Fix ci #885
Workflow file for this run
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| # The purpose of this workflow is to execute `R CMD check` on different R and OS version. | |
| # | |
| # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples | |
| # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help | |
| on: | |
| push: | |
| branches: [main, master] | |
| pull_request: | |
| branches: [main, master] | |
| name: R-CMD-check | |
| jobs: | |
| R-CMD-check: | |
| runs-on: self-hosted #${{ matrix.config.os }} | |
| name: "ubuntu" # ${{ matrix.config.os }} (${{ matrix.config.r }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| # some dependencies can't be installed on windows or mac OS. We only support Linux. Period. | |
| # - { os: macOS-latest, r: "release" } | |
| # - { os: windows-latest, r: "release" } | |
| # TODO devel currently fails because a dependency can't be installed. Hopefully this gets fixed. | |
| # - { os: ubuntu-latest, r: "devel", http-user-agent: "release" } | |
| - { os: ubuntu-22.04, r: "4.2.2" } | |
| - { os: ubuntu-22.04, r: "oldrel-1" } | |
| env: | |
| GITHUB_PAT: ${{ secrets.TOKEN }} | |
| R_KEEP_PKG_SOURCE: yes | |
| CIBERSORTX_EMAIL: ${{ secrets.CIBERSORTX_EMAIL }} | |
| CIBERSORTX_TOKEN: ${{ secrets.CIBERSORTX_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Update system dependencies | |
| # due to recent versions of GLIBC missing | |
| run: | | |
| sudo apt-get update && sudo apt-get install cmake libstdc++6 \ | |
| libcurl4-openssl-dev libssl-dev libxml2-dev libfontconfig1-dev \ | |
| libharfbuzz-dev libfribidi-dev \ | |
| libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev -y | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: 4.2.2 # ${{ matrix.config.r }} | |
| # http-user-agent: ${{ matrix.config.http-user-agent }} | |
| use-public-rspm: true | |
| - name: Install pak | |
| run: Rscript -e "install.packages('pak', repos='https://cran.rstudio.com/')" | |
| #- name: harmony | |
| # run: Rscript -e "pak::pkg_install('omnideconv/harmony')" | |
| # - name: BiocManager | |
| # run: Rscript -e "pak::pkg_install('BiocManager')" | |
| # | |
| # - name: Giotto deps | |
| # run: Rscript -e "BiocManager::install(c('lfa', 'SPARK', 'trendsceek'))" | |
| #- name: Giotto | |
| # run: Rscript -e "pak::pkg_install('drieslab/Giotto@master')" | |
| - name: Install Devtools | |
| run: Rscript -e "pak::pkg_install('devtools')" | |
| - name: Install SpatialExperiment | |
| run: Rscript -e "devtools::install_github('drighelli/SpatialExperiment')" | |
| - name: Install Test Dependencies | |
| run: Rscript -e "pak::pkg_install(c('testthat', 'omnideconv/immunedeconv', 'omnideconv/omnideconv', 'satijalab/seurat@4.4.0'))" # drighelli/SpatialExperiment' | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| dependencies: '"hard"' # do not install suggests | |
| extra-packages: any::rcmdcheck, any::rmarkdown, any::markdown, local::. | |
| needs: check | |
| #error-on: '"error"' | |
| - uses: r-lib/actions/check-r-package@v2 | |
| with: | |
| upload-snapshots: true | |
| error-on: '"error"' |