fix workflow file #38
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| on: [push] | |
| jobs: | |
| job1: | |
| runs-on: ubuntu-latest | |
| container: bioconductor/bioconductor_docker:RELEASE_3_11 | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| steps: | |
| - name: Checkout code | |
| run: | | |
| git clone https://github.com/${{ github.repository }} . | |
| git checkout ${{ github.sha }} | |
| - name: Query dependencies | |
| run: | | |
| install.packages('remotes') | |
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | |
| shell: Rscript {0} | |
| - name: Install system dependencies | |
| if: runner.os == 'Linux' | |
| env: | |
| RHUB_PLATFORM: linux-x86_64-ubuntu-gcc | |
| run: | | |
| apt-get update | |
| apt-get -y install libharfbuzz-dev libfribidi-dev | |
| Rscript -e "remotes::install_github('r-hub/sysreqs')" | |
| sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))") | |
| sudo -s eval "$sysreqs" | |
| - name: Install dependencies | |
| # Change: Add the GH_PAT secret as an environment variable | |
| env: | |
| GITHUB_PAT: ${{ secrets.GH_PAT }} | |
| run: | | |
| options(repos = c(CRAN = "https://cloud.r-project.org")) | |
| remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE) | |
| BiocManager::install("rcmdcheck", update = TRUE, ask = FALSE) | |
| shell: Rscript {0} | |
| - name: Check | |
| env: | |
| _R_CHECK_CRAN_INCOMING_REMOTE_: false | |
| GITHUB_PAT: ${{ secrets.GH_PAT }} # Also add here if check step accesses private repos | |
| run: rcmdcheck::rcmdcheck(args = c("--no-manual"), error_on = "error", check_dir = "check") | |
| shell: Rscript {0} | |
| - uses: docker/build-push-action@v5 | |
| with: | |
| username: ${{ secrets.DOCKER_USERNAME }} | |
| password: ${{ secrets.DOCKER_PASSWORD }} | |
| repository: ludwigg/subtypeheterogeneity | |
| tag_with_ref: true | |
| tag_with_sha: true | |
| tags: latest | |
| - name: Build pkgdown | |
| env: | |
| GITHUB_PAT: ${{ secrets.GH_PAT }} # Also add here for pkgdown | |
| run: | | |
| PATH=$PATH:$HOME/bin/ Rscript -e 'pkgdown::build_site(".")' | |
| - name: Install deploy dependencies | |
| run: | | |
| apt-get update | |
| apt-get -y install rsync | |
| - name: Deploy 🚀 | |
| uses: JamesIves/github-pages-deploy-action@v4 | |
| with: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| BRANCH: gh-pages | |
| FOLDER: docs |