Update versions and some cleanup

.Rbuildignore

@@ -15,3 +15,5 @@
 ^check-r-package$
 ^setup-r-dependencies$
 ^setup-renv$
+^setup-manifest$
+^_pkgdown\.yml$

.github/workflows/check-full.yaml

@@ -35,16 +35,14 @@ jobs:
           - {os: ubuntu-latest,  r: 'oldrel-2'}
           - {os: ubuntu-latest,  r: 'oldrel-3'}
           - {os: ubuntu-latest,  r: 'oldrel-4'}
-
           - {os: ubuntu-22.04-arm, r: 'release' }
 
-
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd
 
       - uses: ./setup-pandoc
 

.github/workflows/check-release.yaml

@@ -16,7 +16,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
     steps:
-      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd
 
       - uses: ./setup-r
         with:

.github/workflows/check-standard.yaml

@@ -30,7 +30,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd
 
       - uses: ./setup-pandoc
 

.github/workflows/lint.yaml

@@ -15,7 +15,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd
 
       - uses: ./setup-r
         with:

.github/workflows/pkgdown.yaml

@@ -23,7 +23,7 @@ jobs:
     permissions:
       contents: write
     steps:
-      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd
 
       - uses: ./setup-pandoc
 

.github/workflows/r-devel-test.yaml

@@ -38,7 +38,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd
 
       - uses: r-hub/actions/debug-shell@v1
 

.github/workflows/rtools.yaml

@@ -27,7 +27,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd
 
       - uses: ./setup-pandoc
 

.github/workflows/scorecard.yml

@@ -32,12 +32,12 @@ jobs:
 
     steps:
       - name: "Checkout code"
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
         with:
           persist-credentials: false
 
       - name: "Run analysis"
-        uses: ossf/scorecard-action@0864cf19026789058feabb7e87baa5f140aac736 # v2.3.1
+        uses: ossf/scorecard-action@4eaacf0543bb3f2c246792bd56e8cdeffafb205a # v2.4.3
         with:
           results_file: results.sarif
           results_format: sarif
@@ -60,7 +60,7 @@ jobs:
       # Upload the results as artifacts (optional). Commenting out will disable uploads of run results in SARIF
       # format to the repository Actions tab.
       - name: "Upload artifact"
-        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4.3.3
+        uses: actions/upload-artifact@bbbca2ddaa5d8feaa63e36b76fdaad77386f024f # v7.0.0
         with:
           name: SARIF file
           path: results.sarif
@@ -69,6 +69,6 @@ jobs:
       # Upload the results to GitHub's code scanning dashboard (optional).
       # Commenting out will disable upload of results to your repo's Code Scanning dashboard
       - name: "Upload to code-scanning"
-        uses: github/codeql-action/upload-sarif@1b1aada464948af03b950897e5eb522f92603cc2 # v3.24.9
+        uses: github/codeql-action/upload-sarif@89a39a4e59826350b863aa6b6252a07ad50cf83e # v4.32.4
         with:
           sarif_file: results.sarif

.github/workflows/setup-pandoc-test.yaml

@@ -26,13 +26,15 @@ jobs:
       matrix:
         config:
           - { os: macos-14         }
-          - { os: macos-13         }
+          - { os: macos-15-intel   }
+          - { os: macos-latest     }
+          - { os: macos-26         }
           - { os: windows-latest   }
           - { os: ubuntu-latest    }
           - { os: ubuntu-22.04-arm }
 
     steps:
-      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd
 
       - uses: ./setup-pandoc
         with:

.github/workflows/setup-r-test.yaml

@@ -39,7 +39,7 @@ jobs:
     name: ${{ github.event.inputs.inpos }} (${{ matrix.r }})
 
     steps:
-    - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b
+    - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd
 
     - uses: ./setup-r
       id: setup-r

.github/workflows/setup-tinytex.yaml

@@ -23,7 +23,7 @@ jobs:
           - { os: ubuntu-latest  }
 
     steps:
-      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd
 
       - uses: ./setup-tinytex
         env:

.github/workflows/test-coverage.yaml

@@ -16,7 +16,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd
 
       - uses: ./setup-r
         with:
@@ -34,15 +34,16 @@ jobs:
             clean = FALSE,
             install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
+          print(cov)
           covr::to_cobertura(cov)
         shell: Rscript {0}
 
-      - uses: codecov/codecov-action@f1b7348826d750ac29741abc9d1623d8da5dcd4f
+      - uses: codecov/codecov-action@671740ac38dd9b0130fbe1cec585b89eea48d3de
         with:
           # Fail if error if not on PR, or if on PR and token is given
           fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
-          file: ./cobertura.xml
-          plugin: noop
+          files: ./cobertura.xml
+          plugins: noop
           disable_search: true
           token: ${{ secrets.CODECOV_TOKEN }}
 
@@ -55,7 +56,7 @@ jobs:
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808
+        uses: actions/upload-artifact@bbbca2ddaa5d8feaa63e36b76fdaad77386f024f
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package

Makefile

@@ -9,11 +9,15 @@ all : $(WORKFLOWS)
 
 $(WORKFLOWS) : .github/workflows/%.yaml: examples/%.yaml Makefile
 	perl -pe 's{r-lib/actions/([\w-]+)\@v2}{./$$1}g' $< | \
-	perl -pe 's{actions/checkout\@v4}{actions/checkout\@0ad4b8fadaa221de15dcec353f45205ec38ea70b}g' | \
-	perl -pe 's{actions/upload-artifact\@v4}{actions/upload-artifact\@65462800fd760344b1a7b4382951275a0abb4808}g' | \
-	perl -pe 's{codecov/codecov-action\@v4}{codecov/codecov-action\@f1b7348826d750ac29741abc9d1623d8da5dcd4f}g' | \
+	perl -pe 's{actions/checkout\@v6}{actions/checkout\@de0fac2e4500dabe0009e67214ff5f5447ce83dd}g' | \
+	perl -pe 's{actions/upload-artifact\@v7}{actions/upload-artifact\@bbbca2ddaa5d8feaa63e36b76fdaad77386f024f}g' | \
+	perl -pe 's{codecov/codecov-action\@v5}{codecov/codecov-action\@671740ac38dd9b0130fbe1cec585b89eea48d3de}g' | \
 	perl -pe 's{JamesIves/github-pages-deploy-action\@v4[.]5[.]0}{JamesIves/github-pages-deploy-action\@65b5dfd4f5bcd3a7403bbc2959c144256167464e}g' | \
-	perl -pe 's{main, master}{main, master, v2-branch}g' > $@
+	perl -pe 's{main, master}{main, master, v2-branch}g' | \
+	if [ "$*" = "check-full" ]; then \
+	  perl -pe 's{(- \{os: ubuntu-latest,  r: \x27oldrel-4\x27\})}{$$1\n          - {os: ubuntu-22.04-arm, r: \x27release\x27 }}g' | \
+	  perl -pe 's{(- uses: \./setup-r-dependencies)}{- uses: gaborcsardi/quarto-actions/setup\@fix/linux-arm64\n\n      $$1}g'; \
+	else cat; fi > $@
 
 .PHONY: clean
 clean:

R/foo.R

@@ -7,3 +7,7 @@ add_one <- function(x) {
 times2 <- function(x) {
   .Call(test_fun, as.integer(x)[1])
 }
+
+plus <- function(x, y) {
+  x + y
+}

check-r-package/README.md

@@ -37,7 +37,7 @@ Inputs available:
 Basic:
 ```yaml
 steps:
-- uses: actions/checkout@v4
+- uses: actions/checkout@v6
 - uses: r-lib/actions/setup-r@v2
 - uses: r-lib/actions/setup-r-dependencies@v2
   with:
@@ -49,7 +49,7 @@ steps:
 With specified inputs:
 ```yaml
 steps:
-- uses: actions/checkout@v4
+- uses: actions/checkout@v6
 - uses: r-lib/actions/setup-r@v2
 - uses: r-lib/actions/setup-r-dependencies@v2
   with:

check-r-package/action.yaml

@@ -62,14 +62,14 @@ runs:
 
     - name: Upload check results
       if: ${{ (failure() && inputs.upload-results != 'never') || (inputs.upload-results != 'false' && inputs.upload-results != 'never') }}
-      uses: actions/upload-artifact@v4
+      uses: actions/upload-artifact@v7
       with:
         name: ${{ inputs.artifact-name || format('{0}-{1}-r{2}-{3}-results', runner.os, runner.arch, matrix.config.r, matrix.config.id || strategy.job-index ) }}
         path: ${{ steps.rcmdcheck.outputs.check-dir-path }}
 
     - name: Upload snapshots
       if: ${{ (failure() && inputs.upload-snapshots == 'always') || inputs.upload-snapshots != 'false' }}
-      uses: actions/upload-artifact@v4
+      uses: actions/upload-artifact@v7
       with:
         name: ${{ inputs.snapshot-artifact-name || format('{0}-{1}-r{2}-{3}-testthat-snapshots', runner.os, runner.arch, matrix.config.r, matrix.config.id || strategy.job-index ) }}
         path: ${{ steps.rcmdcheck.outputs.check-dir-path }}/**/tests*/testthat/_snaps