Merge pull request #149 from omnideconv/fixCI #890
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
| # 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: 4.4.0 # ${{ 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 Seurat | |
| run: Rscript -e "install.packages('Matrix')" | |
| - name: Install Test Dependencies | |
| run: Rscript -e "pak::pkg_install(c('testthat', 'omnideconv/immunedeconv', 'omnideconv/omnideconv'))" # 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"' |