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id-token: write
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concurrency:
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group: "pages"
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cancel-in-progress: false
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Setup Pages
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uses: actions/configure-pages@v4
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- name: Set up R
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uses: r-lib/actions/setup-r@v2
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- name: Install system dependencies
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run: |
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sudo apt-get update
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sudo apt-get install -y libcurl4-openssl-dev libssl-dev libxml2-dev
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- name: Install dependencies
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uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: |
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any::pak
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any::pkgdown
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- name: Install package
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run: |
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pak::pak("local::.")
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shell: Rscript {0}
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- name: Build site
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run: |
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pkgdown::clean_site(force = TRUE)
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pkgdown::build_site()
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shell: Rscript {0}
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- name: Upload artifact
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uses: actions/upload-pages-artifact@v3
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with:
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path: ./docs
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deploy:
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environment:
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name: github-pages
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url: ${{ steps.deployment.outputs.page_url }}
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runs-on: ubuntu-latest
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needs: build
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steps:
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- name: Deploy to GitHub Pages
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id: deployment
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uses: actions/deploy-pages@v4

‎.github/workflows/test.yaml‎

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name: R Package Tests
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on:
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push:
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branches: [ main, master, develop ]
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pull_request:
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branches: [ main, master, develop ]
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workflow_dispatch:
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permissions:
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contents: read
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jobs:
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test:
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: [ubuntu-latest]
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r-version: ['4.3', 'latest']
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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R_KEEP_PKG_SOURCE: yes
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steps:
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- uses: actions/checkout@v4
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- name: Set up R
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uses: r-lib/actions/setup-r@v2
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with:
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r-version: ${{ matrix.r-version }}
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- name: Install system dependencies
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if: runner.os == 'Linux'
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run: |
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sudo apt-get update
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sudo apt-get install -y libcurl4-openssl-dev libssl-dev libxml2-dev
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- name: Install R dependencies
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uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: |
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any::pak
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any::testthat
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- name: Install package
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run: |
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pak::pak("local::.")
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shell: Rscript {0}
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- name: Run tests
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run: |
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test_files <- list.files("tests", pattern = "^test.*\\.R$", full.names = TRUE)
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if (length(test_files) == 0) {
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cat("No test files found\n")
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quit(save = "no", status = 0)
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}
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for (test_file in test_files) {
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cat("\n=====================================\n")
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cat("Running:", test_file, "\n")
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cat("=====================================\n")
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tryCatch(
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source(test_file),
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error = function(e) {
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cat("ERROR in", test_file, ":\n")
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print(e)
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quit(save = "no", status = 1)
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}
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)
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}
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cat("\nAll tests completed successfully!\n")
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shell: Rscript {0}
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- name: Upload test results
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if: always()
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uses: actions/upload-artifact@v4
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with:
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name: test-results-${{ matrix.os }}-r${{ matrix.r-version }}
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path: tests/
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retention-days: 30

‎.gitignore‎

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.gitmodules
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.hgtags
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.project
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.RDataTmp
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.seed
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.settings
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.tm_properties

‎DESCRIPTION‎

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FactoMineR (>= 2.11),
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factoextra (>= 1.0.7),
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nFactors (>= 2.4.1.1)
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Suggests: BiocStyle, knitr, rmarkdown, magrittr
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Suggests: BiocStyle, knitr, rmarkdown, magrittr, pkgdown
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VignetteBuilder: knitr
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RdMacros: Rdpack
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RoxygenNote: 7.3.2

‎R/internalClusterboot.R‎

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}
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c1 <- clustermethod(data, ...)
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randresult <- fossil::rand.index(gold_standard, c1$partition)
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#randresult <- fossil::rand.index(gold_standard, c1$partition)
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randresult <- mclust::adjustedRandIndex(gold_standard, c1$partition)
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#message("Gold standard")
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#message(gold_standard)

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