Merge branch 'develop' into baseline-risk-meta-regression

.github/workflows/R-CMD-check-HTML5.yaml

@@ -16,7 +16,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
       _R_CHECK_RD_VALIDATE_RD2HTML_: TRUE
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - name: Install pdflatex
         run: sudo apt-get install texlive-latex-base texlive-fonts-recommended texlive-fonts-extra texlive-latex-extra

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

@@ -27,7 +27,7 @@ jobs:
       _R_CHECK_DONTTEST_EXAMPLES_: false
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 

.github/workflows/commit-commands.yaml

@@ -14,7 +14,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -31,8 +31,8 @@ jobs:
 
       - name: Commit
         run: |
-          git config --local user.name "$GITHUB_ACTOR"
-          git config --local user.email "[email protected].github.com"
+          git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
+          git config user.name "github-actions[bot]"
           git add man/\* NAMESPACE
           git commit -m 'Document'
           git push
@@ -44,7 +44,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -64,8 +64,8 @@ jobs:
 
       - name: Commit
         run: |
-          git config --local user.name "$GITHUB_ACTOR"
-          git config --local user.email "[email protected].github.com"
+          git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
+          git config user.name "github-actions[bot]"
           git add vignettes/\* tests/testthat/\*.R
           git commit -m 'Build pre-compiled vignettes'
           git push

.github/workflows/pkgdown.yaml

@@ -17,7 +17,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 

.github/workflows/pr-commands.yaml

@@ -14,7 +14,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/pr-fetch@v2
         with:
@@ -35,8 +35,8 @@ jobs:
 
       - name: Commit
         run: |
-          git config --local user.name "$GITHUB_ACTOR"
-          git config --local user.email "[email protected].github.com"
+          git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
+          git config user.name "github-actions[bot]"
           git add man/\* NAMESPACE
           git commit -m 'Document'
 
@@ -51,7 +51,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/pr-fetch@v2
         with:
@@ -75,8 +75,8 @@ jobs:
 
       - name: Commit
         run: |
-          git config --local user.name "$GITHUB_ACTOR"
-          git config --local user.email "[email protected].github.com"
+          git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
+          git config user.name "github-actions[bot]"
           git add vignettes/\* tests/testthat/\*.R
           git commit -m 'Build pre-compiled vignettes'
 

.github/workflows/rhub.yaml

@@ -0,0 +1,95 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+  workflow_dispatch:
+    inputs:
+      config:
+        description: 'A comma separated list of R-hub platforms to use.'
+        type: string
+        default: 'linux,windows,macos'
+      name:
+        description: 'Run name. You can leave this empty now.'
+        type: string
+      id:
+        description: 'Unique ID. You can leave this empty now.'
+        type: string
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      containers: ${{ steps.rhub-setup.outputs.containers }}
+      platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+    steps:
+    # NO NEED TO CHECKOUT HERE
+    - uses: r-hub/actions/setup@v1
+      with:
+        config: ${{ github.event.inputs.config }}
+      id: rhub-setup
+
+  linux-containers:
+    needs: setup
+    if: ${{ needs.setup.outputs.containers != '[]' }}
+    runs-on: ubuntu-latest
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.containers) }}
+    container:
+      image: ${{ matrix.config.container }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+
+  other-platforms:
+    needs: setup
+    if: ${{ needs.setup.outputs.platforms != '[]' }}
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}