New CI flow: Check package against specific CRAN snapshot(s).

.github/actions/setup-r-dependencies/action.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 }}-${{inputs.cache-version }}-${{inputs.dependency_repo }}
+
+      - 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

.github/workflows/Check-package.yaml

@@ -10,6 +10,10 @@ on:
   workflow_dispatch:
   workflow_call:
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 name: Check Package 📦
 
 jobs:
@@ -23,10 +27,15 @@ jobs:
     name: License Check 🃏
     uses: insightsengineering/r.pkg.template/.github/workflows/licenses.yaml@main
 
-  # Runs R CMD check using the local R-CMD-check.yaml workflow
-  check:
-    name: RMD check 📦
-    uses: ./.github/workflows/R-CMD-check.yaml
+  # # Runs R CMD check using the local R-CMD-check.yaml workflow
+  # check:
+  #   name: RMD check 📦
+  #   uses: ./.github/workflows/R-CMD-check.yaml
+
+  # Runs R CMD check with specific version(s) of R and cran-snapshot
+  check-versions:
+    name: RMD check versions 📜
+    uses: ./.github/workflows/R-CMD-check-versions.yaml
 
   # Runs unittests while capturing code:cov and uploads to Codecov io. See local subflow
   test:

.github/workflows/R-CMD-check-versions.yaml

@@ -0,0 +1,74 @@
+---
+# R-CMD check which allows you to lock the R version and date of the CRAN snapshot.
+# This is particularly helpful for ensuring that the package works with internal systems.
+  on:
+    workflow_dispatch:
+    workflow_call:
+
+  name: R-CMD-check-versions
+
+  jobs:
+    R-CMD-check:
+      runs-on: ${{ matrix.os }}
+      name: ${{ matrix.os }} (R ${{ matrix.config.r }}, CRAN ${{ matrix.config.date }})
+      strategy:
+        fail-fast: false
+        matrix:
+          os:
+            - macos-latest
+            - windows-latest
+            - ubuntu-latest
+          config:
+            - date: 'latest'
+              r: 'release'
+            - date: 2023-10-25  # Lock the date of the CRAN snapshot
+              r: 4.3.1
+      env:
+        GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+        R_KEEP_PKG_SOURCE: yes
+
+      steps:
+        - uses: actions/checkout@v4
+        - uses: r-lib/actions/setup-pandoc@v2
+        - uses: r-lib/actions/setup-r@v2
+          with:
+            r-version: ${{ matrix.config.r }}
+            use-public-rspm: false
+
+        - name: Determine the CRAN image to use
+          id: cran-image
+          run: |
+            if [ "${{ matrix.config.date }}" == "latest" ]; then
+              echo "image=https://cloud.r-project.org" >> $GITHUB_OUTPUT
+            else
+              echo "image=https://packagemanager.posit.co/cran/${{ matrix.config.date }}" >> $GITHUB_OUTPUT
+            fi
+          shell: bash
+
+        - name: Debug image
+          run: |
+            echo ${{ steps.cran-image.outputs.image }}
+          shell: bash
+
+        - name: Install R dependencies (custom)
+          uses: ./.github/actions/setup-r-dependencies
+          with:
+            cache: true
+            dependency_repo: ${{ steps.cran-image.outputs.image }}
+            working-directory: ${{ github.workspace }}
+            extra-packages: any::rcmdcheck
+
+        - name: Session info
+          run: |
+            sessionInfo()
+            installed.packages()[,c("Package", "Version")]
+
+          shell: Rscript {0}
+
+        - uses: r-lib/actions/check-r-package@v2
+          with:
+            args: 'c("--no-manual", "--as-cran")'
+            upload-snapshots: true
+            error-on: '"error"'
+            check-dir: '"check"'
+            upload-results: true

.github/workflows/R-CMD-check.yaml

@@ -18,8 +18,8 @@ jobs:
       matrix:
         config:
           - {os: ubuntu-latest,   r: 'release'}
-          - {os: windows-latest, r: 'release'}
-          - {os: macos-latest,    r: 'release'}
+          #- {os: windows-latest, r: 'release'}
+          #- {os: macos-latest,    r: 'release'}
           # - {os: ubuntu-latest,   r: 'oldrel-1'}
           # - {os: ubuntu-latest,   r: 'oldrel-2'}
           # - {os: ubuntu-latest,   r: 'oldrel-3'}

.github/workflows/Release-package.yaml

@@ -10,6 +10,10 @@
     workflow_dispatch:
     workflow_call:
 
+  concurrency:
+    group: ${{ github.workflow }}-${{ github.ref }}
+    cancel-in-progress: true
+
   name: Release Package 🚀
 
   jobs:

DESCRIPTION

@@ -22,7 +22,7 @@ Suggests:
     usethis,
     rmarkdown,
     testthat (>= 3.0.0),
-    kableExtra (>= 1.4),
+    kableExtra,
     testr,
     tidyr,
     pharmaverseadam

README.Rmd

@@ -3,6 +3,15 @@
   always_allow_html: true
 ---
 
+<!-- Add badges here -->
+
+[![Check Package
+📦](https://github.com/hta-pharma/ramnog/actions/workflows/Check-package.yaml/badge.svg)](https://github.com/hta-pharma/ramnog/actions/workflows/Check-package.yaml)
+[![Release Package
+🚀](https://github.com/hta-pharma/ramnog/actions/workflows/Release-package.yaml/badge.svg)](https://github.com/hta-pharma/ramnog/actions/workflows/Release-package.yaml)
+[![codecov.io](https://img.shields.io/codecov/c/gh/hta-pharma/ramnog?style=plastic&label=codecov.io)]((https://app.codecov.io/github/hta-pharma/ramnog?branch=main))
+<!-- Until here -->
+
 # ramnog <a href="https://hta-pharma.github.io/ramnog/"><img src="man/figures/logo.png" align="right" height="138" alt="ramnog website" /></a>
 
 # R packages for AMNOG analyses <a href="https://hta-pharma.github.io/ramnog/"><img src="man/figures/logo.png" align="right" height="138" alt="ramnog website" /></a>

README.md

@@ -1,4 +1,13 @@
 
+<!-- Add badges here -->
+
+[![Check Package
+📦](https://github.com/hta-pharma/ramnog/actions/workflows/Check-package.yaml/badge.svg)](https://github.com/hta-pharma/ramnog/actions/workflows/Check-package.yaml)
+[![Release Package
+🚀](https://github.com/hta-pharma/ramnog/actions/workflows/Release-package.yaml/badge.svg)](https://github.com/hta-pharma/ramnog/actions/workflows/Release-package.yaml)
+[![codecov.io](https://img.shields.io/codecov/c/gh/hta-pharma/ramnog?style=plastic&label=codecov.io)]((https://app.codecov.io/github/hta-pharma/ramnog?branch=main))
+<!-- Until here -->
+
 # ramnog <a href="https://hta-pharma.github.io/ramnog/"><img src="man/figures/logo.png" align="right" height="138" alt="ramnog website" /></a>
 
 # R packages for AMNOG analyses <a href="https://hta-pharma.github.io/ramnog/"><img src="man/figures/logo.png" align="right" height="138" alt="ramnog website" /></a>
@@ -13,7 +22,7 @@ To get started, check out the [Quick Start](articles/ramnog.html) guide
 
 # Packages
 
-<table class="table table-bordered table table-hover table-condensed table-responsive" style="color: black; margin-left: auto; margin-right: auto;">
+<table class="table table-bordered table table-hover table-condensed table-responsive" style="margin-left: auto; margin-right: auto;">
 <thead>
 <tr>
 <th style="text-align:left;color: white !important;background-color: rgba(44, 62, 80, 255) !important;">