From a1f7fa5e8f4697fd8cb95a887be61ae5b249af99 Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com>
Date: Tue, 1 Jul 2025 11:56:14 +0100
Subject: [PATCH 01/11] Improve variable protection

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

diff --git a/DESCRIPTION b/DESCRIPTION
index 95db082..3d03261 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: Rogue
 Title: Identify Rogue Taxa in Sets of Phylogenetic Trees
-Version: 2.1.6.9000
+Version: 2.1.6.9001
 Authors@R: c(person("Martin R.", 'Smith',
                     email = "martin.smith@durham.ac.uk", 
                     role = c("aut", "cre", "cph"), 
diff --git a/NEWS.md b/NEWS.md
index fa48abd..46b168a 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,7 +1,8 @@
-# Rogue v2.1.6.9000 (2025-04-14)
+# Rogue v2.1.6.9001 (2025-04-14)
 
 - Improve tip instability calculation in identical tree sets
   ([#29](https://github.com/ms609/Rogue/issues/29)).
+- Improve variable protection.
 
 
 # Rogue v2.1.6 (2023-11-29)

From 55e0ef90194b5cf44c1fe518f3ed137df7af5dbf Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com>
Date: Tue, 1 Jul 2025 11:57:16 +0100
Subject: [PATCH 02/11] Update rnr

---
 src/rnr | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/rnr b/src/rnr
index dc5ce2a..56d2b8b 160000
--- a/src/rnr
+++ b/src/rnr
@@ -1 +1 @@
-Subproject commit dc5ce2afd36d5262660a39b9119679cc2b274d5d
+Subproject commit 56d2b8bb13e7c3ac5c7d4f76b26b647689405dd5

From f06bc029f0516ac456f1959a9a7da428616b38bb Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com>
Date: Tue, 1 Jul 2025 11:59:40 +0100
Subject: [PATCH 03/11] Create rchk.yml

---
 .github/workflows/rchk.yml | 49 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 49 insertions(+)
 create mode 100644 .github/workflows/rchk.yml

diff --git a/.github/workflows/rchk.yml b/.github/workflows/rchk.yml
new file mode 100644
index 0000000..f07b47e
--- /dev/null
+++ b/.github/workflows/rchk.yml
@@ -0,0 +1,49 @@
+on:
+  push:
+    branches:
+      - main
+      - master
+    paths:
+      - '.github/workflows/rchk.yml'
+      - 'src/**'
+      - 'inst/include/**'
+      - 'memcheck/**'
+      - 'tests/testthat/**.R'
+      - 'vignettes/**.Rmd'
+  pull_request:
+    paths:
+      - '.github/workflows/rchk.yml'
+      - 'src/**'
+      - 'inst/include/**'
+      - 'memcheck/**'
+      - 'tests/testthat/**.R'
+      - 'vignettes/**.Rmd'
+
+name: rchk
+
+jobs:  
+  rchk:
+    runs-on: ubuntu-latest
+    container:
+      image: rhub/ubuntu-rchk
+      options: --user=root
+    steps:
+    - uses: actions/checkout@v4
+      
+    - name: Set up rchk
+      uses: r-lib/actions/run-rchk@v2
+      with:
+        setup-only: true
+        
+    - uses: randy3k/gh-actions/r-install-deps@main
+      with:
+        cache-version: rchk-1
+        
+    - name: Install package
+      run: |
+        remotes::install_local()
+      shell: Rscript {0}
+      
+    - uses: r-lib/actions/run-rchk@v2
+      with:
+        run-only: true

From b096a12a1eb0089f7f1a752cfed0c6d2b157a34e Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com>
Date: Tue, 1 Jul 2025 12:01:07 +0100
Subject: [PATCH 04/11] Revert "Create rchk.yml"

This reverts commit f06bc029f0516ac456f1959a9a7da428616b38bb.
---
 .github/workflows/rchk.yml | 49 --------------------------------------
 1 file changed, 49 deletions(-)
 delete mode 100644 .github/workflows/rchk.yml

diff --git a/.github/workflows/rchk.yml b/.github/workflows/rchk.yml
deleted file mode 100644
index f07b47e..0000000
--- a/.github/workflows/rchk.yml
+++ /dev/null
@@ -1,49 +0,0 @@
-on:
-  push:
-    branches:
-      - main
-      - master
-    paths:
-      - '.github/workflows/rchk.yml'
-      - 'src/**'
-      - 'inst/include/**'
-      - 'memcheck/**'
-      - 'tests/testthat/**.R'
-      - 'vignettes/**.Rmd'
-  pull_request:
-    paths:
-      - '.github/workflows/rchk.yml'
-      - 'src/**'
-      - 'inst/include/**'
-      - 'memcheck/**'
-      - 'tests/testthat/**.R'
-      - 'vignettes/**.Rmd'
-
-name: rchk
-
-jobs:  
-  rchk:
-    runs-on: ubuntu-latest
-    container:
-      image: rhub/ubuntu-rchk
-      options: --user=root
-    steps:
-    - uses: actions/checkout@v4
-      
-    - name: Set up rchk
-      uses: r-lib/actions/run-rchk@v2
-      with:
-        setup-only: true
-        
-    - uses: randy3k/gh-actions/r-install-deps@main
-      with:
-        cache-version: rchk-1
-        
-    - name: Install package
-      run: |
-        remotes::install_local()
-      shell: Rscript {0}
-      
-    - uses: r-lib/actions/run-rchk@v2
-      with:
-        run-only: true

From ed5f5b3b5e5a4b7de5dbee35b6c91ea0e42a8b8e Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com>
Date: Tue, 1 Jul 2025 12:01:48 +0100
Subject: [PATCH 05/11] rhub::rhub_setup()

---
 .github/workflows/rhub.yaml | 95 +++++++++++++++++++++++++++++++++++++
 1 file changed, 95 insertions(+)
 create mode 100644 .github/workflows/rhub.yaml

diff --git a/.github/workflows/rhub.yaml b/.github/workflows/rhub.yaml
new file mode 100644
index 0000000..74ec7b0
--- /dev/null
+++ b/.github/workflows/rhub.yaml
@@ -0,0 +1,95 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+  workflow_dispatch:
+    inputs:
+      config:
+        description: 'A comma separated list of R-hub platforms to use.'
+        type: string
+        default: 'linux,windows,macos'
+      name:
+        description: 'Run name. You can leave this empty now.'
+        type: string
+      id:
+        description: 'Unique ID. You can leave this empty now.'
+        type: string
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      containers: ${{ steps.rhub-setup.outputs.containers }}
+      platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+    steps:
+    # NO NEED TO CHECKOUT HERE
+    - uses: r-hub/actions/setup@v1
+      with:
+        config: ${{ github.event.inputs.config }}
+      id: rhub-setup
+
+  linux-containers:
+    needs: setup
+    if: ${{ needs.setup.outputs.containers != '[]' }}
+    runs-on: ubuntu-latest
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.containers) }}
+    container:
+      image: ${{ matrix.config.container }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+
+  other-platforms:
+    needs: setup
+    if: ${{ needs.setup.outputs.platforms != '[]' }}
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}

From e19941ef6a4fdaefab4b42ced00642f53cd12718 Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com>
Date: Tue, 1 Jul 2025 12:12:57 +0100
Subject: [PATCH 06/11] submoduels

---
 .github/workflows/rhub.yaml | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/rhub.yaml b/.github/workflows/rhub.yaml
index 74ec7b0..6e423a7 100644
--- a/.github/workflows/rhub.yaml
+++ b/.github/workflows/rhub.yaml
@@ -17,11 +17,13 @@ on:
         type: string
         default: 'linux,windows,macos'
       name:
-        description: 'Run name. You can leave this empty now.'
+        description: 'Run name.'
         type: string
+        default: 'run'
       id:
-        description: 'Unique ID. You can leave this empty now.'
+        description: 'Unique ID.'
         type: string
+        default: 'no id'
 
 jobs:
 
@@ -52,6 +54,8 @@ jobs:
 
     steps:
       - uses: r-hub/actions/checkout@v1
+        with:
+          submodules: 'true'
       - uses: r-hub/actions/platform-info@v1
         with:
           token: ${{ secrets.RHUB_TOKEN }}
@@ -77,6 +81,8 @@ jobs:
 
     steps:
       - uses: r-hub/actions/checkout@v1
+        with:
+          submodules: 'true'
       - uses: r-hub/actions/setup-r@v1
         with:
           job-config: ${{ matrix.config.job-config }}

From f276db884fa17b649a03c0390bc25c731500ffe4 Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com>
Date: Tue, 1 Jul 2025 12:18:02 +0100
Subject: [PATCH 07/11] Update checks

---
 .github/workflows/R-CMD-check.yml |  7 +++----
 cran-comments.md                  | 16 ++++++++--------
 2 files changed, 11 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yml b/.github/workflows/R-CMD-check.yml
index 5516bf0..8a2a1b8 100644
--- a/.github/workflows/R-CMD-check.yml
+++ b/.github/workflows/R-CMD-check.yml
@@ -47,10 +47,9 @@ jobs:
         config:
           - {os: windows-latest, r: 'release'}
           - {os: macOS-latest, r: 'release'}
-          - {os: ubuntu-20.04, r: '4.1', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} # Until TreeDist can slough phangorn
-          #- {os: ubuntu-20.04, r: '3.6.3', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-latest, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-latest, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-latest, r: '4.1', rspm: "https://packagemanager.rstudio.com/cran/__linux__/noble/latest"} # Until TreeDist can slough phangorn
+          - {os: ubuntu-latest, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/noble/latest"}
+          - {os: ubuntu-latest, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/noble/latest"}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
diff --git a/cran-comments.md b/cran-comments.md
index 5ab10db..2aecbdf 100644
--- a/cran-comments.md
+++ b/cran-comments.md
@@ -1,17 +1,18 @@
 ## Test environments
 
 * Local PC:
-  - Windows 10, R 4.3.1
+  - Windows 10, R devel
 
 * [GitHub Actions](https://github.com/ms609/Rogue/actions)
-  - Ubuntu 20.04
+  - ubuntu-latest
     - R 4.1
     - R release (tests, examples & vignettes run with valgrind)
     - R devel
-  - Mac OS X 12.6.8, R release
-  - Microsoft Windows Server 2022 10.0.20348, R release
-  
-* R-hub, with `rhub::check_for_cran()` and `devtools::check_win_devel()`
+  - macOS-latest, R release
+  - windows-latest, R release
+  - [R-hub](https://github.com/ms609/Rogue/actions/workflows/rhub.yaml)
+
+* `devtools::check_win_devel()`
 
 ## R CMD check results
 
@@ -21,5 +22,4 @@ There was one NOTE:
 > The Description field should not start with the package name,
   'This package' or similar.
 
-False positive: the word 'Rogue' is used here as an adjective, but happens to
-match the name of the package.
+False positive: the adjective 'Rogue' happens to match the name of the package.

From e157ef9317c2303e6e4636423fa08d0fae0e813c Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com>
Date: Tue, 1 Jul 2025 12:19:32 +0100
Subject: [PATCH 08/11] -latest

---
 .github/workflows/memcheck.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/memcheck.yml b/.github/workflows/memcheck.yml
index 657b0b3..635339f 100644
--- a/.github/workflows/memcheck.yml
+++ b/.github/workflows/memcheck.yml
@@ -24,7 +24,7 @@ name: mem-check
 
 jobs:
   mem-check:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
 
     name: valgrind ${{ matrix.config.test }}
 
@@ -38,7 +38,7 @@ jobs:
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       _R_CHECK_FORCE_SUGGESTS_: false
-      RSPM: https://packagemanager.rstudio.com/cran/__linux__/focal/latest
+      RSPM: https://packagemanager.rstudio.com/cran/__linux__/noble/latest
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:

From d52fd75dcafd6340fcbcb326c382f3f4a5a9d396 Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com>
Date: Tue, 1 Jul 2025 12:24:10 +0100
Subject: [PATCH 09/11] v2.1.7

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

diff --git a/DESCRIPTION b/DESCRIPTION
index 3d03261..0c1ead7 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: Rogue
 Title: Identify Rogue Taxa in Sets of Phylogenetic Trees
-Version: 2.1.6.9001
+Version: 2.1.7
 Authors@R: c(person("Martin R.", 'Smith',
                     email = "martin.smith@durham.ac.uk", 
                     role = c("aut", "cre", "cph"), 
diff --git a/NEWS.md b/NEWS.md
index 46b168a..1c452c8 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# Rogue v2.1.6.9001 (2025-04-14)
+# Rogue v2.1.7 (2025-07-01)
 
 - Improve tip instability calculation in identical tree sets
   ([#29](https://github.com/ms609/Rogue/issues/29)).

From 4193559c8447f5588c86c9cdce21415f0ce4ff85 Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com>
Date: Tue, 1 Jul 2025 12:24:50 +0100
Subject: [PATCH 10/11] Update codemeta.json

---
 codemeta.json | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/codemeta.json b/codemeta.json
index 99c5884..5836849 100644
--- a/codemeta.json
+++ b/codemeta.json
@@ -8,13 +8,13 @@
   "codeRepository": "https://github.com/ms609/Rogue/",
   "issueTracker": "https://github.com/ms609/Rogue/issues/",
   "license": "https://spdx.org/licenses/GPL-3.0",
-  "version": "2.1.6.9000",
+  "version": "2.1.7",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
     "url": "https://r-project.org"
   },
-  "runtimePlatform": "R version 4.5.0 (2025-04-11)",
+  "runtimePlatform": "R Under development (unstable) (2025-04-08 r88126 ucrt)",
   "provider": {
     "@id": "https://cran.r-project.org",
     "@type": "Organization",
@@ -247,7 +247,7 @@
     },
     "SystemRequirements": "C99"
   },
-  "fileSize": "2139.969KB",
+  "fileSize": "2326.252KB",
   "citation": [
     {
       "@type": "ScholarlyArticle",

From a24ae095dcadabdac876c43952977e86af29737d Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com>
Date: Tue, 1 Jul 2025 12:30:30 +0100
Subject: [PATCH 11/11] Update URL

---
 DESCRIPTION          | 2 +-
 R/Rogue-package.R    | 4 +++-
 codemeta.json        | 2 +-
 man/Rogue-package.Rd | 3 ++-
 4 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 0c1ead7..8606ab2 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -59,5 +59,5 @@ ByteCompile: true
 Encoding: UTF-8
 Language: en-GB
 VignetteBuilder: knitr
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Roxygen: list(markdown = TRUE)
diff --git a/R/Rogue-package.R b/R/Rogue-package.R
index 97745eb..3009dce 100644
--- a/R/Rogue-package.R
+++ b/R/Rogue-package.R
@@ -22,7 +22,9 @@
 #'
 #' The latter heuristic is implemented for the relative bipartition
 #' "information" content and Pattengale's criterion
-#' _via_ [RogueNaRok](https://rnr.h-its.org/about) \insertCite{Aberer2013}{Rogue}.
+#' _via_ [RogueNaRok](
+#' https://cme.h-its.org/exelixis/web/software/roguenarok/roguenarok.html)
+#' \insertCite{Aberer2013}{Rogue}.
 #'
 #'
 #' ## Citing "Rogue"
diff --git a/codemeta.json b/codemeta.json
index 5836849..caed4ac 100644
--- a/codemeta.json
+++ b/codemeta.json
@@ -247,7 +247,7 @@
     },
     "SystemRequirements": "C99"
   },
-  "fileSize": "2326.252KB",
+  "fileSize": "2326.285KB",
   "citation": [
     {
       "@type": "ScholarlyArticle",
diff --git a/man/Rogue-package.Rd b/man/Rogue-package.Rd
index aca2caa..bec1ca1 100644
--- a/man/Rogue-package.Rd
+++ b/man/Rogue-package.Rd
@@ -29,7 +29,8 @@ dropping all possible sets of up to \emph{n} leaves
 
 The latter heuristic is implemented for the relative bipartition
 "information" content and Pattengale's criterion
-\emph{via} \href{https://rnr.h-its.org/about}{RogueNaRok} \insertCite{Aberer2013}{Rogue}.
+\emph{via} \href{https://cme.h-its.org/exelixis/web/software/roguenarok/roguenarok.html}{RogueNaRok}
+\insertCite{Aberer2013}{Rogue}.
 \subsection{Citing "Rogue"}{
 
 If you find this package useful in your work, Please consider citing