From e4b4fcda083dd0afe55afcd7dd095aceaa0fb121 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kirill=20M=C3=BCller?= <kirill@cynkra.com>
Date: Sat, 9 Nov 2024 06:09:00 +0100
Subject: [PATCH 1/9] ci: Latest changes

---
 .github/workflows/R-CMD-check.yaml   | 6 +++++-
 .github/workflows/fledge.yaml        | 2 +-
 .github/workflows/install/action.yml | 3 +++
 .github/workflows/pkgdown.yaml       | 2 +-
 4 files changed, 10 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 56ae58c6..2af0024c 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -106,7 +106,7 @@ jobs:
           cache-version: rcc-smoke-2
           needs: check, website
           # Beware of using dev pkgdown here, has brought in dev dependencies in the past
-          extra-packages: any::rcmdcheck r-lib/roxygen2 any::decor r-lib/styler r-lib/pkgdown@f-readme-tweak deps::.
+          extra-packages: any::rcmdcheck r-lib/roxygen2 any::decor r-lib/styler r-lib/pkgdown deps::.
 
       - name: Install package
         run: |
@@ -267,6 +267,8 @@ jobs:
         with:
           results: ${{ runner.os }}-r${{ matrix.r }}
 
+# The status update is taken care of by R-CMD-check-status.yaml
+
   rcc-suggests:
     needs:
       - rcc-smoke
@@ -340,3 +342,5 @@ jobs:
       - uses: ./.github/workflows/check
         with:
           results: ${{ matrix.package }}
+
+# The status update is taken care of by R-CMD-check-status.yaml
diff --git a/.github/workflows/fledge.yaml b/.github/workflows/fledge.yaml
index d880c55d..02e9101f 100644
--- a/.github/workflows/fledge.yaml
+++ b/.github/workflows/fledge.yaml
@@ -43,7 +43,7 @@ jobs:
     env:
       FLEDGE_GHA_CI: true
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
diff --git a/.github/workflows/install/action.yml b/.github/workflows/install/action.yml
index 702aedab..263ddf3a 100644
--- a/.github/workflows/install/action.yml
+++ b/.github/workflows/install/action.yml
@@ -56,6 +56,9 @@ runs:
         echo "_R_CHECK_UNDOC_USE_ALL_NAMES_=true" | tee -a $GITHUB_ENV
         echo "_R_CHECK_URLS_SHOW_301_STATUS_=true" | tee -a $GITHUB_ENV
         echo "_R_CXX_USE_NO_REMAP_=true" | tee -a $GITHUB_ENV
+        # There is no way to disable recency and frequency checks when the incoming checks are run
+        # echo "_R_CHECK_CRAN_INCOMING_=true" | tee -a $GITHUB_ENV
+        echo "_R_CHECK_CRAN_INCOMING_SKIP_LARGE_VERSION_=true" | tee -a $GITHUB_ENV
       shell: bash
 
     - name: Set environment variables (non-Windows only)
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
index 6afddb16..de69b149 100644
--- a/.github/workflows/pkgdown.yaml
+++ b/.github/workflows/pkgdown.yaml
@@ -42,7 +42,7 @@ jobs:
           install-r: false
           cache-version: pkgdown-2
           needs: website
-          extra-packages: r-lib/pkgdown@f-readme-tweak local::.
+          extra-packages: r-lib/pkgdown local::.
 
       - uses: ./.github/workflows/custom/after-install
         if: hashFiles('.github/workflows/custom/after-install/action.yml') != ''

From 38dd76cb6ec29818253dda0e93a14e4af8c5b357 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kirill=20M=C3=BCller?= <krlmlr@users.noreply.github.com>
Date: Sat, 16 Nov 2024 19:02:39 +0100
Subject: [PATCH 2/9] ci: Use stable pak

---
 .github/workflows/install/action.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/install/action.yml b/.github/workflows/install/action.yml
index 263ddf3a..bb42f186 100644
--- a/.github/workflows/install/action.yml
+++ b/.github/workflows/install/action.yml
@@ -95,7 +95,7 @@ runs:
       env:
         GITHUB_PAT: ${{ inputs.token }}
       with:
-        pak-version: devel
+        pak-version: stable
         needs: ${{ inputs.needs }}
         packages: ${{ inputs.packages }}
         extra-packages: ${{ inputs.extra-packages }} ${{ ( matrix.config.covr && 'any::covr' ) || '' }} ${{ steps.get-extra.outputs.packages }}

From fdbdf5878acb5e4832453f2f6b68f453cc372362 Mon Sep 17 00:00:00 2001
From: krlmlr <krlmlr@users.noreply.github.com>
Date: Sun, 17 Nov 2024 06:13:35 +0000
Subject: [PATCH 3/9] chore: Auto-update from GitHub Actions

Run: https://github.com/poissonconsulting/chk/actions/runs/11876513601
---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index a7e0197a..6e71886a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -44,4 +44,4 @@ Config/testthat/edition: 3
 Encoding: UTF-8
 Language: en-US
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.2.9000

From f9d56c9e7eb0af9114510531f37da765329a80d2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kirill=20M=C3=BCller?= <krlmlr@users.noreply.github.com>
Date: Fri, 22 Nov 2024 14:46:19 +0100
Subject: [PATCH 4/9] ci: Correctly detect branch protection (#148)

---
 .github/workflows/fledge.yaml | 16 +++++++++++++---
 1 file changed, 13 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/fledge.yaml b/.github/workflows/fledge.yaml
index 02e9101f..b197fb35 100644
--- a/.github/workflows/fledge.yaml
+++ b/.github/workflows/fledge.yaml
@@ -72,8 +72,18 @@ jobs:
           packages: cynkra/fledge
           cache-version: fledge-1
 
+      - name: Count rulesets
+        # Assume that branch is protected if ruleset exists
+        id: rulesets
+        env:
+          GH_TOKEN: ${{ github.token }}
+        run: |
+          n_rulesets=$(gh api repos/${{ github.repository }}/rulesets -q length)
+          echo "count=${n_rulesets}" >> $GITHUB_OUTPUT
+        shell: bash
+
       - name: Switch to branch if branch protection is enabled
-        if: github.ref_protected == 'true' || inputs.pr == 'true'
+        if: github.ref_protected == 'true' || inputs.pr == 'true' || steps.rulesets.outputs.count > 0
         run: |
           git checkout -b fledge
           git push -f -u origin HEAD
@@ -83,14 +93,14 @@ jobs:
         env:
           GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
         run: |
-          check_default_branch <- ("${{ github.ref_protected == 'true' || inputs.pr == 'true' }}" != "true")
+          check_default_branch <- ("${{ github.ref_protected == 'true' || inputs.pr == 'true' || steps.rulesets.outputs.count > 0 }}" != "true")
           if (fledge::bump_version(which = "dev", no_change_behavior = "noop", check_default_branch = check_default_branch)) {
             fledge::finalize_version(push = TRUE)
           }
         shell: Rscript {0}
 
       - name: Create and merge PR if branch protection is enabled
-        if: github.ref_protected == 'true' || inputs.pr == 'true'
+        if: github.ref_protected == 'true' || inputs.pr == 'true' || steps.rulesets.outputs.count > 0
         env:
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |

From 9e6fd150d1502ba5e05961f1808a4462f1a70c33 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kirill=20M=C3=BCller?= <krlmlr@users.noreply.github.com>
Date: Tue, 26 Nov 2024 10:44:09 +0100
Subject: [PATCH 5/9] ci: Use Ubuntu 24.04 and styler PR (#149)

* ci: Use Ubuntu 24.04 and styler PR

* ci: Use Ubuntu 24.04 for fledge, squash

* ci: Fix macOS (#16)

* ci: Need to install R on Ubuntu 24.04

* ci: Need to install R on Ubuntu 24.04 for fledge

* ci: Use styler from main branch
---
 .github/workflows/R-CMD-check-dev.yaml    | 4 ----
 .github/workflows/R-CMD-check-status.yaml | 2 +-
 .github/workflows/R-CMD-check.yaml        | 5 ++---
 .github/workflows/fledge.yaml             | 7 +++----
 .github/workflows/install/action.yml      | 6 ++++++
 .github/workflows/lock.yaml               | 2 +-
 .github/workflows/pkgdown.yaml            | 3 +--
 .github/workflows/pr-commands.yaml        | 4 ----
 8 files changed, 14 insertions(+), 19 deletions(-)

diff --git a/.github/workflows/R-CMD-check-dev.yaml b/.github/workflows/R-CMD-check-dev.yaml
index 700486fc..bb87451a 100644
--- a/.github/workflows/R-CMD-check-dev.yaml
+++ b/.github/workflows/R-CMD-check-dev.yaml
@@ -27,8 +27,6 @@ jobs:
           token: ${{ secrets.GITHUB_TOKEN }}
 
       - uses: r-lib/actions/setup-r@v2
-        with:
-          install-r: false
 
       - id: set-matrix
         uses: ./.github/workflows/dep-matrix
@@ -70,7 +68,6 @@ jobs:
 
       - uses: ./.github/workflows/install
         with:
-          install-r: false
           cache-version: rcc-dev-base-1
           needs: check
           extra-packages: "any::rcmdcheck any::remotes ."
@@ -118,7 +115,6 @@ jobs:
 
       - uses: ./.github/workflows/install
         with:
-          install-r: false
           cache-version: rcc-dev-${{ matrix.package }}-1
           needs: check
           extra-packages: "any::rcmdcheck any::remotes ."
diff --git a/.github/workflows/R-CMD-check-status.yaml b/.github/workflows/R-CMD-check-status.yaml
index b9bdf4e4..7a4ea62f 100644
--- a/.github/workflows/R-CMD-check-status.yaml
+++ b/.github/workflows/R-CMD-check-status.yaml
@@ -12,7 +12,7 @@ name: rcc-status
 
 jobs:
   rcc-status:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
 
     name: "Update commit status"
 
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 2af0024c..41ae8a5b 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -43,7 +43,7 @@ name: rcc
 
 jobs:
   rcc-smoke:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     outputs:
       sha: ${{ steps.commit.outputs.sha }}
       versions-matrix: ${{ steps.versions-matrix.outputs.matrix }}
@@ -205,7 +205,7 @@ jobs:
         shell: bash
 
   rcc-smoke-check-matrix:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
 
     name: "Check matrix"
 
@@ -294,7 +294,6 @@ jobs:
 
       - uses: ./.github/workflows/install
         with:
-          install-r: false
           cache-version: rcc-dev-${{ matrix.package }}-1
           needs: check
           extra-packages: "any::rcmdcheck any::remotes ."
diff --git a/.github/workflows/fledge.yaml b/.github/workflows/fledge.yaml
index b197fb35..7785ad93 100644
--- a/.github/workflows/fledge.yaml
+++ b/.github/workflows/fledge.yaml
@@ -19,7 +19,7 @@ concurrency:
 
 jobs:
   check_fork:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     outputs:
       is_forked: ${{ steps.check.outputs.is_forked }}
     steps:
@@ -33,7 +33,7 @@ jobs:
         shell: bash
 
   fledge:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     needs: check_fork
     if: needs.check_fork.outputs.is_forked == 'false'
     permissions:
@@ -61,7 +61,6 @@ jobs:
 
       - uses: r-lib/actions/setup-r@v2
         with:
-          install-r: false
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2
@@ -107,7 +106,7 @@ jobs:
           set -x
           gh pr create --base main --head fledge --fill-first
           gh workflow run rcc -f ref=$(git rev-parse HEAD)
-          gh pr merge --merge --auto
+          gh pr merge --squash --auto
         shell: bash
 
       - name: Check release
diff --git a/.github/workflows/install/action.yml b/.github/workflows/install/action.yml
index bb42f186..59673d9c 100644
--- a/.github/workflows/install/action.yml
+++ b/.github/workflows/install/action.yml
@@ -75,6 +75,12 @@ runs:
         echo "_R_CHECK_CRAN_INCOMING_USE_ASPELL_=true" | tee -a $GITHUB_ENV
       shell: bash
 
+    - name: Remove pkg-config@0.29.2
+      if: runner.os == 'macOS'
+      run: |
+        brew uninstall pkg-config@0.29.2
+      shell: bash
+
     - uses: r-lib/actions/setup-pandoc@v2
 
     - uses: r-lib/actions/setup-r@v2
diff --git a/.github/workflows/lock.yaml b/.github/workflows/lock.yaml
index e2a367f8..dd05bc31 100644
--- a/.github/workflows/lock.yaml
+++ b/.github/workflows/lock.yaml
@@ -6,7 +6,7 @@ on:
 
 jobs:
   lock:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     steps:
       - uses: dessant/lock-threads@v5
         with:
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
index de69b149..60d18490 100644
--- a/.github/workflows/pkgdown.yaml
+++ b/.github/workflows/pkgdown.yaml
@@ -16,7 +16,7 @@ concurrency:
 
 jobs:
   pkgdown:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
 
     name: "pkgdown"
 
@@ -39,7 +39,6 @@ jobs:
       - uses: ./.github/workflows/install
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
-          install-r: false
           cache-version: pkgdown-2
           needs: website
           extra-packages: r-lib/pkgdown local::.
diff --git a/.github/workflows/pr-commands.yaml b/.github/workflows/pr-commands.yaml
index a11f4d39..b07a6f3a 100644
--- a/.github/workflows/pr-commands.yaml
+++ b/.github/workflows/pr-commands.yaml
@@ -16,8 +16,6 @@ jobs:
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
       - uses: r-lib/actions/setup-r@v2
-        with:
-          install-r: false
       - name: Configure Git identity
         run: |
           env | sort
@@ -55,8 +53,6 @@ jobs:
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
       - uses: r-lib/actions/setup-r@v2
-        with:
-          install-r: false
       - name: Configure Git identity
         run: |
           env | sort

From ea37912a58d8acbd9c378b80e038d2764813f51f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kirill=20M=C3=BCller?= <krlmlr@users.noreply.github.com>
Date: Tue, 26 Nov 2024 20:36:14 +0100
Subject: [PATCH 6/9] ci: Use Ubuntu 24.04 and styler PR (#150)

* ci: Use Ubuntu 24.04 and styler PR

* ci: Use styler from main branch

* ci: Explicit permissions
---
 .github/workflows/lock.yaml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/lock.yaml b/.github/workflows/lock.yaml
index dd05bc31..6c52f683 100644
--- a/.github/workflows/lock.yaml
+++ b/.github/workflows/lock.yaml
@@ -1,6 +1,10 @@
 name: "Lock threads"
-
+permissions:
+  issues: write
+  pull-requests: write
+  discussions: write
 on:
+  workflow_dispatch:
   schedule:
     - cron: "37 2 * * *"
 

From 5cd0ee0f1105101e38a6fa636824f5eb451e2e4f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kirill=20M=C3=BCller?= <krlmlr@users.noreply.github.com>
Date: Wed, 27 Nov 2024 15:34:41 +0100
Subject: [PATCH 7/9] ci: Ignore errors when removing pkg-config on macOS
 (#151)

---
 .github/workflows/install/action.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/install/action.yml b/.github/workflows/install/action.yml
index 59673d9c..03bcb1eb 100644
--- a/.github/workflows/install/action.yml
+++ b/.github/workflows/install/action.yml
@@ -78,7 +78,7 @@ runs:
     - name: Remove pkg-config@0.29.2
       if: runner.os == 'macOS'
       run: |
-        brew uninstall pkg-config@0.29.2
+        brew uninstall pkg-config@0.29.2 || true
       shell: bash
 
     - uses: r-lib/actions/setup-pandoc@v2

From 9eaeefee22fe920099289a8b925a6a26a4528a3c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kirill=20M=C3=BCller?= <krlmlr@users.noreply.github.com>
Date: Fri, 6 Dec 2024 16:48:27 +0100
Subject: [PATCH 8/9] ci: Use larger retry count for lock-threads workflow
 (#152)

---
 .github/workflows/lock.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/lock.yaml b/.github/workflows/lock.yaml
index 6c52f683..2cd48378 100644
--- a/.github/workflows/lock.yaml
+++ b/.github/workflows/lock.yaml
@@ -12,7 +12,7 @@ jobs:
   lock:
     runs-on: ubuntu-24.04
     steps:
-      - uses: dessant/lock-threads@v5
+      - uses: krlmlr/lock-threads@patch-1
         with:
           github-token: ${{ github.token }}
           issue-inactive-days: "365"

From 4de01753daf148335d99eac504511d747ce120bd Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kirill=20M=C3=BCller?= <krlmlr@users.noreply.github.com>
Date: Sun, 8 Dec 2024 18:25:35 +0100
Subject: [PATCH 9/9] ci: Fetch tags for fledge workflow to avoid unnecessary
 NEWS entries (#153)

* ci: Fetch tags for fledge workflow to avoid unnecessary NEWS entries

* ci: Avoid failure in fledge workflow if no changes
---
 .github/workflows/fledge.yaml | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/fledge.yaml b/.github/workflows/fledge.yaml
index 7785ad93..5b2131ae 100644
--- a/.github/workflows/fledge.yaml
+++ b/.github/workflows/fledge.yaml
@@ -46,6 +46,7 @@ jobs:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
+          fetch-tags: true
 
       - name: Configure Git identity
         run: |
@@ -103,10 +104,14 @@ jobs:
         env:
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
-          set -x
-          gh pr create --base main --head fledge --fill-first
-          gh workflow run rcc -f ref=$(git rev-parse HEAD)
-          gh pr merge --squash --auto
+          set -ex
+          if [ -n "$(git diff main --numstat)" ]; then
+            gh pr create --base main --head fledge --fill-first
+            gh workflow run rcc -f ref=$(git rev-parse HEAD)
+            gh pr merge --squash --auto
+          else
+            echo "No changes."
+          fi
         shell: bash
 
       - name: Check release