deeptime

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
...[truncated]...
, 
+     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

Error(s) in re-building vignettes:
--- re-building 'coord.Rmd' using rmarkdown
--- finished re-building 'coord.Rmd'

--- re-building 'coord_geo.Rmd' using rmarkdown
--- finished re-building 'coord_geo.Rmd'

--- re-building 'geo.Rmd' using rmarkdown

Quitting from geo.Rmd:34-40 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `GET_macrostrat()`:
! Content not found. Check your request.
---
Backtrace:
    ▆
 1. └─rmacrostrat::get_units(column_id = 489, interval_name = "Cretaceous")
 2.   └─rmacrostrat:::GET_macrostrat(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'geo.Rmd' failed with diagnostics:
Content not found. Check your request.
--- failed re-building 'geo.Rmd'

--- re-building 'ggarrange2.Rmd' using rmarkdown
--- finished re-building 'ggarrange2.Rmd'

--- re-building 'phylogenies.Rmd' using rmarkdown
--- finished re-building 'phylogenies.Rmd'

--- re-building 'time.Rmd' using rmarkdown
--- finished re-building 'time.Rmd'

--- re-building 'traits.Rmd' using rmarkdown
--- finished re-building 'traits.Rmd'

SUMMARY: processing the following file failed:
  'geo.Rmd'

Error: Vignette re-building failed.
Execution halted