From 1530eb85f47a2450ad09de5c1cac52085d8dbde0 Mon Sep 17 00:00:00 2001
From: Dan Knight <56950335+dan-knight@users.noreply.github.com>
Date: Wed, 2 Apr 2025 15:41:17 -0700
Subject: [PATCH 1/6] Use renv R CMD check action

---
 .github/workflows/{r-lib-check.yaml => R-CMD-check.yaml} | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)
 rename .github/workflows/{r-lib-check.yaml => R-CMD-check.yaml} (73%)

diff --git a/.github/workflows/r-lib-check.yaml b/.github/workflows/R-CMD-check.yaml
similarity index 73%
rename from .github/workflows/r-lib-check.yaml
rename to .github/workflows/R-CMD-check.yaml
index 184c71c1..d328c27c 100644
--- a/.github/workflows/r-lib-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -1,5 +1,5 @@
 ---
-name: R-CMD-check (r-lib)
+name: R CMD check
 'on':
   workflow_dispatch:
   pull_request:
@@ -13,4 +13,4 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: r-lib/actions/setup-tinytex@v2
-      - uses: uclahs-cds/tool-R-CMD-check-action@CEV
+      - uses: uclahs-cds/tool-R-CMD-check-action@renv

From 1e87f4db9e4930bddeb67497c149ed0acfa227ab Mon Sep 17 00:00:00 2001
From: Dan Knight <danknight@mednet.ucla.edu>
Date: Fri, 13 Jun 2025 17:26:22 -0700
Subject: [PATCH 2/6] Update changelog

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

diff --git a/DESCRIPTION b/DESCRIPTION
index 74c250a3..e6f952d9 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: CancerEvolutionVisualization
 Title: Publication Quality Phylogenetic Tree Plots
 Version: 3.0.0
-Date: 2025-03-12
+Date: 2025-06-13
 Authors@R: c(
 	person("Paul Boutros", role = "cre", email = "PBoutros@mednet.ucla.edu"),
 	person("Adriana Salcedo", role = "aut"),
diff --git a/NEWS.md b/NEWS.md
index bcdf38d8..8f13c44c 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# CancerEvolutionVisualization 3.0.0 (2025-03-12)
+# CancerEvolutionVisualization 3.0.0 (2025-06-13)
 
 ## Added
 * Dendrogram mode
@@ -32,6 +32,7 @@
 * Updated the user guide to reflect new features.
 * Fix bug where the x-axis only renders when y-axis is also rendered.
 * Fix issue when creating polygons with more than 2 siblings
+* Use updated `R CMD check` CI/CD action
 
 ## Bug
 * Resolved issue where the spread parameter was not applied in dendrogram mode.

From d8ff412a59f3f37cbf7e5bf83ebb8a304cb714c0 Mon Sep 17 00:00:00 2001
From: Dan Knight <danknight@mednet.ucla.edu>
Date: Fri, 13 Jun 2025 17:39:03 -0700
Subject: [PATCH 3/6] Install OS graphics dependencies

---
 .github/workflows/R-CMD-check.yaml | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index d328c27c..c6ffe827 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -12,5 +12,11 @@ jobs:
   R-CMD-check:
     runs-on: ubuntu-latest
     steps:
+      - name: Install system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y \
+            libjpeg-dev \
+            libpng-dev
       - uses: r-lib/actions/setup-tinytex@v2
       - uses: uclahs-cds/tool-R-CMD-check-action@renv

From 9f77d2ab44d7e87db9d685549c72607ae9bc664a Mon Sep 17 00:00:00 2001
From: Dan Knight <danknight@mednet.ucla.edu>
Date: Fri, 13 Jun 2025 17:52:34 -0700
Subject: [PATCH 4/6] Suggest rmarkdown dependency

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

diff --git a/DESCRIPTION b/DESCRIPTION
index e6f952d9..788c30c3 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -24,6 +24,7 @@ Imports:
     BoutrosLab.plotting.general
 Suggests:
     testthat,
+	rmarkdown,
 	knitr
 VignetteBuilder: knitr
 LazyLoad: yes

From 8232cde7d4800b5bfebc6b9abb309575da1c08bb Mon Sep 17 00:00:00 2001
From: Dan Knight <danknight@mednet.ucla.edu>
Date: Fri, 13 Jun 2025 18:17:15 -0700
Subject: [PATCH 5/6] Update changelog

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

diff --git a/NEWS.md b/NEWS.md
index a18b56d5..8ececee4 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -17,6 +17,7 @@
 * Add support for 1xn and 1x1 heatmaps.
 * Add `get.colours.in.order` function to get a list of colours and corresponding clone ID order.
 * Add `sample.order` and `clone.order` as input parameters to `create.cluster.heatmap`
+* Suggest rmarkdown dependency for rendering vignettes 
 
 ## Update
 * Fixed angle calculation bug where child angles do not follow

From 921c71bf5c5988c8122d9b95d800238abffa38a4 Mon Sep 17 00:00:00 2001
From: Dan Knight <danknight@mednet.ucla.edu>
Date: Fri, 13 Jun 2025 18:17:56 -0700
Subject: [PATCH 6/6] Reference R CMD check CI/CD action by semver

---
 .github/workflows/R-CMD-check.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index c6ffe827..94be2898 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -19,4 +19,4 @@ jobs:
             libjpeg-dev \
             libpng-dev
       - uses: r-lib/actions/setup-tinytex@v2
-      - uses: uclahs-cds/tool-R-CMD-check-action@renv
+      - uses: uclahs-cds/tool-R-CMD-check-action@v2