added custom R install

.github/actions/setup-r-dependencies.yaml

@@ -0,0 +1,220 @@
+name: 'setup-r-dependencies'
+description: 'Action to setup installation tools and install R dependencies'
+author: 'Jim Hester (modified by Henrik Spiegelhauer)'
+inputs:
+  cache:
+    description: 'A boolean value indicating whether packages should be cached from one to the other'
+    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"'
+  dependency_repo:
+    description: 'Overwrite the default CRAN-like reposity'
+    default: 'NULL'
+  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 details.'
+    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()$arch))'
+          echo "::endgroup::"
+        shell: bash
+
+      - name: Query dependencies
+        id: install
+        run: |
+          # Override the default CRAN-like repository
+          if ("${{ inputs.dependency_repo }}" != "NULL") {
+            options(repos = c(CRAN = "${{ inputs.dependency_repo }}"))
+          }
+
+          # Dependency resolution
+          cat("::group::Dependency resolution\n")
+          cat("os-version=", sessionInfo()$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: Restore R package cache
+        if: inputs.cache == 'true'
+        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, inputs.dependency_repo, hashFiles(format('{0}/.github/pkg.lock', inputs.working-directory ))) }}
+          restore-keys: ${{ steps.install.outputs.os-version }}-${{ steps.install.outputs.r-version }}-${{inputs.cache-version }}-
+
+      - name: Install dependencies
+        run: |
+          # Override the default CRAN-like repository
+          if ("${{ inputs.dependency_repo }}" != "NULL") {
+            options(repos = c(CRAN = "${{ inputs.dependency_repo }}"))
+          }
+
+          # 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