CRAN Package Check Results for Package deeptime

Last updated on 2026-07-21 18:50:56 CEST.

Flavor	Version	Tinstall	Tcheck	Ttotal	Status	Flags
r-devel-linux-x86_64-debian-clang	2.4.0	14.10	348.54	362.64	OK
r-devel-linux-x86_64-debian-gcc	2.4.0	10.57	235.21	245.78	OK
r-devel-linux-x86_64-fedora-clang	2.4.0	24.00	375.50	399.50	OK
r-devel-linux-x86_64-fedora-gcc	2.4.0	10.00	233.63	243.63	OK
r-devel-windows-x86_64	2.4.0	18.00	344.00	362.00	OK
r-patched-linux-x86_64	2.4.0	14.21	330.00	344.21	OK
r-release-linux-x86_64	2.4.0	12.78	332.02	344.80	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	17.00	345.00	362.00	OK
r-oldrel-macos-arm64	2.4.0	4.00	95.00	99.00	OK
r-oldrel-macos-x86_64	2.4.0	11.00	641.00	652.00	ERROR
r-oldrel-windows-x86_64	2.4.0	22.00	491.00	513.00	OK

Check Details

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