Last updated on 2026-08-03 14:50:43 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.4.0 | 14.79 | 348.39 | 363.18 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.4.0 | 8.88 | 242.76 | 251.64 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 2.4.0 | 23.00 | 539.84 | 562.84 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 2.4.0 | 9.00 | 227.11 | 236.11 | OK | |
| r-devel-windows-x86_64 | 2.4.0 | 17.00 | 341.00 | 358.00 | OK | |
| r-patched-linux-x86_64 | 2.4.0 | 14.52 | 331.46 | 345.98 | OK | |
| r-release-linux-x86_64 | 2.4.0 | 13.24 | 329.57 | 342.81 | OK | |
| r-release-macos-arm64 | 2.4.0 | 4.00 | 101.00 | 105.00 | OK | |
| r-release-macos-x86_64 | 2.4.0 | 10.00 | 323.00 | 333.00 | OK | |
| r-release-windows-x86_64 | 2.4.0 | 16.00 | 341.00 | 357.00 | OK | |
| r-oldrel-macos-arm64 | 2.4.0 | 4.00 | 95.00 | 99.00 | OK | |
| r-oldrel-macos-x86_64 | 2.4.0 | 10.00 | 330.00 | 340.00 | ERROR | |
| r-oldrel-windows-x86_64 | 2.4.0 | 22.00 | 473.00 | 495.00 | OK |
Version: 2.4.0
Check: for new files in some other directories
Result: NOTE
Found the following files/directories:
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Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.4.0
Check: examples
Result: ERROR
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
Flavor: r-oldrel-macos-x86_64