diff --git a/.github/workflows/r.yml b/.github/workflows/r.yml index 51afdfc..acedab2 100644 --- a/.github/workflows/r.yml +++ b/.github/workflows/r.yml @@ -25,21 +25,24 @@ jobs: runs-on: ubuntu-24.04 strategy: matrix: - r-version: [4.3] + r-version: [4.5] steps: - uses: actions/checkout@v4 - name: Set up R ${{ matrix.r-version }} uses: r-lib/actions/setup-r@v2 with: r-version: ${{ matrix.r-version }} + use-public-rspm: true - name: Install Linux packages - run: sudo apt-get install -y mono-mcs mono-xbuild libcurl4-openssl-dev libicu-dev pandoc pandoc-citeproc texlive texlive-latex-extra texlive-fonts-extra + run: sudo apt-get install -y libcurl4-openssl-dev libicu-dev pandoc texlive texlive-latex-extra texlive-fonts-extra shell: bash {0} - name: Install dependencies run: | - install.packages(c("remotes", "covr", "rcmdcheck", "rmarkdown", "protViz", "testthat", "knitr", "BiocManager")) - BiocManager::install(c("BiocStyle", "ExperimentHub", "tartar")) - remotes::install_deps(dependencies = TRUE) + install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch)) + cat("Repository being used:\n") + print(getOption("repos")) + pak::pkg_install(c("covr", "rcmdcheck", "rmarkdown", "protViz", "testthat", "knitr", "bioc::BiocStyle", "bioc::ExperimentHub", "bioc::tartare")) + pak::local_install_deps(dependencies = TRUE) shell: Rscript {0} - name: Check run: rcmdcheck::rcmdcheck(build_args = "", args = "", error_on = "error", check_dir = "/tmp/rawrr.Rcheck") @@ -51,4 +54,4 @@ jobs: with: name: rawrr.Rcheck path: /tmp/rawrr.Rcheck - if-no-files-found: warn + if-no-files-found: warn \ No newline at end of file