build_packages #15
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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: Make test artifact | |
run: echo hi from ${{ github.run_id }} > testarti.txt | |
- uses: actions/upload-artifact@v3 | |
with: | |
name: testarti | |
path: testarti.txt | |
- 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 |