From 56e587d9c361da309ceea27bddb23b0a49f40ffc Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com>
Date: Thu, 27 Jun 2024 12:16:47 +0100
Subject: [PATCH] Update R-CMD-check.yml

---
 .github/workflows/R-CMD-check.yml | 19 ++++++++++---------
 1 file changed, 10 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yml b/.github/workflows/R-CMD-check.yml
index 806cb3925..674e726e2 100644
--- a/.github/workflows/R-CMD-check.yml
+++ b/.github/workflows/R-CMD-check.yml
@@ -48,9 +48,9 @@ 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"}
-          - {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: ubuntu-latest, r: '4.1', 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"}
 
     env:
       _R_CHECK_CRAN_INCOMING_: true # Seemingly not set by --as-cran
@@ -71,21 +71,21 @@ jobs:
         uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
+          extra-repositories: https://ms609.github.io/packages/
 
       - name: Install apt packages (Linux)
         if: runner.os == 'Linux'
         run: |
           sudo apt-get update
-          sudo apt-get install -y \
-            texlive-latex-base texlive-fonts-recommended libcurl4-openssl-dev \
-            libglpk40
-
+          sudo apt-get install -y texlive-latex-base texlive-fonts-recommended
+                      
       - name: Set up R dependencies (Windows)
         if: runner.os == 'Windows'
         uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: |
             RcppCore/Rcpp
+            ms609/TreeTools
             ms609/TreeDistData
           needs: |
             check
@@ -96,9 +96,10 @@ jobs:
         uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: |
-            ms609/TreeDistData
             RcppCore/Rcpp
-            phangorn=?ignore-before-r=4.1.0
+            ms609/TreeTools
+            ms609/TreeDistData
+            phangorn=?ignore-before-r=4.4.0
             ggplot2=?ignore-before-r=4.4.0
             hypervolume=?ignore-before-r=4.4.0
             kdensity=?ignore-before-r=4.4.0