Running examples in ‘deeptime-Ex.R’ failed
The error most likely occurred in:

> ### Name: geom_text_clade
> ### Title: Label clades on a phylogenetic tree plotted with ggtree
> ### Aliases: geom_text_clade
> 
> ### ** Examples
> 
> library(ggplot2)
> ## Don't show: 
> if (require(ggtree) && require(phytools)) withAutoprint({ # examplesIf
+ ## End(Don't show)
+ library(ggtree)
+ library(phytools)
+ data(primate.tree)
+ # single annotation
+ revts(ggtree(primate.tree)) +
+   geom_text_clade(label = "Hominoidea", node = 114, extend = c(0.1, 0.1)) +
+   coord_geo_radial()
+ 
+ # data frame of clade labels
+ clades.df <- data.frame(
+   clade = c("Lorisoidea", "Lemuroidea", "Tarsioidea", "Ceboidea",
+             "Cercopithecoidea", "Hominoidea"),
+   node = c(166, 146, 144, 120, 95, 114)
+ )
+ revts(ggtree(primate.tree)) %<+% clades.df +
+   geom_text_clade(aes(label = clade), extend = c(0.1, 0.1)) +
+   coord_geo_radial()
+ 
+ # display with other tip data
+ data(primate.data)
+ activity <- subset(primate.data, select = "Activity_pattern")
+ revts(gheatmap(ggtree(primate.tree), activity, offset = -70,
+                colnames = FALSE, width = 0.03, color = NA)) %<+% clades.df +
+   geom_text_clade(aes(label = clade), extend = c(0.1, 0.1),
+                   position = position_nudge(x = 10)) +
+   coord_geo_radial()
+ ## Don't show: 
+ }) # examplesIf
Loading required package: ggtree
ggtree v3.15.0 Learn more at https://yulab-smu.top/contribution-tree-data/

Please cite:

Guangchuang Yu.  Data Integration, Manipulation and Visualization of
Phylogenetic Trees (1st edition). Chapman and Hall/CRC. 2022,
doi:10.1201/9781003279242, ISBN: 9781032233574
Loading required package: phytools
Loading required package: ape

Attaching package: ‘ape’

The following object is masked from ‘package:ggtree’:

    rotate

Loading required package: maps
> library(ggtree)
> library(phytools)
> data(primate.tree)
> revts(ggtree(primate.tree)) + geom_text_clade(label = "Hominoidea", node = 114, 
+     extend = c(0.1, 0.1)) + coord_geo_radial()
Warning in fortify(data, ...) : Arguments in `...` must be used.
✖ Problematic arguments:
• as.Date = as.Date
• yscale_mapping = yscale_mapping
• hang = hang
ℹ Did you misspell an argument name?
> clades.df <- data.frame(clade = c("Lorisoidea", "Lemuroidea", "Tarsioidea", 
+     "Ceboidea", "Cercopithecoidea", "Hominoidea"), node = c(166, 146, 144, 120, 95, 
+     114))
> revts(ggtree(primate.tree)) %<+% clades.df + geom_text_clade(aes(label = clade), 
+     extend = c(0.1, 0.1)) + coord_geo_radial()
Warning in fortify(data, ...) : Arguments in `...` must be used.
✖ Problematic arguments:
• as.Date = as.Date
• yscale_mapping = yscale_mapping
• hang = hang
ℹ Did you misspell an argument name?
> data(primate.data)
> activity <- subset(primate.data, select = "Activity_pattern")
> revts(gheatmap(ggtree(primate.tree), activity, offset = -70, colnames = FALSE, 
+     width = 0.03, color = NA)) %<+% clades.df + geom_text_clade(aes(label = clade), 
+     extend = c(0.1, 0.1), position = position_nudge(x = 10)) + coord_geo_radial()
Warning in fortify(data, ...) : Arguments in `...` must be used.
✖ Problematic arguments:
• as.Date = as.Date
• yscale_mapping = yscale_mapping
• hang = hang
ℹ Did you misspell an argument name?
Scale for y is already present.
Adding another scale for y, which will replace the existing scale.
Error: <ggtree> object properties are invalid:
- @mapping must be <ggplot2::mapping>, not S3<data.frame>
Execution halted