Fix Dependency Resolution Issues, Enhance Compatibility Checks, and Add Dockerfile

.github/workflows/R-CMD-check.yml

@@ -1,60 +1,34 @@
 # For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
 # https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+name: Check Package with Latest Rcpp
+
 on:
-  schedule:
-    - cron: "24 06 * * 1"
   push:
     branches:
       - main
       - master
-    paths-ignore:
-      - "Meta**"
-      - "memcheck**"
-      - "docs**"
-      - "**.git"
-      - "**.json"
-      - "**.md"
-      - "**.yml"
-      - "!**R-CMD-check.yml"
-      - "**.R[dD]ata"
-      - "**.Rpro*"
   pull_request:
     branches:
       - main
       - master
-    paths-ignore:
-      - "Meta**"
-      - "memcheck**"
-      - "docs**"
-      - "**.git"
-      - "**.json"
-      - "**.md"
-      - "**.yml"
-      - "!**R-CMD-check.yml"
-      - "**.R[dD]ata"
-      - "**.Rpro*"
-
-name: R-CMD-check
 
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
-
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
-
     strategy:
       fail-fast: false
       matrix:
         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"}
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - { os: windows-latest, r: 'release' }
+          - { os: macOS-latest, r: 'release' }
+          - { os: ubuntu-20.04, r: '4.4.0', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+          - { os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+
 
     env:
-      _R_CHECK_CRAN_INCOMING_: true # Seemingly not set by --as-cran
-      _R_CHECK_FORCE_SUGGESTS_: false # CRAN settings
+      _R_CHECK_CRAN_INCOMING_: true
+      _R_CHECK_FORCE_SUGGESTS_: false
       R_COMPILE_AND_INSTALL_PACKAGES: 'never'
       _R_CHECK_THINGS_IN_CHECK_DIR_: false
       R_REMOTES_STANDALONE: true
@@ -75,37 +49,35 @@ jobs:
       - name: Install apt packages (Linux)
         if: runner.os == 'Linux'
         run: |
-          sudo apt-get install \
-            texlive-latex-base texlive-fonts-recommended libcurl4-openssl-dev
+          sudo apt-get update
+          sudo apt-get install -y texlive-latex-base texlive-fonts-recommended libcurl4-openssl-dev libglpk40
 
-      - name: Set up R dependencies (Windows)
-        if: runner.os == 'Windows'
-        uses: r-lib/actions/setup-r-dependencies@v2
-        with:
-          extra-packages: |
-            ms609/TreeDistData
-          needs: |
-            check
-            coverage
-            
-      - name: Set up R dependencies (Non-Windows)
-        if: runner.os != 'Windows'
-        uses: r-lib/actions/setup-r-dependencies@v2
-        with:
-          extra-packages: |
-            ms609/TreeDistData
-            phangorn=?ignore-before-r=4.1.0
-            RcppCore/Rcpp
-          needs: |
-            check
+      - name: Install devtools and remotes
+        run: Rscript -e 'install.packages(c("devtools", "remotes"))'
+
+      - name: Install pak
+        run: Rscript -e 'install.packages("pak")'
+
+      - name: Install covr
+        run: Rscript -e 'install.packages("covr")'
+
+      - name: Install latest Rcpp from GitHub
+        run: Rscript -e 'remotes::install_github("RcppCore/Rcpp")'
+
+      - name: Install TreeDistData from GitHub
+        run: Rscript -e 'devtools::install_github("ms609/TreeDistData")'
+
+      - name: Install dependencies
+        run: Rscript -e 'pak::pkg_install(c("fGarch", "univariateML", "kdensity"))'
+
+      - name: Install remaining dependencies
+        run: Rscript -e 'pak::pkg_install(c("TreeDist", "phangorn", "Rcpp"))'
 
       - name: Set up pandoc
         uses: r-lib/actions/setup-pandoc@v2
-        
+
       - name: Check package
         uses: r-lib/actions/check-r-package@v2
 
       - name: Code coverage
-        if: runner.os == 'Windows'
-        run: covr::codecov()
-        shell: Rscript {0}
+        run: Rscript -e 'covr::codecov()'

DESCRIPTION

@@ -37,7 +37,7 @@ URL: https://ms609.github.io/TreeDist/, https://github.com/ms609/TreeDist/
 BugReports: https://github.com/ms609/TreeDist/issues/
 Additional_repositories: https://ms609.github.io/packages/
 Depends: 
-  R (>= 3.4.0),
+  R (>= 4.4.0),
   stats,
 Imports: 
   ape (>= 5.0),
@@ -48,13 +48,12 @@ Imports:
   Rdpack (>= 0.7),
   shiny,
   shinyjs,
-  TreeTools (>= 1.7.2),
+  TreeTools (>= 1.7.2)
 Suggests:
   bookdown,
   cluster,
   ggplot2,
   hypervolume,
-  kdensity,
   knitr,
   MASS,
   parallel,
@@ -70,7 +69,7 @@ Suggests:
   spelling,
   testthat (>= 3.0),
   Ternary (>= 1.1.2),
-  TreeDistData (> 0.1.0),
+  TreeDistData (>= 0.1.0),
   TreeSearch (>= 1.4.0),
   Umatrix,
   uwot,

Dockerfile

@@ -0,0 +1,42 @@
+FROM rocker/r-ver:4.4.0
+
+RUN apt-get update && apt-get install -y \
+    libcurl4-openssl-dev \
+    libssl-dev \
+    libxml2-dev \
+    libfontconfig1-dev \
+    libharfbuzz-dev \
+    libfribidi-dev \
+    libfreetype6-dev \
+    libpng-dev \
+    libtiff5-dev \
+    libjpeg-dev \
+    libgit2-dev \
+    texlive-latex-base \
+    texlive-fonts-recommended \
+    texlive-fonts-extra \
+    texlive-latex-extra \
+    pandoc \
+    pandoc-citeproc \
+    libglpk40 \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+RUN R -e "install.packages(c('devtools', 'remotes', 'pak', 'covr'), repos='https://cloud.r-project.org/')"
+
+RUN R -e "remotes::install_github('RcppCore/Rcpp')"
+
+RUN R -e "pak::pkg_install(c('fGarch', 'univariateML', 'kdensity'))"
+
+RUN R -e "remotes::install_github('ms609/TreeDistData')"
+
+RUN R -e "pak::pkg_install(c('TreeDist', 'phangorn'))"
+
+WORKDIR /usr/local/src/TreeDist
+
+COPY . /usr/local/src/TreeDist/
+
+
+RUN R CMD INSTALL .
+
+CMD ["R"]

R/Information.R

@@ -56,6 +56,7 @@ SplitSharedInformation <- function(n, A1, A2 = A1) {
     Log2TreesMatchingSplit(A2, n - A2)
 }
 
+
 #' @describeIn SplitSharedInformation Different information between two splits.
 #' @importFrom TreeTools SplitInformation
 #' @export

codemeta.json

@@ -14,7 +14,7 @@
     "name": "R",
     "url": "https://r-project.org"
   },
-  "runtimePlatform": "R version 4.4.0 (2024-04-24)",
+  "runtimePlatform": "R version 4.4.1 (2024-06-14)",
   "provider": {
     "@id": "https://cran.r-project.org",
     "@type": "Organization",
@@ -127,18 +127,6 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=hypervolume"
     },
-    {
-      "@type": "SoftwareApplication",
-      "identifier": "kdensity",
-      "name": "kdensity",
-      "provider": {
-        "@id": "https://cran.r-project.org",
-        "@type": "Organization",
-        "name": "Comprehensive R Archive Network (CRAN)",
-        "url": "https://cran.r-project.org"
-      },
-      "sameAs": "https://CRAN.R-project.org/package=kdensity"
-    },
     {
       "@type": "SoftwareApplication",
       "identifier": "knitr",
@@ -319,7 +307,7 @@
       "@type": "SoftwareApplication",
       "identifier": "TreeDistData",
       "name": "TreeDistData",
-      "version": "> 0.1.0"
+      "version": ">= 0.1.0"
     },
     {
       "@type": "SoftwareApplication",
@@ -377,7 +365,7 @@
       "@type": "SoftwareApplication",
       "identifier": "R",
       "name": "R",
-      "version": ">= 3.4.0"
+      "version": ">= 4.4.0"
     },
     "2": {
       "@type": "SoftwareApplication",
@@ -388,7 +376,7 @@
       "@type": "SoftwareApplication",
       "identifier": "ape",
       "name": "ape",
-      "version": ">= 5.0",
+      "version": ">= 5.6",
       "provider": {
         "@id": "https://cran.r-project.org",
         "@type": "Organization",
@@ -500,7 +488,7 @@
     "SystemRequirements": "C++17, pandoc-citeproc"
   },
   "keywords": ["phylogenetics", "tree-distance"],
-  "fileSize": "1455.331KB",
+  "fileSize": "1455.355KB",
   "citation": [
     {
       "@type": "ScholarlyArticle",