From 69b018e042ad2488758719115b9ffdcaa46519e0 Mon Sep 17 00:00:00 2001
From: ms609-agent <313734811+ms609-agent@users.noreply.github.com>
Date: Wed, 2 Sep 2026 10:07:56 +0100
Subject: [PATCH] Don't attach plotly in landscapes vignette

`library("plotly")` in landscapes.Rmd put `plotly::layout()` on the search
path.  Where vignettes are re-built in a shared R session, this masked
`graphics::layout()` in the subsequently built treespace.Rmd, whose
`plot-mapping-5d` chunk failed with

    no applicable method for 'layout' applied to an object of
    class "c('double', 'numeric')"

Use `plotly::` prefixes instead, and qualify `graphics::layout()` in
treespace.Rmd so the chunk is robust to any future masking.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
---
 vignettes/landscapes.Rmd | 6 +++---
 vignettes/treespace.Rmd  | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/vignettes/landscapes.Rmd b/vignettes/landscapes.Rmd
index 70d7a5875..b9e23050d 100644
--- a/vignettes/landscapes.Rmd
+++ b/vignettes/landscapes.Rmd
@@ -115,9 +115,9 @@ A variety of R add-on packages facilitate three-dimensional plots.
 
 ```{r plot-3d, message = FALSE}
 if (requireNamespace("plotly", quietly = TRUE)) {
-  library("plotly", quietly = TRUE)
-  fig <- plot_ly(x = x, y = y, z = z)
-  fig <- fig %>% add_surface()
+  # Don't attach plotly: it would mask `graphics::layout()` in later vignettes
+  fig <- plotly::plot_ly(x = x, y = y, z = z)
+  fig <- plotly::add_surface(fig)
   fig
 } else {
   print("Run `install.packages('plotly')` to view this output")
diff --git a/vignettes/treespace.Rmd b/vignettes/treespace.Rmd
index 62e2bbec5..3c18cdfea 100644
--- a/vignettes/treespace.Rmd
+++ b/vignettes/treespace.Rmd
@@ -293,7 +293,7 @@ plotSeq <- matrix(0, nDim, nDim)
 plotSeq[upper.tri(plotSeq)] <- seq_len(nDim * (nDim - 1) / 2)
 plotSeq <- t(plotSeq[-nDim, -1])
 plotSeq[nDim * 1:3] <- (nDim * (nDim - 1) / 2) + 1:3
-layout(plotSeq)
+graphics::layout(plotSeq)
 par(mar = rep(0.1, 4))
 
 for (i in 2:nDim) for (j in seq_len(i - 1)) {