• using R version 4.5.2 Patched (2026-01-31 r89382)
• using platform: x86_64-apple-darwin20
• R was compiled by     Apple clang version 14.0.0 (clang-1400.0.29.202)     GNU Fortran (GCC) 14.2.0
• running under: macOS Ventura 13.3.1
• using session charset: UTF-8
• checking for file ‘deeptime/DESCRIPTION’ ... OK
• this is package ‘deeptime’ version ‘2.4.0’
• package encoding: UTF-8
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• checking whether package ‘deeptime’ can be installed ... [12s/40s] OK See the install log for details.
• checking installed package size ... INFO   installed size is 5.3Mb   sub-directories of 1Mb or more:     doc 3.1Mb     help 1.5Mb
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• checking examples ... [18s/56s] 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
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• checking tests ... [73s/250s] OK   Running ‘testthat.R’ [73s/249s]
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• checking package vignettes ... OK
• checking re-building of vignette outputs ... [98s/272s] OK
• checking PDF version of manual ... [11s/18s] OK
• DONE

Status: 1 ERROR