build_packages #10
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: build_packages | |
| on: workflow_dispatch | |
| jobs: | |
| build: | |
| runs-on: windows-latest | |
| strategy: | |
| fail-fast: true | |
| max-parallel: 1 | |
| matrix: | |
| R: [ 'release', 'oldrel' ] | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| name: Build ${{ matrix.R }} | |
| steps: | |
| - name: Test dispatch | |
| uses: codex-/return-dispatch@v1 | |
| id: return_dispatch | |
| with: | |
| token: ${{ secrets.PAT }} | |
| ref: master | |
| repo: patRoon | |
| owner: rickhelmus | |
| workflow: test.yml | |
| #workflow_inputs: { "some_input": "value" } # Optional | |
| #workflow_timeout_seconds: 120 # Default: 300 | |
| - name: Await Run ID ${{ steps.return_dispatch.outputs.run_id }} | |
| uses: Codex-/await-remote-run@v1.0.0 | |
| with: | |
| token: ${{ secrets.PAT }} | |
| repo: patRoon | |
| owner: rickhelmus | |
| run_id: ${{ steps.return_dispatch.outputs.run_id }} | |
| run_timeout_seconds: 300 # Optional | |
| poll_interval_ms: 5000 # Optional | |
| - uses: actions/checkout@v3 | |
| - name: Setup R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.R }} | |
| - name: Pre-Install R deps | |
| run: | | |
| if (getRversion() < "4.3") # workaround, see https://support.bioconductor.org/p/9148444/ | |
| options(BioC_mirror = "http://bioconductor.org") | |
| install.packages(c("miniCRAN", "git2r", "devtools", "BiocManager", "rversions")) | |
| BiocManager::install(c("Rdisop", "GenomeInfoDbData")) # sometimes needed as dependency may not be picked up... | |
| BiocManager::install("ropls") # For KPIC2 | |
| remotes::install_github("cran/InterpretMSSpectrum@1.3.3") # workaround for https://github.com/cbroeckl/RAMClustR/issues/48 | |
| BiocManager::install(c("xcms", "qlcMatrix")) # for cliqueMS | |
| install.packages("RAMClustR") | |
| remotes::install_github(c("blosloos/nontargetData", "blosloos/nontarget")) | |
| remotes::install_github("rickhelmus/KPIC2") | |
| remotes::install_github("souravc83/fastAdaboost") # For Metaclean, removed from CRAN (9/22) | |
| remotes::install_github("KelseyChetnik/MetaClean") | |
| shell: Rscript {0} | |
| - name: Make repos | |
| run: Rscript make_repos.R | |
| - name: Push changes | |
| env: | |
| CI_COMMIT_MESSAGE: Automated GHA update | |
| CI_COMMIT_AUTHOR: GHA | |
| run: | | |
| git config --global user.name "${{ env.CI_COMMIT_AUTHOR }}" | |
| git config --global user.email "notvalid@someemail.com" | |
| git add bin/ | |
| git commit -m "${{ env.CI_COMMIT_MESSAGE }}" | |
| git status | |
| git push |