Update GitHub Actions workflows, and make necessary tweaks to support them (#279)

* Bump Ubuntu version from 18.04 to 20.04

* Fully update GitHub Actions workflows

* Avoid `R_compact_intrange()` in favor of `:`

Closes #280

* Avoid unused variable warning on Windows about `cpp11::preserved`

* Add a remote on r-lib/testthat#1673

* Add old archives to be able to install gcc 4.8

* Depend only on dev testthat now that the PR has been merged

* Set `CC` as well for `pkgbuild:::has_compiler_colored_diagnostics()`

Otherwise this will incorrectly return `TRUE` because it compiles a C program rather than a C++ one to check if color support is available, which adds the `-fdiagnostics-color=always` flag, but g++ 4.8 doesn't actually support that, so the compilation of the C++ code in the vignettes would fail

* NEWS bullet

* Pin to a specific testthat SHA

* Use `seq()` rather than `:` to generate the ALTREP compact-seq vector

Author: DavisVaughan

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

@@ -1,18 +1,14 @@
-# NOTE: This workflow is overkill for most R packages
-# check-standard.yaml is likely a better choice
-# usethis::use_github_action("check-standard") will install it.
+# 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
 #
-# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
-# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+# NOTE: This workflow is overkill for most R packages and
+# check-standard.yaml is likely a better choice.
+# usethis::use_github_action("check-standard") will install it.
 on:
   push:
-    branches:
-      - main
-      - master
+    branches: [main, master]
   pull_request:
-    branches:
-      - main
-      - master
+    branches: [main, master]
 
 name: R-CMD-check
 
@@ -27,92 +23,74 @@ jobs:
       matrix:
         config:
           - {os: macOS-latest,   r: 'release'}
+
           - {os: windows-latest, r: 'release'}
-          - {os: windows-latest, r: '3.6', rspm: "https://packagemanager.rstudio.com/cran/latest"}
-          - {os: ubuntu-18.04,   r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest", http-user-agent: "R/4.1.0 (ubuntu-18.04) R (4.1.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
-          - {os: ubuntu-18.04,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest", custom: 'no-cpp11test'}
-          - {os: ubuntu-18.04,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest", custom: 'gcc 4.8'}
-          - {os: ubuntu-18.04,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
-          - {os: ubuntu-18.04,   r: 'oldrel',  rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
-          - {os: ubuntu-18.04,   r: '3.6',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
-          - {os: ubuntu-18.04,   r: '3.5',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
-          - {os: ubuntu-18.04,   r: '3.4',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
+          # Use 3.6 to trigger usage of RTools35
+          - {os: windows-latest, r: '3.6'}
+
+          # Use older ubuntu to maximise backward compatibility
+          - {os: ubuntu-20.04,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-20.04,   r: 'release'}
+          - {os: ubuntu-20.04,   r: 'release', custom: 'no-cpp11test'}
+          - {os: ubuntu-20.04,   r: 'release', custom: 'gcc 4.8'}
+          - {os: ubuntu-20.04,   r: 'oldrel-1'}
+          - {os: ubuntu-20.04,   r: 'oldrel-2'}
+          - {os: ubuntu-20.04,   r: 'oldrel-3'}
+          - {os: ubuntu-20.04,   r: 'oldrel-4'}
 
     env:
-      RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
-        id: install-r
+      - 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 }}
-
-      - uses: r-lib/actions/setup-pandoc@v1
-
-      - name: Install pak and query dependencies
-        run: |
-          install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/")
-          saveRDS(pak::pkg_deps("local::.", dependencies = TRUE), ".github/r-depends.rds")
-        shell: Rscript {0}
-
-      - name: Restore R package cache
-        uses: actions/cache@v2
-        with:
-          path: |
-            ${{ env.R_LIBS_USER }}/*
-            !${{ env.R_LIBS_USER }}/pak
-          key: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-${{ hashFiles('.github/r-depends.rds') }}
-          restore-keys: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          pak::local_system_requirements(execute = TRUE)
-          pak::pkg_system_requirements("rcmdcheck", execute = TRUE)
-        shell: Rscript {0}
+          use-public-rspm: true
 
       - name : Install compiler version
+        # We check on this old compiler specifically to support CentOS 7,
+        # which uses this gcc version. RStudio products support CentOS 7 through
+        # June 2024.
+        # https://github.com/r-lib/cpp11/pull/78
+        # https://www.rstudio.com/about/platform-support/
+        # Ubuntu 20.04 technically dropped support for gcc 4.8, so we have to
+        # add old archives back in manually to install it
+        # https://github.com/r-lib/cpp11/pull/279
         if: matrix.config.custom == 'gcc 4.8'
         run: |
+          echo "deb http://dk.archive.ubuntu.com/ubuntu/ xenial main" | sudo tee -a /etc/apt/sources.list
+          echo "deb http://dk.archive.ubuntu.com/ubuntu/ xenial universe" | sudo tee -a /etc/apt/sources.list
+          sudo apt update
           sudo apt-get install -y g++-4.8
           mkdir ~/.R/
-          echo $'CXX1X=g++-4.8\nCXX11=g++-4.8' >> ~/.R/Makevars
+          echo $'CXX1X=g++-4.8\nCXX11=g++-4.8\nCC=gcc-4.8' >> ~/.R/Makevars
 
-      - name: install macOS system dependecies
+      - name: Install macOS system dependencies
         if: runner.os == 'macOS'
         run: brew install --cask xquartz
 
-      - name: Install dependencies
-        run: |
-          pak::local_install_dev_deps(upgrade = TRUE)
-          pak::pkg_install("rcmdcheck")
-        shell: Rscript {0}
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - name: Install cpp11 and cpp11test
+      - name: Install cpp11test
         if: matrix.config.custom != 'no-cpp11test'
         run: |
           options(warn = 2)
-          install.packages(".", repos = NULL, type = "source")
-          pak::local_install_dev_deps("cpp11test")
+          pak::local_install_dev_deps("cpp11test", dependencies = TRUE)
           install.packages("cpp11test", repos = NULL, INSTALL_opts = "--install-tests", type = "source")
         shell: Rscript {0}
 
-      - name: Session info
-        run: |
-          options(width = 100)
-          pkgs <- installed.packages()[, "Package"]
-          sessioninfo::session_info(pkgs, include_base = TRUE)
-        shell: Rscript {0}
-
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
 
       - name: Run cpp11test tests
         if: matrix.config.custom != 'no-cpp11test'
@@ -122,20 +100,3 @@ jobs:
           library(cpp11test)
           test_check("cpp11test", reporter = "progress")
         shell: Rscript {0}
-
-      - name: Show testthat output
-        if: always()
-        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
-        shell: bash
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
-        with:
-          name: ${{ matrix.config.os }}-r${{ matrix.config.r }}-results
-          path: check
-
-      - name: Don't use tar from old Rtools to store the cache
-        if: ${{ runner.os == 'Windows' && startsWith(steps.install-r.outputs.installed-r-version, '3.6' ) }}
-        shell: bash
-        run: echo "C:/Program Files/Git/usr/bin" >> $GITHUB_PATH

.github/workflows/format.yaml

@@ -9,7 +9,7 @@ name: format_check
 
 jobs:
   format_check:
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-20.04
     steps:
       - uses: actions/checkout@v2
 

.github/workflows/pkgdown.yaml

@@ -1,35 +1,48 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# 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]
-    tags: ['*']
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
 
 name: pkgdown
 
 jobs:
   pkgdown:
     runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: local::. local::cpp11test pkgdown
+          extra-packages: any::pkgdown, local::., local::cpp11test
           needs: website
 
-      - name: Deploy package
+      - name: Build site
         env:
           CPP11_EVAL: true
-        run: |
-          git config --local user.name "$GITHUB_ACTOR"
-          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
-          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@4.1.4
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/pr-commands.yaml

@@ -1,55 +1,79 @@
+# 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:
   issue_comment:
     types: [created]
+
 name: Commands
+
 jobs:
   document:
-    if: startsWith(github.event.comment.body, '/document')
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/document') }}
     name: document
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v2
-      - uses: r-lib/actions/pr-fetch@v1
+
+      - uses: r-lib/actions/pr-fetch@v2
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
-      - uses: r-lib/actions/setup-r@v1
-      - name: Install dependencies
-        run: Rscript -e 'install.packages(c("remotes", "roxygen2"))' -e 'remotes::install_deps(dependencies = TRUE)'
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::roxygen2
+          needs: pr-document
+
       - name: Document
-        run: Rscript -e 'roxygen2::roxygenise()'
+        run: roxygen2::roxygenise()
+        shell: Rscript {0}
+
       - name: commit
         run: |
-          git config --local user.email "actions@github.com"
-          git config --local user.name "GitHub Actions"
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
           git add man/\* NAMESPACE
           git commit -m 'Document'
-      - uses: r-lib/actions/pr-push@v1
+
+      - uses: r-lib/actions/pr-push@v2
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
+
   style:
-    if: startsWith(github.event.comment.body, '/style')
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/style') }}
     name: style
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v2
-      - uses: r-lib/actions/pr-fetch@v1
+
+      - uses: r-lib/actions/pr-fetch@v2
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
-      - uses: r-lib/actions/setup-r@v1
+
+      - uses: r-lib/actions/setup-r@v2
+
       - name: Install dependencies
-        run: Rscript -e 'install.packages("styler")'
+        run: install.packages("styler")
+        shell: Rscript {0}
+
       - name: Style
-        run: Rscript -e 'styler::style_pkg()'
+        run: styler::style_pkg()
+        shell: Rscript {0}
+
       - name: commit
         run: |
-          git config --local user.email "actions@github.com"
-          git config --local user.name "GitHub Actions"
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
           git add \*.R
           git commit -m 'Style'
-      - uses: r-lib/actions/pr-push@v1
+
+      - uses: r-lib/actions/pr-push@v2
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}