From e7f351ac93f8e4c1f3fb7c9f4fa74b56ed59f62c Mon Sep 17 00:00:00 2001
From: Timothy Weigand <68024672+tmweigand@users.noreply.github.com>
Date: Sun, 5 Apr 2026 17:55:42 -0400
Subject: [PATCH 1/2] switch to ctxR github for bug fix

---
 .github/workflows/bookdown.yml      | 3 +++
 .github/workflows/test_bookdown.yml | 3 +++
 2 files changed, 6 insertions(+)

diff --git a/.github/workflows/bookdown.yml b/.github/workflows/bookdown.yml
index 00b7642..c5be8c7 100644
--- a/.github/workflows/bookdown.yml
+++ b/.github/workflows/bookdown.yml
@@ -40,6 +40,9 @@ jobs:
           # Pin factoextra
           Rscript -e 'remotes::install_version("factoextra", version = "1.0.7", repos = "https://cran.rstudio.com")'
 
+          # Install ctxR from GitHub
+          Rscript -e 'remotes::install_github("USEPA/ctxR")'
+
           # Now install remaining CRAN deps from DESCRIPTION
           Rscript -e 'remotes::install_deps(dependencies = TRUE, upgrade = "never")'
 
diff --git a/.github/workflows/test_bookdown.yml b/.github/workflows/test_bookdown.yml
index ff083fc..0ef13dd 100644
--- a/.github/workflows/test_bookdown.yml
+++ b/.github/workflows/test_bookdown.yml
@@ -43,6 +43,9 @@ jobs:
           # Pin factoextra
           Rscript -e 'remotes::install_version("factoextra", version = "1.0.7", repos = "https://cran.rstudio.com")'
 
+          # Install ctxR from GitHub
+          Rscript -e 'remotes::install_github("USEPA/ctxR")'
+
           # Now install remaining CRAN deps from DESCRIPTION
           Rscript -e 'remotes::install_deps(dependencies = TRUE, upgrade = "never")'
 

From 4deb8b27d2c7b438a11d2255f1c3586f040bd16b Mon Sep 17 00:00:00 2001
From: Timothy Weigand <68024672+tmweigand@users.noreply.github.com>
Date: Sun, 5 Apr 2026 21:38:46 -0400
Subject: [PATCH 2/2] adds github_token for pulling ctxR

---
 .github/workflows/bookdown.yml      | 4 +++-
 .github/workflows/test_bookdown.yml | 4 +++-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/bookdown.yml b/.github/workflows/bookdown.yml
index c5be8c7..3871261 100644
--- a/.github/workflows/bookdown.yml
+++ b/.github/workflows/bookdown.yml
@@ -28,6 +28,8 @@ jobs:
           brew install pandoc
 
       - name: Install CRAN & Bioconductor packages
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
           Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes")'
 
@@ -41,7 +43,7 @@ jobs:
           Rscript -e 'remotes::install_version("factoextra", version = "1.0.7", repos = "https://cran.rstudio.com")'
 
           # Install ctxR from GitHub
-          Rscript -e 'remotes::install_github("USEPA/ctxR")'
+          Rscript -e 'remotes::install_github("USEPA/ctxR", auth_token = Sys.getenv("GITHUB_TOKEN"))'
 
           # Now install remaining CRAN deps from DESCRIPTION
           Rscript -e 'remotes::install_deps(dependencies = TRUE, upgrade = "never")'
diff --git a/.github/workflows/test_bookdown.yml b/.github/workflows/test_bookdown.yml
index 0ef13dd..48faf40 100644
--- a/.github/workflows/test_bookdown.yml
+++ b/.github/workflows/test_bookdown.yml
@@ -31,6 +31,8 @@ jobs:
           brew install pandoc
 
       - name: Install CRAN & Bioconductor packages
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
           Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes")'
 
@@ -44,7 +46,7 @@ jobs:
           Rscript -e 'remotes::install_version("factoextra", version = "1.0.7", repos = "https://cran.rstudio.com")'
 
           # Install ctxR from GitHub
-          Rscript -e 'remotes::install_github("USEPA/ctxR")'
+          Rscript -e 'remotes::install_github("USEPA/ctxR", auth_token = Sys.getenv("GITHUB_TOKEN"))'
 
           # Now install remaining CRAN deps from DESCRIPTION
           Rscript -e 'remotes::install_deps(dependencies = TRUE, upgrade = "never")'