fix CI

Author: MelodyJIN-Y

.github/workflows/pkgdown.yml

@@ -141,17 +141,37 @@ jobs:
         run: |
           if (!requireNamespace("BiocManager", quietly = TRUE))
               install.packages("BiocManager")
+          if (!requireNamespace("remotes", quietly = TRUE))
+              install.packages("remotes")
+          # smoother (destiny dependency) was archived from CRAN on
+          # 2025-12-19, so BiocManager::install("destiny") can no longer
+          # resolve it from PPM. Install the last archived version first.
+          if (!requireNamespace("smoother", quietly = TRUE))
+              remotes::install_version(
+                  "smoother", version = "1.3",
+                  repos = "https://cloud.r-project.org",
+                  upgrade = "never"
+              )
           BiocManager::install(
               c("ComplexHeatmap",   # Module 5 heatmap
                 "slingshot",        # Module 6 principal-curve pseudotime
                 "destiny",          # Module 6 diffusion pseudotime (DPT)
                 "scater"),          # Module 6 SCE helpers / plotting
               update = FALSE, ask = FALSE
           )
-          if (!requireNamespace("remotes", quietly = TRUE))
-              install.packages("remotes")
-          remotes::install_github("jiadongm/PhiSpace/pkg", upgrade = "never")
-          remotes::install_github("meiosis97/NeighbourNet", upgrade = "never")
+          # Use pak for the GitHub installs. The remotes package (>=2.5)
+          # errors with "can't convert package edgeR with RemoteType
+          # 'bioconductor' to remote" when a Bioconductor-installed
+          # transitive dependency is already on the library path; pak
+          # resolves Bioconductor remotes correctly.
+          if (!requireNamespace("pak", quietly = TRUE))
+              install.packages("pak")
+          pak::pkg_install(
+              c("github::jiadongm/PhiSpace/pkg",
+                "github::meiosis97/NeighbourNet"),
+              ask = FALSE,
+              upgrade = FALSE
+          )
         shell: Rscript {0}
 
       # Install local package (needed for pkgdown to build reference docs)

vignettes/00_setup.Rmd

@@ -200,6 +200,22 @@ if (!pkgbuild::has_build_tools(debug = FALSE)) {
 if (!requireNamespace("BiocManager", quietly = TRUE)) {
     install.packages("BiocManager")
 }
+if (!requireNamespace("remotes", quietly = TRUE)) {
+    install.packages("remotes")
+}
+
+# `smoother` is a transitive dependency of `destiny` that was archived
+# from CRAN on 2025-12-19. BiocManager / install.packages can no longer
+# resolve it, so install the last archived version directly before
+# pulling destiny.
+if (!requireNamespace("smoother", quietly = TRUE)) {
+    remotes::install_version(
+        "smoother", version = "1.3",
+        repos = "https://cloud.r-project.org",
+        upgrade = "never"
+    )
+}
+
 BiocManager::install(
     c("ComplexHeatmap",   # Module 5 heatmap
       "slingshot",        # Module 6 principal-curve pseudotime
@@ -209,11 +225,20 @@ BiocManager::install(
 )
 
 # 3. GitHub-only packages — source-only, will trigger compilation.
-if (!requireNamespace("remotes", quietly = TRUE)) {
-    install.packages("remotes")
+#    We use `pak` rather than `remotes::install_github` because newer
+#    versions of remotes raise "can't convert package edgeR with
+#    RemoteType 'bioconductor' to remote" when a Bioconductor-installed
+#    package (like edgeR) is on the library path. pak handles
+#    Bioconductor remotes correctly.
+if (!requireNamespace("pak", quietly = TRUE)) {
+    install.packages("pak")
 }
-remotes::install_github("jiadongm/PhiSpace/pkg", upgrade = "never")
-remotes::install_github("meiosis97/NeighbourNet", upgrade = "never")
+pak::pkg_install(
+    c("github::jiadongm/PhiSpace/pkg",
+      "github::meiosis97/NeighbourNet"),
+    ask = FALSE,
+    upgrade = FALSE
+)
 ```
 
 ### 3c. Verify every package loaded successfully