action.yaml

name: 'setup-r-dependencies'
description: 'Action to setup installation tools and install R dependencies'
author: 'Jim Hester'
inputs:
  cache:
    description: 'Whether packages should be cached across runs or not. If `"always"` is provided, the package cache will be saved even if the workflow fails.'
    required: true
    default: true
  cache-version:
    description: 'The version of the cache, change this from the default (1) to start over with a fresh cache. Ignored if cache: false'
    required: true
    default: 1
  extra-packages:
    description: 'Any extra packages to install outside of the packages listed in the dependencies'
  needs:
    description: 'Any extra Config/Needs fields which need to be included when installing dependencies'
  packages:
    description: 'Which package(s) to install.'
    default: 'deps::., any::sessioninfo'
  pak-version:
    description: 'Which pak version to use. Possible values are "stable", "rc" and "devel".'
    default: 'stable'
  working-directory:
    description: 'Using the working-directory keyword, you can specify the working directory of where "pkg_deps" command searches for dependencies in the "DESCRIPTION" file.'
    default: '.'
  dependencies:
    description: 'Types of dependencies to install. Must be an R expression. Note that it often needs to be quoted in YAML, see the README for details.'
    default: '"all"'
  upgrade:
    description: 'Whether to install the latest available versions of the dependencies. Must be an R expression. See the README for details if you need quoting.'
    default: 'FALSE'
  lockfile-create-lib:
    description: 'The package library to consider when creating the pak lockfile. This is passed to the `lib` argument of `pak::lockfile_create()`. Defaults to an empty library, for reproducibility. Must be an R expression. Note that it often needs to be quoted in YAML, see the README for detail\
s.'
    default: 'NULL'
  install-pandoc:
    description: 'Whether to install pandoc. By default it is installed if it is not on the PATH and the local package suggests or depends on the rmarkdown package.'
  pandoc-version:
    description: 'Pandoc version to install.'
    default: '3.1.11'
runs:
  using: "composite"
  steps:
      - name: Set site library path
        run: |
          # Set site library path
          cat("::group::Set site library path\n")
          if (Sys.getenv("RENV_PROJECT") != "") {
            message("renv project detected, no need to set R_LIBS_SITE")
            cat(sprintf("R_LIB_FOR_PAK=%s\n", .libPaths()[1]), file = Sys.getenv("GITHUB_ENV"), append = TRUE)
            q("no")
          }
          lib <- Sys.getenv("R_LIBS_SITE")
          if (lib == "") {
            lib <- file.path(dirname(.Library), "site-library")
            cat(sprintf("R_LIBS_SITE=%s\n", lib), file = Sys.getenv("GITHUB_ENV"), append = TRUE)
            cat(sprintf("R_LIB_FOR_PAK=%s\n", lib), file = Sys.getenv("GITHUB_ENV"), append = TRUE)
            message("Setting R_LIBS_SITE to ", lib)
          } else {
            message("R_LIBS_SITE is already set to ", lib)
            cat(sprintf("R_LIB_FOR_PAK=%s\n", strsplit(lib, .Platform$path.sep)[[1]][[1]]), file = Sys.getenv("GITHUB_ENV"), append = TRUE)
          }
          cat("::endgroup::\n")
        shell: Rscript {0}

      - name: Install pak (Windows)
        if: runner.os == 'Windows'
        run: |
          # Install pak
          cat("::group::Install pak\n")
          lib <- Sys.getenv("R_LIB_FOR_PAK")
          dir.create(lib, showWarnings = FALSE, recursive = TRUE)
          install.packages("pak", lib = lib, repos = sprintf(
            "https://r-lib.github.io/p/pak/%s/%s/%s/%s",
            "${{ inputs.pak-version }}",
            .Platform$pkgType,
            R.Version()$os,
            R.Version()$arch
          ))
          cat("::endgroup::\n")
        shell: Rscript {0}

      - name: Install pak (Unix)
        if: runner.os != 'Windows'
        run: |
          # Install pak
          echo "::group::Install pak"
          if which sudo >/dev/null; then SUDO="sudo -E --preserve-env=PATH env"; else SUDO=""; fi
          $SUDO R -q -e 'dir.create(Sys.getenv("R_LIB_FOR_PAK"), recursive = TRUE, showWarnings = FALSE)'
          $SUDO R -q -e 'install.packages("pak", lib = Sys.getenv("R_LIB_FOR_PAK"), repos = sprintf("https://r-lib.github.io/p/pak/%s/%s/%s/%s", "${{ inputs.pak-version }}", .Platform$pkgType, R.Version()$os, R.Version()$arch))'
          echo "::endgroup::"
        shell: bash

      - name: Query dependencies
        id: install
        run: |
          # Dependency resolution
          cat("::group::Dependency resolution\n")
          cat("os-version=", sessionInfo()$running, "\n", file = Sys.getenv("GITHUB_OUTPUT"), sep = "", append = TRUE)
          r_version <-
            if (grepl("development", R.version.string)) {
              pdf(tempfile())
              ge_ver <- attr(recordPlot(), "engineVersion")
              dev.off()
              paste0("R version ", getRversion(), " (ge:", ge_ver, "; iid:", .Internal(internalsID()), ")")
            } else {
              R.version.string
            }
          cat("r-version=", r_version, "\n", file = Sys.getenv("GITHUB_OUTPUT"), sep = "", append = TRUE)
          needs <- sprintf("Config/Needs/%s", strsplit("${{ inputs.needs }}", "[[:space:],]+")[[1]])
          deps <- strsplit("${{ inputs.packages }}", "[[:space:],]+")[[1]]
          extra_deps <- strsplit("${{ inputs.extra-packages }}", "[[:space:],]+")[[1]]
          dir.create(".github", showWarnings=FALSE)
          Sys.setenv("PKGCACHE_HTTP_VERSION" = "2")
          library(pak, lib.loc = Sys.getenv("R_LIB_FOR_PAK"))
          pak::lockfile_create(
            c(deps, extra_deps),
            lockfile = ".github/pkg.lock",
            upgrade = (${{ inputs.upgrade }}),
            dependencies = c(needs, (${{ inputs.dependencies }})),
            lib = ${{ inputs.lockfile-create-lib }}
          )
          cat("::endgroup::\n")
          cat("::group::Show Lockfile\n")
          writeLines(readLines(".github/pkg.lock"))
          cat("::endgroup::\n")
        shell: Rscript {0}
        working-directory: ${{ inputs.working-directory }}

      - name: R package cache
        if: inputs.cache != 'false'
        uses: actions/cache@v4
        with:
          path: |
            ${{ env.R_LIBS_USER }}/*
            !${{ env.R_LIBS_USER }}/pak
          key: ${{ format('{0}-{1}-{2}-{3}', steps.install.outputs.os-version, steps.install.outputs.r-version, inputs.cache-version, hashFiles(format('{0}/.github/pkg.lock', inputs.working-directory ))) }}
          restore-keys: ${{ format('{0}-{1}-{2}-', steps.install.outputs.os-version, steps.install.outputs.r-version, inputs.cache-version) }}
          # Used to save package installation on troublesome Actions
          save-always: ${{ inputs.cache == 'always' }}

      - name: Install dependencies
        run: |
          # Install/Update packages
          cat("::group::Install/update packages\n")
          Sys.setenv("PKGCACHE_HTTP_VERSION" = "2")
          library(pak, lib.loc = Sys.getenv("R_LIB_FOR_PAK"))
          pak::lockfile_install(".github/pkg.lock")
          ## Clean up lock file
          unlink(".github/pkg.lock")
          cat("::endgroup::\n")
        shell: Rscript {0}
        working-directory: ${{ inputs.working-directory }}

      - name: Check whether pandoc needs to be installed
        id: check-pandoc
        run: |
          cat("::group::Check if package needs pandoc\n")
          o <- '${{ inputs.install-pandoc }}'
          if (! o %in% c('true', 'false')) {
            if (Sys.which("pandoc") != "") {
              o <- 'false'
            } else if (file.exists("DESCRIPTION")) {
              deptypes <- list(direct = "all", indirect = character())
              deps <- pak::pkg_deps(".", dependencies = deptypes)
              if ("rmarkdown" %in% deps$package) {
                o <- 'true'
              } else {
                o <- 'false'
              }
            } else {
              o <- 'false'
            }
          }
          cat("install=", o, "\n", file = Sys.getenv("GITHUB_OUTPUT"), sep = "", append = TRUE)
          cat("::endgroup::\n")
        shell: Rscript {0}
        working-directory: ${{ inputs.working-directory }}

      - name: Install pandoc if needed
        if: ${{ steps.check-pandoc.outputs.install == 'true' }}
        uses: r-lib/actions/setup-pandoc@v2
        with:
          pandoc-version: ${{ inputs.pandoc-version }}

      - name: Session info
        run: |
          # Session info
          cat("::group::Session info\n")
          if (requireNamespace("sessioninfo", quietly = TRUE)) {
            if (packageVersion("sessioninfo") >= "1.2.1") {
              sessioninfo::session_info(pkgs = "installed", include_base = TRUE)
            } else {
              options(width = 200)
              sessioninfo::session_info(rownames(installed.packages()), include_base=TRUE)
            }
          } else {
            sessionInfo()
          }
          cat("::endgroup::\n")
        shell: Rscript {0}
        working-directory: ${{ inputs.working-directory }}

      - name: Don't use tar 1.30 from Rtools35 to store the cache
        if: runner.os == 'Windows'
        shell: bash
        run: |
          if command -v /c/Rtools/bin/tar && /c/Rtools/bin/tar --version | grep -q 'tar (GNU tar) 1.30'
            then echo 'C:/Program Files/Git/usr/bin' >> $GITHUB_PATH
          fi