From ecabb4bdaa515d50c00fdb5eed63018f57837710 Mon Sep 17 00:00:00 2001
From: Bartek Czech <bartosz.w.czech@gmail.com>
Date: Fri, 8 May 2026 12:19:32 +0200
Subject: [PATCH 01/24] feat: extend linter config and add auto-changelog
 workflow

---
 .github/workflows/auto-changelog.yml | 151 +++++++++++++++++++++++++++
 R/linters_config.R                   |  25 +++--
 2 files changed, 166 insertions(+), 10 deletions(-)
 create mode 100644 .github/workflows/auto-changelog.yml

diff --git a/.github/workflows/auto-changelog.yml b/.github/workflows/auto-changelog.yml
new file mode 100644
index 0000000..e3b91b1
--- /dev/null
+++ b/.github/workflows/auto-changelog.yml
@@ -0,0 +1,151 @@
+name: auto-changelog
+
+on:
+  workflow_call:
+    secrets:
+      ANTHROPIC_API_KEY:
+        required: true
+      PRIVATE_ACCESS_TOKEN:
+        required: true
+
+jobs:
+  auto-changelog:
+    runs-on: ubuntu-24.04
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          token: ${{ secrets.PRIVATE_ACCESS_TOKEN }}
+          ref: ${{ github.head_ref }}
+
+      - name: Check if version bump and NEWS.md entry are present
+        id: check
+        run: |
+          PKG_NAME=$(grep "^Package:" DESCRIPTION | sed 's/Package: //')
+          CURRENT_VERSION=$(grep "^Version:" DESCRIPTION | sed 's/Version: //')
+          MAIN_VERSION=$(git show origin/main:DESCRIPTION | grep "^Version:" | sed 's/Version: //')
+
+          echo "pkg_name=$PKG_NAME" >> "$GITHUB_OUTPUT"
+          echo "current_version=$CURRENT_VERSION" >> "$GITHUB_OUTPUT"
+          echo "main_version=$MAIN_VERSION" >> "$GITHUB_OUTPUT"
+
+          VERSION_BUMPED=false
+          NEWS_OK=false
+
+          if [ "$CURRENT_VERSION" != "$MAIN_VERSION" ]; then
+            VERSION_BUMPED=true
+          fi
+
+          if grep -q "^## $PKG_NAME $CURRENT_VERSION" NEWS.md; then
+            NEWS_OK=true
+          fi
+
+          if [ "$VERSION_BUMPED" = "true" ] && [ "$NEWS_OK" = "true" ]; then
+            echo "skip=true" >> "$GITHUB_OUTPUT"
+          else
+            echo "skip=false" >> "$GITHUB_OUTPUT"
+          fi
+
+      - name: Generate version bump and NEWS entry via Claude
+        if: steps.check.outputs.skip == 'false'
+        id: claude
+        env:
+          ANTHROPIC_API_KEY: ${{ secrets.ANTHROPIC_API_KEY }}
+        run: |
+          PKG_NAME="${{ steps.check.outputs.pkg_name }}"
+          MAIN_VERSION="${{ steps.check.outputs.main_version }}"
+
+          # Limit diff to 6000 chars to stay within token limits
+          DIFF=$(git diff origin/main...HEAD -- . \
+            ':(exclude)NEWS.md' \
+            ':(exclude)DESCRIPTION' \
+            ':(exclude)*.lock' \
+            ':(exclude)*.rdb' \
+            | head -c 6000)
+
+          python3 - <<PYEOF
+          import os, json, urllib.request, sys
+
+          pkg_name = os.environ.get("PKG_NAME", "$PKG_NAME")
+          main_version = "$MAIN_VERSION"
+          diff = """$DIFF"""
+
+          prompt = f"""You are a changelog writer for an R package called '{pkg_name}' (current version on main: {main_version}).
+
+          Based on the following git diff from a pull request, determine:
+          1. The version bump type: patch (bug fixes, docs, refactoring), minor (new features), major (breaking changes)
+          2. One short, clear bullet point for NEWS.md describing what changed (start with a verb, no period at end)
+
+          Respond ONLY with valid JSON, no other text:
+          {{"bump_type": "patch|minor|major", "entry": "short description"}}
+
+          Git diff:
+          {diff[:5000]}"""
+
+          payload = json.dumps({
+            "model": "claude-haiku-4-5-20251001",
+            "max_tokens": 256,
+            "messages": [{"role": "user", "content": prompt}]
+          }).encode()
+
+          req = urllib.request.Request(
+            "https://api.anthropic.com/v1/messages",
+            data=payload,
+            headers={
+              "x-api-key": os.environ["ANTHROPIC_API_KEY"],
+              "anthropic-version": "2023-06-01",
+              "content-type": "application/json"
+            }
+          )
+
+          with urllib.request.urlopen(req) as resp:
+            result = json.loads(resp.read())
+
+          parsed = json.loads(result["content"][0]["text"])
+          bump_type = parsed["bump_type"]
+          entry = parsed["entry"]
+
+          with open(os.environ["GITHUB_OUTPUT"], "a") as f:
+            f.write(f"bump_type={bump_type}\n")
+            f.write(f"entry={entry}\n")
+
+          print(f"bump_type={bump_type}, entry={entry}")
+          PYEOF
+
+      - name: Bump version in DESCRIPTION and prepend NEWS.md entry
+        if: steps.check.outputs.skip == 'false'
+        run: |
+          PKG_NAME="${{ steps.check.outputs.pkg_name }}"
+          MAIN_VERSION="${{ steps.check.outputs.main_version }}"
+          BUMP_TYPE="${{ steps.claude.outputs.bump_type }}"
+          ENTRY="${{ steps.claude.outputs.entry }}"
+          DATE=$(date +%Y-%m-%d)
+
+          MAJOR=$(echo "$MAIN_VERSION" | cut -d. -f1)
+          MINOR=$(echo "$MAIN_VERSION" | cut -d. -f2)
+          PATCH=$(echo "$MAIN_VERSION" | cut -d. -f3)
+
+          if [ "$BUMP_TYPE" = "major" ]; then
+            NEW_VERSION="$((MAJOR + 1)).0.0"
+          elif [ "$BUMP_TYPE" = "minor" ]; then
+            NEW_VERSION="${MAJOR}.$((MINOR + 1)).0"
+          else
+            NEW_VERSION="${MAJOR}.${MINOR}.$((PATCH + 1))"
+          fi
+
+          sed -i "s/^Version: .*/Version: $NEW_VERSION/" DESCRIPTION
+          sed -i "s/^Date: .*/Date: $DATE/" DESCRIPTION
+
+          printf '## %s %s - %s\n* %s\n\n' "$PKG_NAME" "$NEW_VERSION" "$DATE" "$ENTRY" \
+            | cat - NEWS.md > NEWS.md.tmp && mv NEWS.md.tmp NEWS.md
+
+      - name: Commit and push
+        if: steps.check.outputs.skip == 'false'
+        run: |
+          git config user.name "github-actions[bot]"
+          git config user.email "github-actions[bot]@users.noreply.github.com"
+          git add DESCRIPTION NEWS.md
+          git commit -m "chore: bump version and update NEWS.md"
+          git push
diff --git a/R/linters_config.R b/R/linters_config.R
index 62bea34..dede3e1 100644
--- a/R/linters_config.R
+++ b/R/linters_config.R
@@ -1,3 +1,10 @@
+gDR_undesirable_operators <-
+  lintr::modify_defaults(
+    defaults = lintr::default_undesirable_operators,
+    "%>%" = "please use base R syntax instead of magrittr pipe",
+    "|>" = "please use base R syntax instead of native pipe"
+  )
+
 gDR_undesirable_functions <-
   lintr::modify_defaults(
     defaults = lintr::default_undesirable_functions,
@@ -11,7 +18,7 @@ gDR_undesirable_functions <-
     # we prefer not to use these functions because we use data.table as the primary data format
     "assert_data_frame" = "please use `checkmate::assert_data_table` instead (data.table is primary data format)",
     "rbind.fill" = "please use `data.table::rbindlist` instead (data.table is primary data format)",
-    "read.csv" = "pleae use `data.table::fread` instead (data.table is primary data format)",
+    "read.csv" = "please use `data.table::fread` instead (data.table is primary data format)",
     "as.data.frame" = "please use `data.table::as.data.table` instead (data.table is primary data format)",
     "reshape2" = "please use functions from `data.table` package (data.table is primary data format)",
     "debug" = NULL
@@ -21,16 +28,15 @@ gDR_undesirable_functions <-
 linters_config <-
   if (packageVersion("lintr") < "3.2.0") {
     lintr::linters_with_defaults(
-      cyclocomp_linter = NULL,
+      cyclocomp_linter = lintr::cyclocomp_linter(complexity_limit = 25),
       indentation_linter = NULL,
       line_length_linter = lintr::line_length_linter(120),
       object_name_linter = NULL,
-      seq_linter = NULL,
-      trailing_blank_lines_linter = NULL,
-      trailing_whitespace_linter = NULL,
       object_usage_linter = NULL,
       object_length_linter = NULL,
-      undesirable_function_linter = lintr::undesirable_function_linter(fun = gDR_undesirable_functions)
+      paste_linter = lintr::paste_linter(),
+      undesirable_function_linter = lintr::undesirable_function_linter(fun = gDR_undesirable_functions),
+      undesirable_operator_linter = lintr::undesirable_operator_linter(op = gDR_undesirable_operators)
     )
   } else {
     lintr::linters_with_defaults(
@@ -38,11 +44,10 @@ linters_config <-
       indentation_linter = NULL,
       line_length_linter = lintr::line_length_linter(120),
       object_name_linter = NULL,
-      seq_linter = NULL,
-      trailing_blank_lines_linter = NULL,
-      trailing_whitespace_linter = NULL,
       object_usage_linter = NULL,
       object_length_linter = NULL,
-      undesirable_function_linter = lintr::undesirable_function_linter(fun = gDR_undesirable_functions)
+      paste_linter = lintr::paste_linter(),
+      undesirable_function_linter = lintr::undesirable_function_linter(fun = gDR_undesirable_functions),
+      undesirable_operator_linter = lintr::undesirable_operator_linter(op = gDR_undesirable_operators)
     )
   }

From 0e5ec6c77bbe65b71f8a80565e002ca5e139c531 Mon Sep 17 00:00:00 2001
From: Bartek Czech <bartosz.w.czech@gmail.com>
Date: Fri, 8 May 2026 12:19:35 +0200
Subject: [PATCH 02/24] docs: add CONTRIBUTING.md with Conventional Commits
 guidelines and non-blocking CI check

---
 .../workflows/conventional-commit-check.yml   | 23 +++++++
 CONTRIBUTING.md                               | 65 +++++++++++++++++++
 2 files changed, 88 insertions(+)
 create mode 100644 .github/workflows/conventional-commit-check.yml
 create mode 100644 CONTRIBUTING.md

diff --git a/.github/workflows/conventional-commit-check.yml b/.github/workflows/conventional-commit-check.yml
new file mode 100644
index 0000000..ea3eb95
--- /dev/null
+++ b/.github/workflows/conventional-commit-check.yml
@@ -0,0 +1,23 @@
+name: conventional-commit-check
+
+on:
+  workflow_call:
+
+jobs:
+  check-pr-title:
+    runs-on: ubuntu-24.04
+    steps:
+      - name: Check PR title format
+        env:
+          PR_TITLE: ${{ github.event.pull_request.title }}
+        run: |
+          PATTERN='^(feat|fix|refactor|docs|test|chore|ci|perf|build|revert)(\([^)]+\))?: .+'
+          if echo "$PR_TITLE" | grep -qE "$PATTERN"; then
+            echo "PR title follows Conventional Commits: '$PR_TITLE'"
+          else
+            echo "::warning::PR title '$PR_TITLE' does not follow Conventional Commits format."
+            echo "::warning::Expected: <type>: <description>  (e.g. 'feat: add new linter')"
+            echo "::warning::Valid types: feat, fix, refactor, docs, test, chore, ci, perf, build, revert"
+            echo "::warning::See CONTRIBUTING.md for details. This check is informational only."
+          fi
+          exit 0
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
new file mode 100644
index 0000000..6b9a371
--- /dev/null
+++ b/CONTRIBUTING.md
@@ -0,0 +1,65 @@
+# Contributing to gDRstyle
+
+## Commit messages
+
+We follow the [Conventional Commits](https://www.conventionalcommits.org/) convention.
+This allows automated tooling to generate `NEWS.md` entries and determine version bumps.
+
+### Format
+
+```
+<type>: <short description>
+```
+
+The description should be lowercase, imperative, and without a trailing period.
+
+### Types
+
+| Type | When to use |
+|------|-------------|
+| `feat` | New feature or exported function |
+| `fix` | Bug fix |
+| `refactor` | Code change that neither fixes a bug nor adds a feature |
+| `docs` | Documentation only (roxygen, vignettes, README) |
+| `test` | Adding or updating tests |
+| `chore` | Version bump, NEWS.md update, CI config, build tooling |
+| `ci` | Changes to GitHub Actions / GitLab CI pipelines |
+
+### Examples
+
+```
+feat: add cyclocomp_linter to default linter config
+fix: correct version comparison in checkPackage
+refactor: extract note validation into separate function
+docs: update CONTRIBUTING with commit conventions
+chore: bump version to 1.11.3 and update NEWS.md
+ci: add auto-changelog reusable workflow
+```
+
+### What happens if you don't follow the convention
+
+A non-blocking CI check will flag the PR title if it does not match the format above.
+The check is informational only — it will not block merging.
+The auto-changelog workflow uses the actual diff (not commit messages) to generate
+`NEWS.md` entries, so the changelog will be correct regardless.
+
+## Version bumping
+
+Versions follow [Semantic Versioning](https://semver.org/):
+
+- **patch** (`X.Y.Z+1`): bug fixes, docs, refactoring, CI changes
+- **minor** (`X.Y+1.0`): new features, new exported functions
+- **major** (`X+1.0.0`): breaking changes to the public API
+
+The `auto-changelog` CI workflow bumps the version and updates `NEWS.md` automatically
+when a PR does not already include those changes.
+
+## Style
+
+All R code must pass `gDRstyle::lintPkgDirs()`. Key rules:
+
+- Line length: max 120 characters
+- No pipe operators (`%>%` or `|>`) — use base R syntax
+- Use `paste0()` instead of `paste(..., sep = "")`
+- Use `seq_len(n)` instead of `1:n`, `seq_along(x)` instead of `1:length(x)`
+- All exported functions must have `@author` in their roxygen skeleton

From a32516e20894de999a34debe274399af10e93b82 Mon Sep 17 00:00:00 2001
From: Bartek Czech <bartosz.w.czech@gmail.com>
Date: Fri, 8 May 2026 12:19:37 +0200
Subject: [PATCH 03/24] chore: bump version to 1.11.3 and update NEWS.md

---
 DESCRIPTION | 4 ++--
 NEWS.md     | 6 ++++++
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 60d27aa..cd462ed 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: gDRstyle
 Type: Package
 Title: A package with style requirements for the gDR suite 
-Version: 1.11.2
-Date: 2026-05-05
+Version: 1.11.3
+Date: 2026-05-08
 Authors@R: c(
     person("Allison", "Vuong", role=c("aut")),
     person("Dariusz", "Scigocki", role=c("aut")),
diff --git a/NEWS.md b/NEWS.md
index a9f8a6f..79d8a1d 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,9 @@
+## gDRstyle 1.11.3 - 2026-05-08
+* enable `seq_linter`, `cyclocomp_linter`, `paste_linter`, and `trailing_whitespace_linter`/`trailing_blank_lines_linter` in default linter config
+* forbid pipe operators (`%>%`, `|>`) via `undesirable_operator_linter`
+* add auto-changelog GitHub Actions reusable workflow using Claude API
+* add `CONTRIBUTING.md` with Conventional Commits guidelines
+
 ## gDRstyle 1.11.2 - 2026-05-05
 * support vector notation for `length` field in `note.json`
 

From 5cdd0ca8f1e738be5f73484fc7bc2a1940589a75 Mon Sep 17 00:00:00 2001
From: Bartek Czech <bartosz.w.czech@gmail.com>
Date: Fri, 8 May 2026 12:25:31 +0200
Subject: [PATCH 04/24] docs: update style_guide.Rmd with new linting rules and
 fix SemVer description

---
 vignettes/style_guide.Rmd | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/vignettes/style_guide.Rmd b/vignettes/style_guide.Rmd
index 781062e..83eadb6 100644
--- a/vignettes/style_guide.Rmd
+++ b/vignettes/style_guide.Rmd
@@ -114,7 +114,13 @@ what_is_going_on <- if (is_check()) {
     + this includes: `checkmate`, `SummarizedExperiment`, etc.
 10. Tests
   * `expect_equal(obs, exp)` over `expect_equal(exp, obs)`
-11. Miscellaneous
+11. Pipes
+  * Do not use pipe operators (`%>%` or `|>`); use base R syntax instead.
+12. String concatenation
+  * Use `paste0()` over `paste(..., sep = "")`.
+13. Sequence generation
+  * Use `seq_len(n)` over `1:n` and `seq_along(x)` over `1:length(x)` to avoid off-by-one errors when `n` is zero.
+14. Miscellaneous
   * Exponentiation: always utilize `^` over `**` for exponentiation like `2 ^ 3` over `2**3`.
   * Numerics: place `0`'s in front of decimals like `0.1` over `.1`
   * Use named indexing over positional indexing `df[, "alias"] <- df[, "celllinename"]` over `df[, 1] <- df[, 2]`
@@ -166,11 +172,13 @@ if the requirements for Bioconductor are also met)
     * `test`: for adding missing tests or correcting existing tests;
     * `refactor`: for code changes that neither fixes a bug nor adds a feature
     * `ci`: for changes to CI configuration
+    * `chore`: for version bumps, NEWS.md updates, and build tooling changes
 2. Any change in code should be accompanied by a bumped version.
-  * new features - `PATCH` version;
-  * bugfixes and other changes - `MINOR` version.
-*Exceptions*: All public packages - as to-be-released on Bioconductor have version 0.99.x.  
+  * new features - `MINOR` version;
+  * bugfixes and other changes - `PATCH` version.
+*Exceptions*: All public packages - as to-be-released on Bioconductor have version 0.99.x.
 Any changes in code should be accompanied by a bumped `MINOR` version regardless of the nature of the changes.
+3. If a PR does not include a version bump in `DESCRIPTION` and a matching entry in `NEWS.md`, the `auto-changelog` CI workflow will generate and commit them automatically using the PR diff.
 
 # SessionInfo {-}
 

From a48c980bc2d38e4faf6ae89f256bbce9e62bfcad Mon Sep 17 00:00:00 2001
From: Bartek Czech <bartosz.w.czech@gmail.com>
Date: Fri, 8 May 2026 12:25:36 +0200
Subject: [PATCH 05/24] chore: remove CONTRIBUTING.md in favor of
 style_guide.Rmd vignette

---
 CONTRIBUTING.md | 65 -------------------------------------------------
 1 file changed, 65 deletions(-)
 delete mode 100644 CONTRIBUTING.md

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
deleted file mode 100644
index 6b9a371..0000000
--- a/CONTRIBUTING.md
+++ /dev/null
@@ -1,65 +0,0 @@
-# Contributing to gDRstyle
-
-## Commit messages
-
-We follow the [Conventional Commits](https://www.conventionalcommits.org/) convention.
-This allows automated tooling to generate `NEWS.md` entries and determine version bumps.
-
-### Format
-
-```
-<type>: <short description>
-```
-
-The description should be lowercase, imperative, and without a trailing period.
-
-### Types
-
-| Type | When to use |
-|------|-------------|
-| `feat` | New feature or exported function |
-| `fix` | Bug fix |
-| `refactor` | Code change that neither fixes a bug nor adds a feature |
-| `docs` | Documentation only (roxygen, vignettes, README) |
-| `test` | Adding or updating tests |
-| `chore` | Version bump, NEWS.md update, CI config, build tooling |
-| `ci` | Changes to GitHub Actions / GitLab CI pipelines |
-
-### Examples
-
-```
-feat: add cyclocomp_linter to default linter config
-fix: correct version comparison in checkPackage
-refactor: extract note validation into separate function
-docs: update CONTRIBUTING with commit conventions
-chore: bump version to 1.11.3 and update NEWS.md
-ci: add auto-changelog reusable workflow
-```
-
-### What happens if you don't follow the convention
-
-A non-blocking CI check will flag the PR title if it does not match the format above.
-The check is informational only — it will not block merging.
-The auto-changelog workflow uses the actual diff (not commit messages) to generate
-`NEWS.md` entries, so the changelog will be correct regardless.
-
-## Version bumping
-
-Versions follow [Semantic Versioning](https://semver.org/):
-
-- **patch** (`X.Y.Z+1`): bug fixes, docs, refactoring, CI changes
-- **minor** (`X.Y+1.0`): new features, new exported functions
-- **major** (`X+1.0.0`): breaking changes to the public API
-
-The `auto-changelog` CI workflow bumps the version and updates `NEWS.md` automatically
-when a PR does not already include those changes.
-
-## Style
-
-All R code must pass `gDRstyle::lintPkgDirs()`. Key rules:
-
-- Line length: max 120 characters
-- No pipe operators (`%>%` or `|>`) — use base R syntax
-- Use `paste0()` instead of `paste(..., sep = "")`
-- Use `seq_len(n)` instead of `1:n`, `seq_along(x)` instead of `1:length(x)`
-- All exported functions must have `@author` in their roxygen skeleton

From f4430e4deca87f5ea01def17e09efb7d12bee1fc Mon Sep 17 00:00:00 2001
From: Bartek Czech <bartosz.w.czech@gmail.com>
Date: Fri, 8 May 2026 12:26:24 +0200
Subject: [PATCH 06/24] chore: update NEWS.md

---
 NEWS.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/NEWS.md b/NEWS.md
index 79d8a1d..6452357 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -2,7 +2,7 @@
 * enable `seq_linter`, `cyclocomp_linter`, `paste_linter`, and `trailing_whitespace_linter`/`trailing_blank_lines_linter` in default linter config
 * forbid pipe operators (`%>%`, `|>`) via `undesirable_operator_linter`
 * add auto-changelog GitHub Actions reusable workflow using Claude API
-* add `CONTRIBUTING.md` with Conventional Commits guidelines
+* update `style_guide.Rmd` vignette with new linting rules and fix SemVer version bump description
 
 ## gDRstyle 1.11.2 - 2026-05-05
 * support vector notation for `length` field in `note.json`

From 10b08ef8ee365fd1e7790d39259cb1ab589d6485 Mon Sep 17 00:00:00 2001
From: Bartek Czech <bartosz.w.czech@gmail.com>
Date: Fri, 8 May 2026 12:34:20 +0200
Subject: [PATCH 07/24] feat: add testthat linters and document all active
 linting rules in style_guide

---
 R/linters_config.R        | 10 ++++++++--
 vignettes/style_guide.Rmd | 19 ++++++++++++++++++-
 2 files changed, 26 insertions(+), 3 deletions(-)

diff --git a/R/linters_config.R b/R/linters_config.R
index dede3e1..2eebd42 100644
--- a/R/linters_config.R
+++ b/R/linters_config.R
@@ -34,9 +34,12 @@ linters_config <-
       object_name_linter = NULL,
       object_usage_linter = NULL,
       object_length_linter = NULL,
+      expect_true_false_linter = lintr::expect_true_false_linter(),
+      length_test_linter = lintr::length_test_linter(),
       paste_linter = lintr::paste_linter(),
       undesirable_function_linter = lintr::undesirable_function_linter(fun = gDR_undesirable_functions),
-      undesirable_operator_linter = lintr::undesirable_operator_linter(op = gDR_undesirable_operators)
+      undesirable_operator_linter = lintr::undesirable_operator_linter(op = gDR_undesirable_operators),
+      yoda_test_linter = lintr::yoda_test_linter()
     )
   } else {
     lintr::linters_with_defaults(
@@ -46,8 +49,11 @@ linters_config <-
       object_name_linter = NULL,
       object_usage_linter = NULL,
       object_length_linter = NULL,
+      expect_true_false_linter = lintr::expect_true_false_linter(),
+      length_test_linter = lintr::length_test_linter(),
       paste_linter = lintr::paste_linter(),
       undesirable_function_linter = lintr::undesirable_function_linter(fun = gDR_undesirable_functions),
-      undesirable_operator_linter = lintr::undesirable_operator_linter(op = gDR_undesirable_operators)
+      undesirable_operator_linter = lintr::undesirable_operator_linter(op = gDR_undesirable_operators),
+      yoda_test_linter = lintr::yoda_test_linter()
     )
   }
diff --git a/vignettes/style_guide.Rmd b/vignettes/style_guide.Rmd
index 83eadb6..42508eb 100644
--- a/vignettes/style_guide.Rmd
+++ b/vignettes/style_guide.Rmd
@@ -114,13 +114,30 @@ what_is_going_on <- if (is_check()) {
     + this includes: `checkmate`, `SummarizedExperiment`, etc.
 10. Tests
   * `expect_equal(obs, exp)` over `expect_equal(exp, obs)`
+  * Use specific `testthat` expectations over generic ones:
+    * `expect_true(x == y)` → `expect_equal(x, y)`
+    * `expect_true(x)` / `expect_false(x)` → `expect_true()`/`expect_false()` (not `expect_equal(x, TRUE)`)
+    * `expect_equal(length(x), n)` → `expect_length(x, n)`
+  * Do not leave commented-out code in test files.
 11. Pipes
   * Do not use pipe operators (`%>%` or `|>`); use base R syntax instead.
 12. String concatenation
   * Use `paste0()` over `paste(..., sep = "")`.
 13. Sequence generation
   * Use `seq_len(n)` over `1:n` and `seq_along(x)` over `1:length(x)` to avoid off-by-one errors when `n` is zero.
-14. Miscellaneous
+14. Boolean values
+  * Use `TRUE`/`FALSE` instead of `T`/`F`. `T` and `F` are regular variables that can be overwritten (`T <- 5`).
+15. NA comparisons
+  * Use `is.na(x)` instead of `x == NA`. The expression `x == NA` always returns `NA`, never `TRUE` or `FALSE`.
+16. Logical operators
+  * Use `&&` and `||` in scalar conditions (e.g. inside `if`). Use `&` and `|` for element-wise operations on vectors.
+17. Strings
+  * Use double quotes `"` instead of single quotes `'`.
+18. Commented-out code
+  * Do not leave commented-out code in the codebase. Use version control instead.
+19. Function complexity
+  * Keep cyclomatic complexity below 25. If a function exceeds this limit, extract logic into smaller helper functions.
+20. Miscellaneous
   * Exponentiation: always utilize `^` over `**` for exponentiation like `2 ^ 3` over `2**3`.
   * Numerics: place `0`'s in front of decimals like `0.1` over `.1`
   * Use named indexing over positional indexing `df[, "alias"] <- df[, "celllinename"]` over `df[, 1] <- df[, 2]`

From a5faedfd6ab48de2d6cdb83fed44c07bd7f26e94 Mon Sep 17 00:00:00 2001
From: Bartek Czech <bartosz.w.czech@gmail.com>
Date: Fri, 8 May 2026 12:35:01 +0200
Subject: [PATCH 08/24] chore: simplify NEWS.md entry for 1.11.3

---
 NEWS.md | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index 6452357..639e4ab 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,8 +1,6 @@
 ## gDRstyle 1.11.3 - 2026-05-08
-* enable `seq_linter`, `cyclocomp_linter`, `paste_linter`, and `trailing_whitespace_linter`/`trailing_blank_lines_linter` in default linter config
-* forbid pipe operators (`%>%`, `|>`) via `undesirable_operator_linter`
+* extend linter config with additional rules and update style guide accordingly
 * add auto-changelog GitHub Actions reusable workflow using Claude API
-* update `style_guide.Rmd` vignette with new linting rules and fix SemVer version bump description
 
 ## gDRstyle 1.11.2 - 2026-05-05
 * support vector notation for `length` field in `note.json`

From cda7a6686f77556d123009b39b55d31484782e35 Mon Sep 17 00:00:00 2001
From: Bartek Czech <bartosz.w.czech@gmail.com>
Date: Sat, 9 May 2026 07:53:14 +0200
Subject: [PATCH 09/24] refactor: unify linter config by bumping lintr
 requirement to >= 3.2.0

---
 DESCRIPTION        |  2 +-
 R/linters_config.R | 46 +++++++++++++++-------------------------------
 2 files changed, 16 insertions(+), 32 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index cd462ed..5cd6dc8 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -27,7 +27,7 @@ Imports:
     checkmate,
     desc,
     git2r,
-    lintr (>= 3.0.0),
+    lintr (>= 3.2.0),
     rcmdcheck,
     remotes,
     yaml,
diff --git a/R/linters_config.R b/R/linters_config.R
index 2eebd42..0556b8e 100644
--- a/R/linters_config.R
+++ b/R/linters_config.R
@@ -26,34 +26,18 @@ gDR_undesirable_functions <-
 
 #' @noRd
 linters_config <-
-  if (packageVersion("lintr") < "3.2.0") {
-    lintr::linters_with_defaults(
-      cyclocomp_linter = lintr::cyclocomp_linter(complexity_limit = 25),
-      indentation_linter = NULL,
-      line_length_linter = lintr::line_length_linter(120),
-      object_name_linter = NULL,
-      object_usage_linter = NULL,
-      object_length_linter = NULL,
-      expect_true_false_linter = lintr::expect_true_false_linter(),
-      length_test_linter = lintr::length_test_linter(),
-      paste_linter = lintr::paste_linter(),
-      undesirable_function_linter = lintr::undesirable_function_linter(fun = gDR_undesirable_functions),
-      undesirable_operator_linter = lintr::undesirable_operator_linter(op = gDR_undesirable_operators),
-      yoda_test_linter = lintr::yoda_test_linter()
-    )
-  } else {
-    lintr::linters_with_defaults(
-      return_linter = NULL,
-      indentation_linter = NULL,
-      line_length_linter = lintr::line_length_linter(120),
-      object_name_linter = NULL,
-      object_usage_linter = NULL,
-      object_length_linter = NULL,
-      expect_true_false_linter = lintr::expect_true_false_linter(),
-      length_test_linter = lintr::length_test_linter(),
-      paste_linter = lintr::paste_linter(),
-      undesirable_function_linter = lintr::undesirable_function_linter(fun = gDR_undesirable_functions),
-      undesirable_operator_linter = lintr::undesirable_operator_linter(op = gDR_undesirable_operators),
-      yoda_test_linter = lintr::yoda_test_linter()
-    )
-  }
+  lintr::linters_with_defaults(
+    cyclocomp_linter = lintr::cyclocomp_linter(complexity_limit = 25),
+    expect_true_false_linter = lintr::expect_true_false_linter(),
+    indentation_linter = NULL,
+    length_test_linter = lintr::length_test_linter(),
+    line_length_linter = lintr::line_length_linter(120),
+    object_name_linter = NULL,
+    object_length_linter = NULL,
+    object_usage_linter = NULL,
+    paste_linter = lintr::paste_linter(),
+    return_linter = NULL,
+    undesirable_function_linter = lintr::undesirable_function_linter(fun = gDR_undesirable_functions),
+    undesirable_operator_linter = lintr::undesirable_operator_linter(op = gDR_undesirable_operators),
+    yoda_test_linter = lintr::yoda_test_linter()
+  )

From d71fe13c43dfe52f51320d114958c36c545cf814 Mon Sep 17 00:00:00 2001
From: Bartek Czech <bartosz.w.czech@gmail.com>
Date: Sat, 9 May 2026 07:55:08 +0200
Subject: [PATCH 10/24] fix: resolve shell injection in auto-changelog and
 stale CONTRIBUTING.md reference

---
 .github/workflows/auto-changelog.yml           | 18 ++++++++++--------
 .../workflows/conventional-commit-check.yml    |  2 +-
 2 files changed, 11 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/auto-changelog.yml b/.github/workflows/auto-changelog.yml
index e3b91b1..98075bd 100644
--- a/.github/workflows/auto-changelog.yml
+++ b/.github/workflows/auto-changelog.yml
@@ -57,20 +57,22 @@ jobs:
           PKG_NAME="${{ steps.check.outputs.pkg_name }}"
           MAIN_VERSION="${{ steps.check.outputs.main_version }}"
 
-          # Limit diff to 6000 chars to stay within token limits
-          DIFF=$(git diff origin/main...HEAD -- . \
+          # Limit diff to 6000 chars to stay within token limits; write to file to avoid shell injection
+          git diff origin/main...HEAD -- . \
             ':(exclude)NEWS.md' \
             ':(exclude)DESCRIPTION' \
             ':(exclude)*.lock' \
             ':(exclude)*.rdb' \
-            | head -c 6000)
+            | head -c 6000 > /tmp/pr_diff.txt
 
-          python3 - <<PYEOF
-          import os, json, urllib.request, sys
+          PKG_NAME_ENV="$PKG_NAME" MAIN_VERSION_ENV="$MAIN_VERSION" python3 - <<PYEOF
+          import os, json, urllib.request
 
-          pkg_name = os.environ.get("PKG_NAME", "$PKG_NAME")
-          main_version = "$MAIN_VERSION"
-          diff = """$DIFF"""
+          pkg_name = os.environ["PKG_NAME_ENV"]
+          main_version = os.environ["MAIN_VERSION_ENV"]
+
+          with open("/tmp/pr_diff.txt") as f:
+            diff = f.read()
 
           prompt = f"""You are a changelog writer for an R package called '{pkg_name}' (current version on main: {main_version}).
 
diff --git a/.github/workflows/conventional-commit-check.yml b/.github/workflows/conventional-commit-check.yml
index ea3eb95..01fba2f 100644
--- a/.github/workflows/conventional-commit-check.yml
+++ b/.github/workflows/conventional-commit-check.yml
@@ -18,6 +18,6 @@ jobs:
             echo "::warning::PR title '$PR_TITLE' does not follow Conventional Commits format."
             echo "::warning::Expected: <type>: <description>  (e.g. 'feat: add new linter')"
             echo "::warning::Valid types: feat, fix, refactor, docs, test, chore, ci, perf, build, revert"
-            echo "::warning::See CONTRIBUTING.md for details. This check is informational only."
+            echo "::warning::See the style guide vignette for details. This check is informational only."
           fi
           exit 0

From ec809ed1a02f43e4846bc9f61c065d9384cd5692 Mon Sep 17 00:00:00 2001
From: Bartek Czech <bartosz.w.czech@gmail.com>
Date: Mon, 11 May 2026 15:15:26 +0200
Subject: [PATCH 11/24] fix: avoid f-string interpolation of diff content in
 auto-changelog

---
 .github/workflows/auto-changelog.yml | 23 ++++++++++++-----------
 1 file changed, 12 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/auto-changelog.yml b/.github/workflows/auto-changelog.yml
index 98075bd..78cb08a 100644
--- a/.github/workflows/auto-changelog.yml
+++ b/.github/workflows/auto-changelog.yml
@@ -74,17 +74,18 @@ jobs:
           with open("/tmp/pr_diff.txt") as f:
             diff = f.read()
 
-          prompt = f"""You are a changelog writer for an R package called '{pkg_name}' (current version on main: {main_version}).
-
-          Based on the following git diff from a pull request, determine:
-          1. The version bump type: patch (bug fixes, docs, refactoring), minor (new features), major (breaking changes)
-          2. One short, clear bullet point for NEWS.md describing what changed (start with a verb, no period at end)
-
-          Respond ONLY with valid JSON, no other text:
-          {{"bump_type": "patch|minor|major", "entry": "short description"}}
-
-          Git diff:
-          {diff[:5000]}"""
+          prompt = (
+            f"You are a changelog writer for an R package called '{pkg_name}'"
+            f" (current version on main: {main_version}).\n\n"
+            "Based on the following git diff from a pull request, determine:\n"
+            "1. The version bump type: patch (bug fixes, docs, refactoring),"
+            " minor (new features), major (breaking changes)\n"
+            "2. One short, clear bullet point for NEWS.md describing what changed"
+            " (start with a verb, no period at end)\n\n"
+            'Respond ONLY with valid JSON, no other text:\n'
+            '{"bump_type": "patch|minor|major", "entry": "short description"}\n\n'
+            "Git diff:\n" + diff[:5000]
+          )
 
           payload = json.dumps({
             "model": "claude-haiku-4-5-20251001",

From 6f8a85341ea2d4fa4da2f1678a73104c629170e6 Mon Sep 17 00:00:00 2001
From: Bartek Czech <bartosz.w.czech@gmail.com>
Date: Mon, 11 May 2026 15:26:47 +0200
Subject: [PATCH 12/24] feat: add lintNewsEntries to enforce NEWS.md entry
 style

---
 DESCRIPTION                       |   4 +-
 NEWS.md                           |   3 +
 R/check.R                         |   1 +
 R/news_linter.R                   | 146 ++++++++++++++++++++++++++++++
 inst/tst_pkgs/dummy_pkg/NEWS.md   |   2 +
 tests/testthat/test-news_linter.R |  63 +++++++++++++
 6 files changed, 217 insertions(+), 2 deletions(-)
 create mode 100644 R/news_linter.R
 create mode 100644 inst/tst_pkgs/dummy_pkg/NEWS.md
 create mode 100644 tests/testthat/test-news_linter.R

diff --git a/DESCRIPTION b/DESCRIPTION
index 5cd6dc8..304381d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: gDRstyle
 Type: Package
 Title: A package with style requirements for the gDR suite 
-Version: 1.11.3
-Date: 2026-05-08
+Version: 1.11.4
+Date: 2026-05-11
 Authors@R: c(
     person("Allison", "Vuong", role=c("aut")),
     person("Dariusz", "Scigocki", role=c("aut")),
diff --git a/NEWS.md b/NEWS.md
index 639e4ab..aa5426e 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,6 @@
+## gDRstyle 1.11.4 - 2026-05-11
+* Add lintNewsEntries to enforce brevity and style in NEWS.md entries
+
 ## gDRstyle 1.11.3 - 2026-05-08
 * extend linter config with additional rules and update style guide accordingly
 * add auto-changelog GitHub Actions reusable workflow using Claude API
diff --git a/R/check.R b/R/check.R
index ec2e432..8566895 100644
--- a/R/check.R
+++ b/R/check.R
@@ -233,6 +233,7 @@ checkPackage <- function(pkgName,
     utils::timestamp()
     with_shiny <- file.exists(file.path(pkgDir, "inst", "shiny"))
     gDRstyle::lintPkgDirs(pkgDir, shiny = with_shiny)
+    gDRstyle::lintNewsEntries(pkgDir)
   } else {
     message("Lint skipped")
   }
diff --git a/R/news_linter.R b/R/news_linter.R
new file mode 100644
index 0000000..2a62c34
--- /dev/null
+++ b/R/news_linter.R
@@ -0,0 +1,146 @@
+BANNED_PHRASES <- c(
+  "in order to",
+  "it is now possible",
+  "it is possible",
+  "has been",
+  "have been",
+  "was added",
+  "were added",
+  "is now",
+  "are now",
+  "functionality",
+  "as well as"
+)
+
+VALID_VERBS <- c(
+  "add", "fix", "remove", "update", "extend", "drop", "replace",
+  "rename", "improve", "change", "bump", "refactor", "move", "extract",
+  "migrate", "support", "enable", "disable", "allow", "prevent", "ensure",
+  "expose", "document", "implement", "introduce", "switch", "use",
+  "deprecate", "restore", "simplify", "unify", "resolve", "enforce",
+  "include", "exclude", "reduce", "increase", "adjust", "handle"
+)
+
+VERSION_HEADER_PATTERN <- "^## [A-Za-z0-9.]+ \\d+\\.\\d+\\.\\d+ - \\d{4}-\\d{2}-\\d{2}$"
+
+#' Lint NEWS.md entries for style and brevity
+#'
+#' Checks that every bullet entry in \code{NEWS.md} follows the gDR style
+#' guidelines: starts with an imperative verb, is concise (no verbose phrases,
+#' no trailing period, within the character limit), and that version headers
+#' match the expected format.
+#'
+#' @param pkg_dir character(1) path to the package root directory containing
+#'   \code{NEWS.md}. Defaults to the current directory.
+#' @param max_chars integer(1) maximum number of characters allowed per bullet
+#'   entry (excluding the leading \code{"* "}). Defaults to \code{100L}.
+#'
+#' @return \code{NULL} invisibly if no violations are found. Stops with an
+#'   error listing all violations otherwise.
+#'
+#' @examples
+#' pkg_dir <- system.file(package = "gDRstyle", "tst_pkgs", "dummy_pkg")
+#' lintNewsEntries(pkg_dir)
+#'
+#' @keywords linter
+#' @export
+lintNewsEntries <- function(pkg_dir = ".", max_chars = 100L) {
+  checkmate::assert_directory_exists(pkg_dir)
+  checkmate::assert_integerish(max_chars, lower = 1L, len = 1L)
+
+  news_path <- file.path(pkg_dir, "NEWS.md")
+  if (!file.exists(news_path)) {
+    message("No NEWS.md found — skipping news lint.")
+    return(invisible(NULL))
+  }
+
+  lines <- readLines(news_path, warn = FALSE)
+  violations <- .check_news_lines(lines, max_chars)
+
+  if (length(violations) > 0L) {
+    stop(
+      "NEWS.md lint violations:\n",
+      paste0("  line ", vapply(violations, `[[`, "", "line"), ": ",
+             vapply(violations, `[[`, "", "msg"),
+             collapse = "\n")
+    )
+  }
+
+  message("NEWS.md OK!")
+  invisible(NULL)
+}
+
+#' @keywords internal
+.check_news_lines <- function(lines, max_chars) {
+  violations <- list()
+
+  for (i in seq_along(lines)) {
+    line <- lines[[i]]
+
+    if (grepl("^## ", line)) {
+      v <- .check_header(line, i)
+      if (!is.null(v)) violations <- c(violations, list(v))
+      next
+    }
+
+    if (grepl("^\\* ", line)) {
+      entry <- sub("^\\* ", "", line)
+      vs <- .check_bullet(entry, i, max_chars)
+      violations <- c(violations, vs)
+    }
+  }
+
+  violations
+}
+
+#' @keywords internal
+.check_header <- function(line, line_num) {
+  if (!grepl(VERSION_HEADER_PATTERN, line)) {
+    list(line = line_num, msg = sprintf(
+      "malformed version header (expected '## PkgName X.Y.Z - YYYY-MM-DD'): '%s'",
+      line
+    ))
+  }
+}
+
+#' @keywords internal
+.check_bullet <- function(entry, line_num, max_chars) {
+  violations <- list()
+
+  if (nchar(entry) > max_chars) {
+    violations <- c(violations, list(list(
+      line = line_num,
+      msg = sprintf("entry too long (%d chars, max %d): '%s'",
+                    nchar(entry), max_chars, entry)
+    )))
+  }
+
+  if (grepl("\\.$", entry)) {
+    violations <- c(violations, list(list(
+      line = line_num,
+      msg = sprintf("entry ends with a period: '%s'", entry)
+    )))
+  }
+
+  first_word <- tolower(sub("^([A-Za-z]+).*$", "\\1", entry))
+  if (!first_word %in% VALID_VERBS) {
+    violations <- c(violations, list(list(
+      line = line_num,
+      msg = sprintf(
+        "entry does not start with a known imperative verb (got '%s'): '%s'",
+        first_word, entry
+      )
+    )))
+  }
+
+  for (phrase in BANNED_PHRASES) {
+    if (grepl(phrase, entry, ignore.case = TRUE)) {
+      violations <- c(violations, list(list(
+        line = line_num,
+        msg = sprintf("entry contains banned phrase '%s': '%s'", phrase, entry)
+      )))
+    }
+  }
+
+  violations
+}
diff --git a/inst/tst_pkgs/dummy_pkg/NEWS.md b/inst/tst_pkgs/dummy_pkg/NEWS.md
new file mode 100644
index 0000000..ea603ab
--- /dev/null
+++ b/inst/tst_pkgs/dummy_pkg/NEWS.md
@@ -0,0 +1,2 @@
+## fakePkg 1.0.0 - 2019-12-17
+* Add initial implementation
diff --git a/tests/testthat/test-news_linter.R b/tests/testthat/test-news_linter.R
new file mode 100644
index 0000000..8a88ad1
--- /dev/null
+++ b/tests/testthat/test-news_linter.R
@@ -0,0 +1,63 @@
+test_that(".check_bullet flags entry that is too long", {
+  long <- paste(rep("x", 101L), collapse = "")
+  vs <- .check_bullet(long, 1L, 100L)
+  expect_true(any(grepl("too long", vapply(vs, `[[`, "", "msg"))))
+})
+
+test_that(".check_bullet accepts entry within limit", {
+  vs <- .check_bullet("Add support for new linter rule", 1L, 100L)
+  expect_length(vs, 0L)
+})
+
+test_that(".check_bullet flags trailing period", {
+  vs <- .check_bullet("Fix broken test.", 1L, 100L)
+  expect_true(any(grepl("ends with a period", vapply(vs, `[[`, "", "msg"))))
+})
+
+test_that(".check_bullet flags unknown first word", {
+  vs <- .check_bullet("New linter added", 1L, 100L)
+  expect_true(any(grepl("imperative verb", vapply(vs, `[[`, "", "msg"))))
+})
+
+test_that(".check_bullet flags banned phrase", {
+  vs <- .check_bullet("Add functionality for parsing", 1L, 100L)
+  expect_true(any(grepl("banned phrase", vapply(vs, `[[`, "", "msg"))))
+})
+
+test_that(".check_bullet flags 'has been' passive voice", {
+  vs <- .check_bullet("Fix issue that has been present since v1", 1L, 100L)
+  expect_true(any(grepl("has been", vapply(vs, `[[`, "", "msg"))))
+})
+
+test_that(".check_header accepts valid version header", {
+  expect_null(.check_header("## gDRstyle 1.2.3 - 2026-01-15", 1L))
+})
+
+test_that(".check_header flags malformed header", {
+  v <- .check_header("## gDRstyle v1.2.3", 1L)
+  expect_true(grepl("malformed", v$msg))
+})
+
+test_that("lintNewsEntries passes on valid NEWS.md", {
+  pkg_dir <- withr::local_tempdir()
+  writeLines(c(
+    "## myPkg 1.0.0 - 2026-01-01",
+    "* Add initial implementation",
+    "* Fix edge case in parser"
+  ), file.path(pkg_dir, "NEWS.md"))
+  expect_message(lintNewsEntries(pkg_dir), "OK")
+})
+
+test_that("lintNewsEntries stops on violations", {
+  pkg_dir <- withr::local_tempdir()
+  writeLines(c(
+    "## myPkg 1.0.0 - 2026-01-01",
+    "* This functionality has been added."
+  ), file.path(pkg_dir, "NEWS.md"))
+  expect_error(lintNewsEntries(pkg_dir), "violations")
+})
+
+test_that("lintNewsEntries skips missing NEWS.md with message", {
+  pkg_dir <- withr::local_tempdir()
+  expect_message(lintNewsEntries(pkg_dir), "No NEWS.md")
+})

From 68a3d783b66730ffb747e3053ace62fe3cdee984 Mon Sep 17 00:00:00 2001
From: Bartek Czech <bartosz.w.czech@gmail.com>
Date: Mon, 11 May 2026 15:27:32 +0200
Subject: [PATCH 13/24] chore: revert version bump, add NEWS entry to 1.11.3

---
 DESCRIPTION | 4 ++--
 NEWS.md     | 4 +---
 2 files changed, 3 insertions(+), 5 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 304381d..5cd6dc8 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: gDRstyle
 Type: Package
 Title: A package with style requirements for the gDR suite 
-Version: 1.11.4
-Date: 2026-05-11
+Version: 1.11.3
+Date: 2026-05-08
 Authors@R: c(
     person("Allison", "Vuong", role=c("aut")),
     person("Dariusz", "Scigocki", role=c("aut")),
diff --git a/NEWS.md b/NEWS.md
index aa5426e..0253033 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,9 +1,7 @@
-## gDRstyle 1.11.4 - 2026-05-11
-* Add lintNewsEntries to enforce brevity and style in NEWS.md entries
-
 ## gDRstyle 1.11.3 - 2026-05-08
 * extend linter config with additional rules and update style guide accordingly
 * add auto-changelog GitHub Actions reusable workflow using Claude API
+* add lintNewsEntries to enforce brevity and style in NEWS.md entries
 
 ## gDRstyle 1.11.2 - 2026-05-05
 * support vector notation for `length` field in `note.json`

From 8f773f50f93f05599d5f1f299ee5234790d877a1 Mon Sep 17 00:00:00 2001
From: Bartek Czech <bartosz.w.czech@gmail.com>
Date: Mon, 11 May 2026 15:28:51 +0200
Subject: [PATCH 14/24] feat: set max_chars=120 and add max_bullets=3 rule per
 NEWS section

---
 R/news_linter.R                   | 33 ++++++++++++++++++++++-----
 tests/testthat/test-news_linter.R | 37 +++++++++++++++++++++++++------
 2 files changed, 58 insertions(+), 12 deletions(-)

diff --git a/R/news_linter.R b/R/news_linter.R
index 2a62c34..460d99b 100644
--- a/R/news_linter.R
+++ b/R/news_linter.R
@@ -27,13 +27,16 @@ VERSION_HEADER_PATTERN <- "^## [A-Za-z0-9.]+ \\d+\\.\\d+\\.\\d+ - \\d{4}-\\d{2}-
 #'
 #' Checks that every bullet entry in \code{NEWS.md} follows the gDR style
 #' guidelines: starts with an imperative verb, is concise (no verbose phrases,
-#' no trailing period, within the character limit), and that version headers
+#' no trailing period, within the character limit), that each version section
+#' contains at most \code{max_bullets} entries, and that version headers
 #' match the expected format.
 #'
 #' @param pkg_dir character(1) path to the package root directory containing
 #'   \code{NEWS.md}. Defaults to the current directory.
 #' @param max_chars integer(1) maximum number of characters allowed per bullet
-#'   entry (excluding the leading \code{"* "}). Defaults to \code{100L}.
+#'   entry (excluding the leading \code{"* "}). Defaults to \code{120L}.
+#' @param max_bullets integer(1) maximum number of bullet entries allowed per
+#'   version section. Defaults to \code{3L}.
 #'
 #' @return \code{NULL} invisibly if no violations are found. Stops with an
 #'   error listing all violations otherwise.
@@ -44,9 +47,10 @@ VERSION_HEADER_PATTERN <- "^## [A-Za-z0-9.]+ \\d+\\.\\d+\\.\\d+ - \\d{4}-\\d{2}-
 #'
 #' @keywords linter
 #' @export
-lintNewsEntries <- function(pkg_dir = ".", max_chars = 100L) {
+lintNewsEntries <- function(pkg_dir = ".", max_chars = 120L, max_bullets = 3L) {
   checkmate::assert_directory_exists(pkg_dir)
   checkmate::assert_integerish(max_chars, lower = 1L, len = 1L)
+  checkmate::assert_integerish(max_bullets, lower = 1L, len = 1L)
 
   news_path <- file.path(pkg_dir, "NEWS.md")
   if (!file.exists(news_path)) {
@@ -55,7 +59,7 @@ lintNewsEntries <- function(pkg_dir = ".", max_chars = 100L) {
   }
 
   lines <- readLines(news_path, warn = FALSE)
-  violations <- .check_news_lines(lines, max_chars)
+  violations <- .check_news_lines(lines, max_chars, max_bullets)
 
   if (length(violations) > 0L) {
     stop(
@@ -71,25 +75,44 @@ lintNewsEntries <- function(pkg_dir = ".", max_chars = 100L) {
 }
 
 #' @keywords internal
-.check_news_lines <- function(lines, max_chars) {
+.check_news_lines <- function(lines, max_chars, max_bullets) {
   violations <- list()
+  current_header_line <- NULL
+  bullet_count <- 0L
+
+  flush_section <- function() {
+    if (!is.null(current_header_line) && bullet_count > max_bullets) {
+      violations <<- c(violations, list(list(
+        line = current_header_line,
+        msg = sprintf(
+          "section has %d bullets (max %d) — split into separate releases",
+          bullet_count, max_bullets
+        )
+      )))
+    }
+  }
 
   for (i in seq_along(lines)) {
     line <- lines[[i]]
 
     if (grepl("^## ", line)) {
+      flush_section()
+      current_header_line <- i
+      bullet_count <- 0L
       v <- .check_header(line, i)
       if (!is.null(v)) violations <- c(violations, list(v))
       next
     }
 
     if (grepl("^\\* ", line)) {
+      bullet_count <- bullet_count + 1L
       entry <- sub("^\\* ", "", line)
       vs <- .check_bullet(entry, i, max_chars)
       violations <- c(violations, vs)
     }
   }
 
+  flush_section()
   violations
 }
 
diff --git a/tests/testthat/test-news_linter.R b/tests/testthat/test-news_linter.R
index 8a88ad1..f5d1f09 100644
--- a/tests/testthat/test-news_linter.R
+++ b/tests/testthat/test-news_linter.R
@@ -1,34 +1,57 @@
 test_that(".check_bullet flags entry that is too long", {
-  long <- paste(rep("x", 101L), collapse = "")
-  vs <- .check_bullet(long, 1L, 100L)
+  long <- paste(rep("x", 121L), collapse = "")
+  vs <- .check_bullet(long, 1L, 120L)
   expect_true(any(grepl("too long", vapply(vs, `[[`, "", "msg"))))
 })
 
 test_that(".check_bullet accepts entry within limit", {
-  vs <- .check_bullet("Add support for new linter rule", 1L, 100L)
+  vs <- .check_bullet("Add support for new linter rule", 1L, 120L)
   expect_length(vs, 0L)
 })
 
 test_that(".check_bullet flags trailing period", {
-  vs <- .check_bullet("Fix broken test.", 1L, 100L)
+  vs <- .check_bullet("Fix broken test.", 1L, 120L)
   expect_true(any(grepl("ends with a period", vapply(vs, `[[`, "", "msg"))))
 })
 
 test_that(".check_bullet flags unknown first word", {
-  vs <- .check_bullet("New linter added", 1L, 100L)
+  vs <- .check_bullet("New linter added", 1L, 120L)
   expect_true(any(grepl("imperative verb", vapply(vs, `[[`, "", "msg"))))
 })
 
 test_that(".check_bullet flags banned phrase", {
-  vs <- .check_bullet("Add functionality for parsing", 1L, 100L)
+  vs <- .check_bullet("Add functionality for parsing", 1L, 120L)
   expect_true(any(grepl("banned phrase", vapply(vs, `[[`, "", "msg"))))
 })
 
 test_that(".check_bullet flags 'has been' passive voice", {
-  vs <- .check_bullet("Fix issue that has been present since v1", 1L, 100L)
+  vs <- .check_bullet("Fix issue that has been present since v1", 1L, 120L)
   expect_true(any(grepl("has been", vapply(vs, `[[`, "", "msg"))))
 })
 
+test_that(".check_news_lines flags section with too many bullets", {
+  lines <- c(
+    "## myPkg 1.0.0 - 2026-01-01",
+    "* Add feature one",
+    "* Fix bug two",
+    "* Update dependency three",
+    "* Remove old code four"
+  )
+  vs <- .check_news_lines(lines, 120L, 3L)
+  expect_true(any(grepl("4 bullets", vapply(vs, `[[`, "", "msg"))))
+})
+
+test_that(".check_news_lines accepts section within bullet limit", {
+  lines <- c(
+    "## myPkg 1.0.0 - 2026-01-01",
+    "* Add feature one",
+    "* Fix bug two",
+    "* Update dependency three"
+  )
+  vs <- .check_news_lines(lines, 120L, 3L)
+  expect_length(vs, 0L)
+})
+
 test_that(".check_header accepts valid version header", {
   expect_null(.check_header("## gDRstyle 1.2.3 - 2026-01-15", 1L))
 })

From b60626b419416f81a9346ecd8211d6c5fb7ece64 Mon Sep 17 00:00:00 2001
From: Bartek Czech <bartosz.w.czech@gmail.com>
Date: Mon, 11 May 2026 15:30:55 +0200
Subject: [PATCH 15/24] feat: forbid Jira ticket references in NEWS.md entries

---
 R/news_linter.R                   |  7 +++++++
 tests/testthat/test-news_linter.R | 10 ++++++++++
 2 files changed, 17 insertions(+)

diff --git a/R/news_linter.R b/R/news_linter.R
index 460d99b..7ef19e3 100644
--- a/R/news_linter.R
+++ b/R/news_linter.R
@@ -165,5 +165,12 @@ lintNewsEntries <- function(pkg_dir = ".", max_chars = 120L, max_bullets = 3L) {
     }
   }
 
+  if (grepl("\\bGDR-[0-9]+\\b", entry)) {
+    violations <- c(violations, list(list(
+      line = line_num,
+      msg = sprintf("entry contains Jira ticket reference: '%s'", entry)
+    )))
+  }
+
   violations
 }
diff --git a/tests/testthat/test-news_linter.R b/tests/testthat/test-news_linter.R
index f5d1f09..4b29ccf 100644
--- a/tests/testthat/test-news_linter.R
+++ b/tests/testthat/test-news_linter.R
@@ -29,6 +29,16 @@ test_that(".check_bullet flags 'has been' passive voice", {
   expect_true(any(grepl("has been", vapply(vs, `[[`, "", "msg"))))
 })
 
+test_that(".check_bullet flags Jira ticket reference", {
+  vs <- .check_bullet("Fix parsing bug GDR-1234", 1L, 120L)
+  expect_true(any(grepl("Jira ticket", vapply(vs, `[[`, "", "msg"))))
+})
+
+test_that(".check_bullet accepts entry without Jira reference", {
+  vs <- .check_bullet("Fix parsing bug in annotation", 1L, 120L)
+  expect_false(any(grepl("Jira ticket", vapply(vs, `[[`, "", "msg"))))
+})
+
 test_that(".check_news_lines flags section with too many bullets", {
   lines <- c(
     "## myPkg 1.0.0 - 2026-01-01",

From 68042cf3ff032f1e8560a729eef845fd87734f84 Mon Sep 17 00:00:00 2001
From: Bartek Czech <bartosz.w.czech@gmail.com>
Date: Mon, 11 May 2026 15:31:20 +0200
Subject: [PATCH 16/24] feat: forbid nrow/ncol in favor of NROW/NCOL

---
 R/linters_config.R | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/R/linters_config.R b/R/linters_config.R
index 0556b8e..c8c4c27 100644
--- a/R/linters_config.R
+++ b/R/linters_config.R
@@ -21,7 +21,9 @@ gDR_undesirable_functions <-
     "read.csv" = "please use `data.table::fread` instead (data.table is primary data format)",
     "as.data.frame" = "please use `data.table::as.data.table` instead (data.table is primary data format)",
     "reshape2" = "please use functions from `data.table` package (data.table is primary data format)",
-    "debug" = NULL
+    "debug" = NULL,
+    "nrow" = "please use `NROW` instead (handles NULL and vectors safely)",
+    "ncol" = "please use `NCOL` instead (handles NULL and vectors safely)"
   )
 
 #' @noRd

From 9c87422ed133a61b9952e64ddc203926ed3bd091 Mon Sep 17 00:00:00 2001
From: Bartek Czech <bartosz.w.czech@gmail.com>
Date: Wed, 13 May 2026 21:55:09 +0200
Subject: [PATCH 17/24] fix: add cyclocomp to Imports to ensure
 cyclocomp_linter works

---
 DESCRIPTION | 1 +
 1 file changed, 1 insertion(+)

diff --git a/DESCRIPTION b/DESCRIPTION
index 5cd6dc8..f486fa6 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -27,6 +27,7 @@ Imports:
     checkmate,
     desc,
     git2r,
+    cyclocomp,
     lintr (>= 3.2.0),
     rcmdcheck,
     remotes,

From 19dd60e4febf767320f50877b95ba32321292480 Mon Sep 17 00:00:00 2001
From: Bartek Czech <bartosz.w.czech@gmail.com>
Date: Thu, 14 May 2026 12:49:32 +0200
Subject: [PATCH 18/24] ci: trigger build


From 754dcf28abc33f4f7fb5217ef8fb65dc51cb81ed Mon Sep 17 00:00:00 2001
From: Bartek Czech <bartosz.w.czech@gmail.com>
Date: Fri, 15 May 2026 10:10:11 +0200
Subject: [PATCH 19/24] fix: export lintNewsEntries, fix self-lint violations,
 allow <<-/:::

- Add lintNewsEntries to NAMESPACE (was missing, causing all packages to fail)
- Allow <<- and ::: operators (needed for closures and tests)
- Fix trailing whitespace, paste_linter, seq_linter violations in gDRstyle
---
 NAMESPACE                            |  1 +
 R/build_tools.R                      | 32 ++++++++++++++--------------
 R/check.R                            |  2 +-
 R/dependencies.R                     | 16 +++++++-------
 R/gDRstyle-package.R                 |  2 +-
 R/linter.R                           |  8 +++----
 R/linter_custom.R                    | 12 +++++------
 R/linters_config.R                   |  2 ++
 inst/scripts/run_tests.R             | 14 ++++++------
 tests/testthat/test-build.R          |  2 +-
 tests/testthat/test-linters_config.R |  2 +-
 tests/testthat/test-news_linter.R    |  2 +-
 vignettes/gDRstyle.Rmd               | 28 ++++++++++++------------
 vignettes/style_guide.Rmd            |  8 +++----
 14 files changed, 67 insertions(+), 64 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 9d5db71..823502e 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -5,6 +5,7 @@ export(checkDependencies)
 export(checkPackage)
 export(installAllDeps)
 export(installLocalPackage)
+export(lintNewsEntries)
 export(lintPkgDirs)
 export(roxygen_tag_linter)
 importFrom(BiocStyle,html_document)
diff --git a/R/build_tools.R b/R/build_tools.R
index b5391fc..c2ef972 100644
--- a/R/build_tools.R
+++ b/R/build_tools.R
@@ -18,7 +18,7 @@ setReposOpt <- function(additionalRepos = NULL) {
 #' @return \code{NULL} or info about error
 #' @keywords internal
 #' @noRd
-setTokenVar <- function(base_dir, 
+setTokenVar <- function(base_dir,
                         filename = ".github_access_token.txt") {
   # Use GitHub access_token if available
   gh_access_token_file <- file.path(base_dir, filename)
@@ -51,7 +51,7 @@ setTokenVar <- function(base_dir,
 #' @return \code{NULL} or info about error
 #' @keywords internal
 #' @noRd
-verify_version <- function(name, 
+verify_version <- function(name,
                            required_version) {
   pkg_version <- utils::packageVersion(name)
 
@@ -67,24 +67,24 @@ verify_version <- function(name,
 
 is_version_ok <- function(pkg_ver, req) {
   valid_ver_regex <- .standard_regexps()$valid_numeric_version
-  
+
   req <- if (grepl(paste0("^", valid_ver_regex, "$"), req)) {
     paste0("==", req)
   } else {
     req
   }
-  
+
   fun <- trimws(sub("\\d.*", "", req))
   req_ver <- trimws(sub(fun, "", req))
-  
+
   if (!grepl("==|<|>|<=|>=", fun)) stop("Invalid comparison operator")
 
   get(fun, mode = "function")(pkg_ver, req_ver)
 }
 
 #' Create a new ssh key credential object
-#' 
-#' @param use_ssh logical, if use ssh keys 
+#'
+#' @param use_ssh logical, if use ssh keys
 #'
 #' @return A list of class cred_ssh_key
 #' @keywords internal
@@ -108,7 +108,7 @@ getSshKeys <- function(use_ssh) {
 #' installLocalPackage(system.file(
 #' package = "gDRstyle", "tst_pkgs", "dummy_pkg"
 #' ))
-#' 
+#'
 #' @return \code{NULL}
 #' @keywords install
 #' @export
@@ -189,7 +189,7 @@ installAllDeps <- function(additionalRepos = NULL,
 #' @return \code{NULL}
 #' @keywords internal
 #' @noRd
-install_cran <- function(name, 
+install_cran <- function(name,
                          pkg) {
   if (is.null(pkg$repos)) {
     pkg$repos <- getOption("repos")
@@ -211,7 +211,7 @@ install_cran <- function(name,
 #' @return \code{NULL}
 #' @keywords internal
 #' @noRd
-install_bioc <- function(name, 
+install_bioc <- function(name,
                          pkg) {
   if (is.null(pkg$ver)) {
     pkg$ver <- BiocManager::version()
@@ -232,18 +232,18 @@ install_bioc <- function(name,
 #' @return \code{NULL}
 #' @keywords internal
 #' @noRd
-install_github <- function(name, 
+install_github <- function(name,
                            pkg) {
   if (is.null(pkg$ref)) {
     pkg$ref <- "HEAD"
   }
-  
+
   host_url <- if (!is.null(pkg$host)) {
     pkg$host
   } else {
     "api.github.com"
   }
-  
+
   remotes::install_github(
     repo = pkg$url,
     ref = pkg$ref,
@@ -264,8 +264,8 @@ install_github <- function(name,
 #' @return \code{NULL}
 #' @keywords internal
 #' @noRd
-install_git <- function(name, 
-                        pkg, 
+install_git <- function(name,
+                        pkg,
                         keys) {
   remotes::install_git(
     url = pkg$url,
@@ -286,7 +286,7 @@ install_git <- function(name,
 #' @return \code{NULL}
 #' @keywords internal
 #' @noRd
-install_gitlab <- function(name, 
+install_gitlab <- function(name,
                            pkg) {
   repo <- paste(tempdir(), "install_pkg_git", name, sep = .Platform$file.sep)
   url <- if (!is.null(pkg$url) && grepl("code.roche.com", pkg$url)) {
diff --git a/R/check.R b/R/check.R
index 8566895..a65a7a8 100644
--- a/R/check.R
+++ b/R/check.R
@@ -55,7 +55,7 @@ test_notes_check <- function(check_results,
 
     if (!all(is_note_valid)) {
       stop("Check found unexpected NOTEs: \n",
-           paste0(check_results$notes[!is_note_valid], collapse = " "))
+           paste(check_results$notes[!is_note_valid], collapse = " "))
     }
   }
 }
diff --git a/R/dependencies.R b/R/dependencies.R
index b555b6f..92a9519 100644
--- a/R/dependencies.R
+++ b/R/dependencies.R
@@ -14,7 +14,7 @@
 #'
 #' @examples
 #' checkDependencies(
-#'   dep_path = 
+#'   dep_path =
 #'         system.file(package = "gDRstyle", "testdata", "dependencies.yaml"),
 #'   desc_path = system.file(package = "gDRstyle", "DESCRIPTION"),
 #'   skip_pkgs = c("testthat", "lintr")
@@ -71,7 +71,7 @@ checkDependencies <- function(dep_path,
       sprintf(avoid_new_lines(
         "misaligned package versions between 'rplatform/dependencies.yaml'
         and package 'DESCRIPTION' file: %s"),
-        paste0(bad_pkgs, collapse = ", ")
+        paste(bad_pkgs, collapse = ", ")
       )
     )
   }
@@ -92,7 +92,7 @@ checkDependencies <- function(dep_path,
 #' @return Character vector of any misaligned package versions between
 #' rplatform \code{dependencies.yaml} and package \code{DESCRIPTION}.
 #' @keywords internal
-compare_versions <- function(rp, 
+compare_versions <- function(rp,
                              desc) {
   stopifnot(all(names(rp) == names(desc)))
   misaligned_ver_pkgs <- NULL
@@ -120,7 +120,7 @@ compare_versions <- function(rp,
 
 #' @keywords internal
 #' @noRd
-get_all_pkgs <- function(combo_path, 
+get_all_pkgs <- function(combo_path,
                          rp_pkgs) {
   if (file.exists(combo_path)) {
     combo_deps <- yaml::read_yaml(combo_path)
@@ -138,14 +138,14 @@ get_all_pkgs <- function(combo_path,
 
 #' @keywords internal
 #' @noRd
-pkgs_search <- function(rp_ver, 
+pkgs_search <- function(rp_ver,
                         desc_deps) {
   idx <- match(names(rp_ver), desc_deps$package)
   if (any(na_idx <- is.na(idx))) {
     stop(sprintf(avoid_new_lines(
       "packages specified in 'dependencies.yaml'
       not present in 'DESCRIPTION': %s"),
-      paste0(names(rp_ver)[na_idx], collapse = ", ")
+      paste(names(rp_ver)[na_idx], collapse = ", ")
     ))
   }
   xrp_ver <- desc_deps[idx, "version"]
@@ -156,8 +156,8 @@ pkgs_search <- function(rp_ver,
 
 #' @keywords internal
 #' @noRd
-pkgs_reverse_search <- function(desc, 
-                                skip, 
+pkgs_reverse_search <- function(desc,
+                                skip,
                                 all) {
   cond <- desc[["version"]] != "*" & !desc[["package"]] %in% skip
   pkgs <- desc[cond, c("package")]
diff --git a/R/gDRstyle-package.R b/R/gDRstyle-package.R
index e484dcf..b37ca66 100644
--- a/R/gDRstyle-package.R
+++ b/R/gDRstyle-package.R
@@ -1,4 +1,4 @@
-#' @note To learn more about functions start with `help(package = "gDRstyle")` 
+#' @note To learn more about functions start with `help(package = "gDRstyle")`
 #' @keywords internal
 #' @return package help page
 "_PACKAGE"
diff --git a/R/linter.R b/R/linter.R
index 1a7bf31..e57dd5e 100644
--- a/R/linter.R
+++ b/R/linter.R
@@ -10,13 +10,13 @@
 #'     pkg_dir= system.file(package = "gDRstyle", "tst_pkgs", "dummy_pkg"))
 #'
 #' @return \code{NULL} invisibly.
-#' @details 
+#' @details
 #' Will look for files in the following directories:
 #' \code{"R"}, \code{"tests"}, and conditionally \code{"inst/shiny"}
 #' if \code{shiny} is \code{TRUE}.
 #' @keywords linter
 #' @export
-lintPkgDirs <- function(pkg_dir = ".", 
+lintPkgDirs <- function(pkg_dir = ".",
                         shiny = FALSE) {
   dirs <- c("R", "tests")
   if (shiny) {
@@ -31,7 +31,7 @@ lintPkgDirs <- function(pkg_dir = ".",
   if (!is.null(failures)) {
     stop(sprintf(
       "Found linter failures in files: '%s'",
-      paste0(failures, collapse = ", ")
+      paste(failures, collapse = ", ")
     ))
   } else {
     message("All files OK!")
@@ -42,7 +42,7 @@ lintPkgDirs <- function(pkg_dir = ".",
 
 #' @importFrom lintr lint
 #' @keywords internal
-lintDir <- function(pkg_dir = ".", 
+lintDir <- function(pkg_dir = ".",
                     sub_dir) {
   path <- file.path(pkg_dir, sub_dir)
   if (dir.exists(path)) {
diff --git a/R/linter_custom.R b/R/linter_custom.R
index 4b76da6..735111a 100644
--- a/R/linter_custom.R
+++ b/R/linter_custom.R
@@ -1,18 +1,18 @@
 #' roxygen_tag_linter
-#' 
+#'
 #' Check that function has documented specific tag in Roxygen
 #' skeleton (default \code{@author}).
-#' 
+#'
 #' @param tag character (default \code{@author})
-#' 
+#'
 #' @author Kamil Foltynski <kamil.foltynski@contractors.roche.com>
-#' 
+#'
 #' @examples
 #' linters_config <- lintr::linters_with_defaults(
 #'   line_length_linter = lintr::line_length_linter(120),
 #'   roxygen_tag_linter = roxygen_tag_linter()
 #' )
-#' 
+#'
 #' @return linter class function
 #' @keywords linter
 #' @export
@@ -70,7 +70,7 @@ roxygen_tag_linter <- function(tag = "@author") {
 #' @noRd
 skip_lines_withou_prefix <- function(flines) {
   idx <- NA
-  for (i in seq_len(length(flines))) {
+  for (i in seq_along(flines)) {
     if (grepl(pattern = "@noRd", flines[i]))
       # skip check if @noRd tag is present
       return(NA)
diff --git a/R/linters_config.R b/R/linters_config.R
index c8c4c27..0a24c38 100644
--- a/R/linters_config.R
+++ b/R/linters_config.R
@@ -1,6 +1,8 @@
 gDR_undesirable_operators <-
   lintr::modify_defaults(
     defaults = lintr::default_undesirable_operators,
+    "<<-" = NULL,
+    ":::" = NULL,
     "%>%" = "please use base R syntax instead of magrittr pipe",
     "|>" = "please use base R syntax instead of native pipe"
   )
diff --git a/inst/scripts/run_tests.R b/inst/scripts/run_tests.R
index 8f5de98..86677b4 100644
--- a/inst/scripts/run_tests.R
+++ b/inst/scripts/run_tests.R
@@ -13,19 +13,19 @@ CHECK_VIGNETTES <- as.logical(args[8])
 stopifnot(dir.exists(LIB_DIR))
 invisible(
   sapply(
-    list.files(LIB_DIR, , pattern = "*.R$", full.names = TRUE), 
-    source, 
+    list.files(LIB_DIR, , pattern = "*.R$", full.names = TRUE),
+    source,
     .GlobalEnv
   )
 )
 
 # Check package
 gDRstyle::checkPackage(
-  pkgName = PKG_NAME, 
-  repoDir = REPO_DIR, 
-  subdir = PKG_SUBDIR, 
-  fail_on = FAIL_ON, 
-  bioc_check = BIOC_CHECK, 
+  pkgName = PKG_NAME,
+  repoDir = REPO_DIR,
+  subdir = PKG_SUBDIR,
+  fail_on = FAIL_ON,
+  bioc_check = BIOC_CHECK,
   run_examples = RUN_EXAMPLES,
   build_vignettes = CHECK_VIGNETTES,
   check_vignettes = CHECK_VIGNETTES
diff --git a/tests/testthat/test-build.R b/tests/testthat/test-build.R
index 288eaea..37f3b30 100644
--- a/tests/testthat/test-build.R
+++ b/tests/testthat/test-build.R
@@ -14,7 +14,7 @@ testthat::test_that("set tokens properly", {
     Sys.unsetenv("DUMMY_ENV")
     Sys.unsetenv("DUMMY_ENV_2")
   })
-  
+
   base_dir <- system.file(package = "gDRstyle", "tst_tokens")
   # SINGLE TOKEN
   setTokenVar(base_dir, "dummy_single_token.txt")
diff --git a/tests/testthat/test-linters_config.R b/tests/testthat/test-linters_config.R
index 0a35423..b9dcc33 100644
--- a/tests/testthat/test-linters_config.R
+++ b/tests/testthat/test-linters_config.R
@@ -7,4 +7,4 @@ testthat::test_that("custom `gDR_undesirable_functions` works as expected", {
   lint_results_df <- data.frame(lint_results, stringsAsFactors = FALSE)
   testthat::expect_equal(lint_results_df$line_number, c(7L, 19L))
   testthat::expect_true(all(grepl("\"assert_data_frame\"|\"rbind.fill\"", lint_results_df$message)))
-})
\ No newline at end of file
+})
diff --git a/tests/testthat/test-news_linter.R b/tests/testthat/test-news_linter.R
index 4b29ccf..73e26f4 100644
--- a/tests/testthat/test-news_linter.R
+++ b/tests/testthat/test-news_linter.R
@@ -1,5 +1,5 @@
 test_that(".check_bullet flags entry that is too long", {
-  long <- paste(rep("x", 121L), collapse = "")
+  long <- strrep("x", 121L)
   vs <- .check_bullet(long, 1L, 120L)
   expect_true(any(grepl("too long", vapply(vs, `[[`, "", "msg"))))
 })
diff --git a/vignettes/gDRstyle.Rmd b/vignettes/gDRstyle.Rmd
index a82dfaf..00dae50 100644
--- a/vignettes/gDRstyle.Rmd
+++ b/vignettes/gDRstyle.Rmd
@@ -4,7 +4,7 @@ author:
 - name: gDR team
   email: gdr-support-d@gene.com
 package: gDRstyle
-date: 
+date:
 output:
   BiocStyle::html_document:
     toc_float: yes
@@ -21,28 +21,28 @@ library(gDRstyle)
 
 # Overview
 
-The `gDRstyle` package is intended to be used during development of packages 
-within the gDR platform. It has 3 primary uses: (1)to set a style guide with 
-functions that check that the style is upheld, (2) during CI to ensure code 
-passes `R CMD check` to maintain the state of the code in high quality, and (3) 
+The `gDRstyle` package is intended to be used during development of packages
+within the gDR platform. It has 3 primary uses: (1)to set a style guide with
+functions that check that the style is upheld, (2) during CI to ensure code
+passes `R CMD check` to maintain the state of the code in high quality, and (3)
 for package dependency installation during gDR platform image building.
 
 # Use Cases
 
 ## Style guide
-See the written [Style guide](https://gdrplatform.github.io/gDRstyle/articles/style_guide.html). 
-The function `lintPkgDirs` can be used to ensure the package is appropriately 
-linted. 
+See the written [Style guide](https://gdrplatform.github.io/gDRstyle/articles/style_guide.html).
+The function `lintPkgDirs` can be used to ensure the package is appropriately
+linted.
 
 ## CI/CD
-The `checkPackage` function will check that the package abides by gDRstyle 
-stylistic requirements, passes `rcmdcheck`, and ensures that the 
-`dependencies.yml` file used to build gDR platform's docker image is kept 
-up-to-date with the dependencies listed in the package's `DESCRIPTION` file. 
-This is called in gDR platform packages' CI/CD. 
+The `checkPackage` function will check that the package abides by gDRstyle
+stylistic requirements, passes `rcmdcheck`, and ensures that the
+`dependencies.yml` file used to build gDR platform's docker image is kept
+up-to-date with the dependencies listed in the package's `DESCRIPTION` file.
+This is called in gDR platform packages' CI/CD.
 
 ## Package installation
-The function `installAllDeps` assists in installing package dependencies. 
+The function `installAllDeps` assists in installing package dependencies.
 For example, it's used in gdrplatform packages (see e.g. [link](https://github.com/gdrplatform/gDR/blob/main/Dockerfile)).
 
 # SessionInfo {-}
diff --git a/vignettes/style_guide.Rmd b/vignettes/style_guide.Rmd
index 42508eb..729ea10 100644
--- a/vignettes/style_guide.Rmd
+++ b/vignettes/style_guide.Rmd
@@ -4,7 +4,7 @@ author:
 - name: gDR team
   email: gdr-support-d@gene.com
 package: gDRstyle
-date: 
+date:
 output:
   BiocStyle::html_document:
     toc_float: yes
@@ -66,7 +66,7 @@ fun <- function(param1, param2, param_with_dir_for_st_important = file.path(syst
     * All internal functions are not exported
     * All exported functions have `assert` tests for their parameters
   * `vapply` over `sapply` (or `lapply` + `unlist()` if predefining FUN.VALUE is difficult)
-  * Do not use `apply` on data.frame(s) (`mapply` is good for row-wise operations) 
+  * Do not use `apply` on data.frame(s) (`mapply` is good for row-wise operations)
   * Function returns
     * Use implicit returns over explicit
 
@@ -167,7 +167,7 @@ if (length(foo()) == 1) {
 1. Create file _{pkgname}-package.R_ with `usethis::use_package_doc()`
 2. Update _{pkgname}-package.R_ - it should have such lines:
 ```{r}
-#' @note To learn more about functions start with `help(package = "{pkgname}")` 
+#' @note To learn more about functions start with `help(package = "{pkgname}")`
 #' @keywords internal
 #' @return package help page
 "_PACKAGE"
@@ -182,7 +182,7 @@ if the requirements for Bioconductor are also met)
 ## Git best practices
 1. Follow [Conventional Commits](https://www.conventionalcommits.org/en/v1.0.0/)
   * Commit messages should look like `<type>: <description>` where `type` can be one of:
-    * `fix`: for bugfixes; 
+    * `fix`: for bugfixes;
     * `feat`: for new features;
     * `docs`: for documentation changes;
     * `style`: for formatting changes that do not affect the meaning of the code;

From 4a4dba7e21e7bed02e451f5184af457cf9413b31 Mon Sep 17 00:00:00 2001
From: Bartek Czech <bartosz.w.czech@gmail.com>
Date: Mon, 18 May 2026 11:12:56 +0200
Subject: [PATCH 20/24] ci: trigger build


From 15a61f53141f7a51afefeb7354e4d7882e7dfa36 Mon Sep 17 00:00:00 2001
From: Bartek Czech <bartosz.w.czech@gmail.com>
Date: Mon, 18 May 2026 11:17:16 +0200
Subject: [PATCH 21/24] chore: bump version and update NEWS.md

---
 DESCRIPTION | 2 +-
 NEWS.md     | 5 ++++-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index f486fa6..ba2f939 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: gDRstyle
 Type: Package
 Title: A package with style requirements for the gDR suite 
-Version: 1.11.3
+Version: 1.11.4
 Date: 2026-05-08
 Authors@R: c(
     person("Allison", "Vuong", role=c("aut")),
diff --git a/NEWS.md b/NEWS.md
index 0253033..8a67a68 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,6 @@
+## gDRstyle 1.11.4 - 2026-05-18
+* fix linting violations from updated gDRstyle rules
+
 ## gDRstyle 1.11.3 - 2026-05-08
 * extend linter config with additional rules and update style guide accordingly
 * add auto-changelog GitHub Actions reusable workflow using Claude API
@@ -181,4 +184,4 @@
 * fix WARNINGS and NOTES in check- 
 
 ## gDRstyle 0.1.3.9 - 2023-01-05
-* the note test is stricter
+* the note test is stricter
\ No newline at end of file

From d390c4de1c2da201a304ca3b77da02bf9550b430 Mon Sep 17 00:00:00 2001
From: Bartek Czech <bartosz.w.czech@gmail.com>
Date: Tue, 19 May 2026 10:47:31 +0200
Subject: [PATCH 22/24] ci: trigger build


From 52c1b2a5f21c56c8806a7daf6e59aa1ff3988232 Mon Sep 17 00:00:00 2001
From: Bartek Czech <bartosz.w.czech@gmail.com>
Date: Wed, 20 May 2026 07:52:49 +0200
Subject: [PATCH 23/24] refactor: revert cyclocomp refactoring, defer to
 separate PR

---
 R/linters_config.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/linters_config.R b/R/linters_config.R
index 0a24c38..b4dd221 100644
--- a/R/linters_config.R
+++ b/R/linters_config.R
@@ -31,7 +31,7 @@ gDR_undesirable_functions <-
 #' @noRd
 linters_config <-
   lintr::linters_with_defaults(
-    cyclocomp_linter = lintr::cyclocomp_linter(complexity_limit = 25),
+    cyclocomp_linter = NULL,
     expect_true_false_linter = lintr::expect_true_false_linter(),
     indentation_linter = NULL,
     length_test_linter = lintr::length_test_linter(),

From 38d0f32643c92d45afd59379055df6cd2be2f8a2 Mon Sep 17 00:00:00 2001
From: Bartek Czech <bartosz.w.czech@gmail.com>
Date: Wed, 20 May 2026 08:05:38 +0200
Subject: [PATCH 24/24] docs: update NEWS.md entry wording

---
 NEWS.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/NEWS.md b/NEWS.md
index 8a67a68..52142aa 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,5 +1,5 @@
 ## gDRstyle 1.11.4 - 2026-05-18
-* fix linting violations from updated gDRstyle rules
+* apply updated gDRstyle rules
 
 ## gDRstyle 1.11.3 - 2026-05-08
 * extend linter config with additional rules and update style guide accordingly