Move variable unprotection

.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

.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:

.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 }}

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Rogue
 Title: Identify Rogue Taxa in Sets of Phylogenetic Trees
-Version: 2.1.6.9000
+Version: 2.1.7
 Authors@R: c(person("Martin R.", 'Smith',
                     email = "martin.smith@durham.ac.uk", 
                     role = c("aut", "cre", "cph"), 
@@ -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)

NEWS.md

@@ -1,7 +1,8 @@
-# Rogue v2.1.6.9000 (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)).
+- Improve variable protection.
 
 
 # Rogue v2.1.6 (2023-11-29)

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"

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": "2326.285KB",
   "citation": [
     {
       "@type": "ScholarlyArticle",

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.