Update the GitHub repo #137
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| # 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: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - {os: windows-latest, r: 'release'} | |
| - {os: macOS-latest, r: 'devel', http-user-agent: 'release'} | |
| - {os: macOS-latest, r: 'release'} | |
| - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} | |
| - {os: ubuntu-latest, r: 'release'} | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| R_KEEP_PKG_SOURCE: yes | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| http-user-agent: ${{ matrix.config.http-user-agent }} | |
| use-public-rspm: true | |
| - uses: r-lib/actions/setup-tinytex@v2 | |
| - name: Install libraries for Linux | |
| if: runner.os == 'Linux' | |
| run: | | |
| sudo apt-get install texlive-fonts-extra texlive-lang-european texlive-latex-recommended | |
| sudo apt-get install libcurl4-openssl-dev | |
| - name: Install dependencies | |
| run: | | |
| install.packages("remotes") | |
| remotes::install_deps(dependencies = TRUE) | |
| remotes::install_cran("rcmdcheck") | |
| install.packages("BiocManager") | |
| BiocManager::install(c("DESeq2", "DSS")) | |
| install.packages('tinytex') | |
| install.packages('aods3') | |
| tinytex::parse_install(text = "! LaTeX Error: File `authblk.sty' not found.") | |
| tinytex::parse_install(text = "! LaTeX Error: File `soul.sty' not found.") | |
| tinytex::parse_install(text = "! LaTeX Error: File `placeins.sty' not found.") | |
| tinytex::parse_install(text = "! LaTeX Error: File `ragged2e.sty' not found.") | |
| tinytex::parse_install(text = "! LaTeX Error: File `footmisc.sty' not found.") | |
| tinytex::parse_install(text = "! LaTeX Error: File `marginfix.sty' not found.") | |
| tinytex::parse_install(text = "! LaTeX Error: File `changepage.sty' not found.") | |
| tinytex::parse_install(text = "! LaTeX Error: File `caption.sty' not found.") | |
| tinytex::parse_install(text = "! LaTeX Error: File `xstring.sty' not found.") | |
| tinytex::parse_install(text = "! LaTeX Error: File `mathtools.sty' not found.") | |
| tinytex::parse_install(text = "! LaTeX Error: File `multirow.sty' not found.") | |
| tinytex::tlmgr_install(c("bera", "titlesec", "fancyhdr", "enumitem", "parskip", "nowidow", "parnotes")) | |
| shell: Rscript {0} | |
| # - name: Install Windows dependencies | |
| # if: runner.os == 'Windows' | |
| # run: | | |
| # install.packages("BiocManager") | |
| # BiocManager::install("RCurl",type="binary",force=TRUE) | |
| # Sys.setenv(LOCAL_CPPFLAGS = "-I/mingw$(WIN)/include/libxml2") | |
| # install.packages("XML") | |
| # shell: Rscript {0} | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| # pak-version: devel | |
| # extra-packages: any::rcmdcheck, any::XML | |
| extra-packages: any::rcmdcheck | |
| needs: check | |
| # See https://github.com/r-lib/actions/issues/559 for the XML issue | |
| - uses: r-lib/actions/check-r-package@v2 | |
| with: | |
| args: 'c("--no-manual", "--as-cran")' | |
| error-on: '"error"' | |
| check-dir: '"check"' |