diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 3769a52..7527b21 100755
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -9,17 +9,16 @@ on:
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.os }}
+    env:
+      # Read the private settylab/ccflowR Remote during pak dependency resolution.
+      GITHUB_PAT: ${{ secrets.SETTYLAB_CI_PAT }}
     strategy:
       fail-fast: false
       matrix:
+        # R >= 4.3 only: the package needs SeuratObject (>= 5.0.0), which pulls
+        # Matrix (>= 1.6.4) requiring R >= 4.4 — R 4.2 cannot solve the graph.
         os: [ubuntu-latest, macos-latest, windows-latest]
-        r-version: ['4.2', '4.3', '4.4']
-        exclude:
-          # Reduce matrix size
-          - os: macos-latest
-            r-version: '4.2'
-          - os: windows-latest
-            r-version: '4.2'
+        r-version: ['4.3', '4.4']
 
     steps:
       - uses: actions/checkout@v4
@@ -45,6 +44,9 @@ jobs:
   test-coverage:
     runs-on: ubuntu-latest
     needs: R-CMD-check
+    env:
+      # Read the private settylab/ccflowR Remote during pak dependency resolution.
+      GITHUB_PAT: ${{ secrets.SETTYLAB_CI_PAT }}
     steps:
       - uses: actions/checkout@v4
 
@@ -68,6 +70,9 @@ jobs:
 
   lint:
     runs-on: ubuntu-latest
+    env:
+      # Read the private settylab/ccflowR Remote during pak dependency resolution.
+      GITHUB_PAT: ${{ secrets.SETTYLAB_CI_PAT }}
     steps:
       - uses: actions/checkout@v4
 
diff --git a/notebooks/01-getting-started.ipynb b/notebooks/01-getting-started.ipynb
index 2bb3e90..f4ad4b0 100644
--- a/notebooks/01-getting-started.ipynb
+++ b/notebooks/01-getting-started.ipynb
@@ -718,14 +718,14 @@
     "    stop(\"No ligand-target links remain for plotting. Try lowering the filtering threshold or increasing TOP_N_LIGANDS.\")\n",
     "}\n",
     "\n",
-    "nichenetr::make_heatmap_ggplot(\n",
+    "print(nichenetr::make_heatmap_ggplot(\n",
     "    vis_matrix,\n",
     "    y_name = \"Predicted target gene\",\n",
     "    x_name = \"Prioritized ligand\",\n",
     "    legend_title = \"Regulatory\\npotential\",\n",
     "    color = \"purple\",\n",
     "    x_axis_position = \"top\"\n",
-    ")"
+    "))\n"
    ],
    "id": "cell01-034"
   },
diff --git a/notebooks/02-standard-workflow.ipynb b/notebooks/02-standard-workflow.ipynb
index 59759e6..3ce8eac 100644
--- a/notebooks/02-standard-workflow.ipynb
+++ b/notebooks/02-standard-workflow.ipynb
@@ -515,7 +515,7 @@
     "activity_matrix <- as.matrix(activity_scores[, \"aupr_corrected\", drop = FALSE])\n",
     "rownames(activity_matrix) <- activity_scores$test_ligand\n",
     "colnames(activity_matrix) <- \"AUPR_c\"\n",
-    "activity_matrix <- activity_matrix[best_ligands, , drop = FALSE]\n",
+    "activity_matrix <- activity_matrix[rev(best_ligands), , drop = FALSE]  # rev() so the highest score is the TOP row\n",
     "\n",
     "nichenetr::make_heatmap_ggplot(\n",
     "    activity_matrix,\n",
@@ -555,13 +555,13 @@
     "}\n",
     "vis_matrix <- vis_matrix[rowSums(vis_matrix) > 0, , drop = FALSE]\n",
     "\n",
-    "nichenetr::make_heatmap_ggplot(\n",
+    "print(nichenetr::make_heatmap_ggplot(\n",
     "    vis_matrix,\n",
     "    y_name = \"Target Gene\",\n",
     "    x_name = \"Predicted Ligand\",\n",
     "    legend_title = \"Regulatory\\nPotential\",\n",
     "    color = \"purple\"\n",
-    ")"
+    "))\n"
    ],
    "id": "cell02-036"
   },