CRAN Package Check Results for Package deeptime

Last updated on 2026-08-03 23:50:33 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	10.01	237.69	247.70	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	17.00	344.00	361.00	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	463.00	473.00	ERROR
r-oldrel-windows-x86_64	2.4.0	24.00	481.00	505.00	OK

Check Details

Version: 2.4.0
Check: for new files in some other directories
Result: NOTE Found the following files/directories: ‘~/tmp/scratch/Rtmp01u1No’ ‘~/tmp/scratch/Rtmp0SyLWn’ ‘~/tmp/scratch/Rtmp0YPT9U’ ‘~/tmp/scratch/Rtmp2fDBcn’ ‘~/tmp/scratch/Rtmp3Kx19m’ ‘~/tmp/scratch/Rtmp4EjvdR’ ‘~/tmp/scratch/Rtmp4JtRSP’ ‘~/tmp/scratch/Rtmp4crHOF’ ‘~/tmp/scratch/Rtmp5XdXEq’ ‘~/tmp/scratch/Rtmp5lzF1J’ ‘~/tmp/scratch/Rtmp5rk20R’ ‘~/tmp/scratch/Rtmp6IK6Rd’ ‘~/tmp/scratch/Rtmp6Jjy6W’ ‘~/tmp/scratch/Rtmp7Y6px2’ ‘~/tmp/scratch/Rtmp86CzUL’ ‘~/tmp/scratch/Rtmp8DFN4X’ ‘~/tmp/scratch/Rtmp8M8ZiG’ ‘~/tmp/scratch/Rtmp8xO9nr’ ‘~/tmp/scratch/Rtmp90apEJ’ ‘~/tmp/scratch/Rtmp92g9FA’ ‘~/tmp/scratch/Rtmp9EsvIG’ ‘~/tmp/scratch/Rtmp9fNsht’ ‘~/tmp/scratch/Rtmp9mXMvg’ ‘~/tmp/scratch/RtmpAP0VXw’ ‘~/tmp/scratch/RtmpAaHEYA’ ‘~/tmp/scratch/RtmpAfOmWw’ ‘~/tmp/scratch/RtmpAzbqrh’ ‘~/tmp/scratch/RtmpB84P2Y’ ‘~/tmp/scratch/RtmpBWloex’ ‘~/tmp/scratch/RtmpBeSWsx’ ‘~/tmp/scratch/RtmpBoIKGh’ ‘~/tmp/scratch/RtmpCTKVrA’ ‘~/tmp/scratch/RtmpDJtMYJ’ ‘~/tmp/scratch/RtmpDSoJhk’ ‘~/tmp/scratch/RtmpDbok79’ ‘~/tmp/scratch/RtmpDhmioD’ ‘~/tmp/scratch/RtmpEDJAaE’ ‘~/tmp/scratch/RtmpEf5l0f’ ‘~/tmp/scratch/RtmpEutPKi’ ‘~/tmp/scratch/RtmpEzX9m0’ ‘~/tmp/scratch/RtmpF51BWq’ ‘~/tmp/scratch/RtmpFWHUEb’ ‘~/tmp/scratch/RtmpFWndxG’ ‘~/tmp/scratch/RtmpFpQrka’ ‘~/tmp/scratch/RtmpGAJXvC’ ‘~/tmp/scratch/RtmpGDVj89’ ‘~/tmp/scratch/RtmpGYw8xD’ ‘~/tmp/scratch/RtmpGwG5h3’ ‘~/tmp/scratch/RtmpGzwQCQ’ ‘~/tmp/scratch/RtmpHCLnWu’ ‘~/tmp/scratch/RtmpHKG1WL’ ‘~/tmp/scratch/RtmpHbh4kO’ ‘~/tmp/scratch/RtmpIE9pSc’ ‘~/tmp/scratch/RtmpIXhfZx’ ‘~/tmp/scratch/RtmpJ6YWrG’ ‘~/tmp/scratch/RtmpJgEYTp’ ‘~/tmp/scratch/RtmpKAta8Q’ ‘~/tmp/scratch/RtmpKdFb7R’ ‘~/tmp/scratch/RtmpL94pCP’ ‘~/tmp/scratch/RtmpMJflF5’ ‘~/tmp/scratch/RtmpMNbOvr’ ‘~/tmp/scratch/RtmpMVcq9D’ ‘~/tmp/scratch/RtmpN1sypX’ ‘~/tmp/scratch/RtmpNQUd0I’ ‘~/tmp/scratch/RtmpNTnFcv’ ‘~/tmp/scratch/RtmpNjBWVl’ ‘~/tmp/scratch/RtmpNkPvD0’ ‘~/tmp/scratch/RtmpNmj1jO’ ‘~/tmp/scratch/RtmpOidzES’ ‘~/tmp/scratch/RtmpP4YRbJ’ ‘~/tmp/scratch/RtmpPUAACv’ ‘~/tmp/scratch/RtmpQnVLWx’ ‘~/tmp/scratch/RtmpRAFMhf’ ‘~/tmp/scratch/RtmpRiLSTK’ ‘~/tmp/scratch/RtmpRvKEiS’ ‘~/tmp/scratch/RtmpRyQbS3’ ‘~/tmp/scratch/RtmpS8OzMZ’ ‘~/tmp/scratch/RtmpS9Vott’ ‘~/tmp/scratch/RtmpSf3LFM’ ‘~/tmp/scratch/RtmpSrcvbM’ ‘~/tmp/scratch/RtmpSzZYOH’ ‘~/tmp/scratch/RtmpSzjGFm’ ‘~/tmp/scratch/RtmpTIWGqg’ ‘~/tmp/scratch/RtmpTMkSaN’ ‘~/tmp/scratch/RtmpUA3Bty’ ‘~/tmp/scratch/RtmpUBjB3r’ ‘~/tmp/scratch/RtmpUzmx9s’ ‘~/tmp/scratch/RtmpVBwXAo’ ‘~/tmp/scratch/RtmpVJZgvW’ ‘~/tmp/scratch/RtmpVOdtiP’ ‘~/tmp/scratch/RtmpVp4sRB’ ‘~/tmp/scratch/RtmpWB54c4’ ‘~/tmp/scratch/RtmpWVceWJ’ ‘~/tmp/scratch/RtmpWVm1ZB’ ‘~/tmp/scratch/RtmpWtlH59’ ‘~/tmp/scratch/RtmpWza3dG’ ‘~/tmp/scratch/RtmpX5gg1N’ ‘~/tmp/scratch/RtmpXBJO3Z’ ‘~/tmp/scratch/RtmpXDVkhJ’ ‘~/tmp/scratch/RtmpY3Uf7J’ ‘~/tmp/scratch/RtmpY7J7HV’ ‘~/tmp/scratch/RtmpYJw5iZ’ ‘~/tmp/scratch/RtmpYUFDLl’ ‘~/tmp/scratch/RtmpYm8y6G’ ‘~/tmp/scratch/RtmpYyNhUI’ ‘~/tmp/scratch/RtmpZGxgFX’ ‘~/tmp/scratch/RtmpaLpUAm’ ‘~/tmp/scratch/RtmpawSEVR’ ‘~/tmp/scratch/RtmpbHr5ZF’ ‘~/tmp/scratch/RtmpbNkyVm’ ‘~/tmp/scratch/RtmpbmRA7f’ ‘~/tmp/scratch/Rtmpcozkm2’ ‘~/tmp/scratch/RtmpdBYQAw’ ‘~/tmp/scratch/Rtmpf0bOZS’ ‘~/tmp/scratch/Rtmpf3263v’ ‘~/tmp/scratch/RtmpfD34TM’ ‘~/tmp/scratch/RtmpflTcI9’ ‘~/tmp/scratch/RtmpgYojxU’ ‘~/tmp/scratch/RtmpgwgYSM’ ‘~/tmp/scratch/RtmpgyhmRW’ ‘~/tmp/scratch/Rtmphb5Afq’ ‘~/tmp/scratch/Rtmpi2jiPR’ ‘~/tmp/scratch/RtmpiACgAH’ ‘~/tmp/scratch/RtmpiYtzJn’ ‘~/tmp/scratch/RtmpidffWM’ ‘~/tmp/scratch/RtmpiygMbq’ ‘~/tmp/scratch/RtmpjvahLl’ ‘~/tmp/scratch/RtmpkINr14’ ‘~/tmp/scratch/RtmplJnPj7’ ‘~/tmp/scratch/RtmplXjkfO’ ‘~/tmp/scratch/RtmpmDkWR7’ ‘~/tmp/scratch/RtmpmJ4Oq9’ ‘~/tmp/scratch/RtmpmMXYLK’ ‘~/tmp/scratch/RtmpmTIpz5’ ‘~/tmp/scratch/Rtmpmfi2zU’ ‘~/tmp/scratch/RtmpnMy78m’ ‘~/tmp/scratch/RtmpnYNfJg’ ‘~/tmp/scratch/RtmpntKx6i’ ‘~/tmp/scratch/Rtmpnv3HtZ’ ‘~/tmp/scratch/Rtmpo96kQC’ ‘~/tmp/scratch/RtmpoLnTPF’ ‘~/tmp/scratch/RtmpoTrAqD’ ‘~/tmp/scratch/RtmpoTuvAo’ ‘~/tmp/scratch/RtmpoXGDve’ ‘~/tmp/scratch/RtmpoxTelO’ ‘~/tmp/scratch/RtmppgWnTu’ ‘~/tmp/scratch/Rtmpr11PE8’ ‘~/tmp/scratch/RtmprT2F5c’ ‘~/tmp/scratch/RtmprlxYKu’ ‘~/tmp/scratch/RtmprnutXM’ ‘~/tmp/scratch/Rtmps2Msga’ ‘~/tmp/scratch/RtmpsAVSix’ ‘~/tmp/scratch/RtmpsbRkbP’ ‘~/tmp/scratch/Rtmpsi6yWo’ ‘~/tmp/scratch/Rtmpt8w4Mx’ ‘~/tmp/scratch/RtmptKbmW1’ ‘~/tmp/scratch/RtmptRIMUF’ ‘~/tmp/scratch/RtmptY6oNM’ ‘~/tmp/scratch/Rtmpue3IrL’ ‘~/tmp/scratch/Rtmpui5Js4’ ‘~/tmp/scratch/RtmpvBoUyP’ ‘~/tmp/scratch/Rtmpvdr7L3’ ‘~/tmp/scratch/RtmpwBKfMU’ ‘~/tmp/scratch/RtmpwFOBxJ’ ‘~/tmp/scratch/Rtmpx0ljHa’ ‘~/tmp/scratch/RtmpyN61Sb’ ‘~/tmp/scratch/RtmpyjEnJB’ ‘~/tmp/scratch/Rtmpz6QOJ4’ ‘~/tmp/scratch/Rtmpzes4Km’ ‘~/tmp/scratch/RtmpzsF9Yg’ ‘~/tmp/scratch/RtmpzuR5JR’ ‘~/tmp/scratch/xvfb-run.0wbWAl’ ‘~/tmp/scratch/xvfb-run.1XjFyt’ ‘~/tmp/scratch/xvfb-run.2VpbTJ’ ‘~/tmp/scratch/xvfb-run.2WM3jX’ ‘~/tmp/scratch/xvfb-run.3ksHAq’ ‘~/tmp/scratch/xvfb-run.4jire9’ ‘~/tmp/scratch/xvfb-run.5GWRHL’ ‘~/tmp/scratch/xvfb-run.6B4Yft’ ‘~/tmp/scratch/xvfb-run.6ynTTV’ ‘~/tmp/scratch/xvfb-run.7io56D’ ‘~/tmp/scratch/xvfb-run.7qy8jG’ ‘~/tmp/scratch/xvfb-run.8dGnaI’ ‘~/tmp/scratch/xvfb-run.8pbUCP’ ‘~/tmp/scratch/xvfb-run.9R1vWR’ ‘~/tmp/scratch/xvfb-run.9WjfZ7’ ‘~/tmp/scratch/xvfb-run.9mQVi7’ ‘~/tmp/scratch/xvfb-run.9zRQ5b’ ‘~/tmp/scratch/xvfb-run.BT4rog’ ‘~/tmp/scratch/xvfb-run.CCYIE8’ ‘~/tmp/scratch/xvfb-run.CfX6EX’ ‘~/tmp/scratch/xvfb-run.D16kI3’ ‘~/tmp/scratch/xvfb-run.DgWCZV’ ‘~/tmp/scratch/xvfb-run.EE1pgT’ ‘~/tmp/scratch/xvfb-run.EUp9ut’ ‘~/tmp/scratch/xvfb-run.FNkRZL’ ‘~/tmp/scratch/xvfb-run.FrUwZM’ ‘~/tmp/scratch/xvfb-run.HRwkTf’ ‘~/tmp/scratch/xvfb-run.HYKCKY’ ‘~/tmp/scratch/xvfb-run.Ih49b2’ ‘~/tmp/scratch/xvfb-run.IqwBo1’ ‘~/tmp/scratch/xvfb-run.Jd1GVa’ ‘~/tmp/scratch/xvfb-run.Js1Ry3’ ‘~/tmp/scratch/xvfb-run.KiuNLl’ ‘~/tmp/scratch/xvfb-run.KmBB6Y’ ‘~/tmp/scratch/xvfb-run.LebZyU’ ‘~/tmp/scratch/xvfb-run.MY8l8A’ ‘~/tmp/scratch/xvfb-run.O6CUR9’ ‘~/tmp/scratch/xvfb-run.PmdSYs’ ‘~/tmp/scratch/xvfb-run.QAeTEp’ ‘~/tmp/scratch/xvfb-run.Qqxl2T’ ‘~/tmp/scratch/xvfb-run.RZiRSW’ ‘~/tmp/scratch/xvfb-run.RdFEgK’ ‘~/tmp/scratch/xvfb-run.VZGr3v’ ‘~/tmp/scratch/xvfb-run.WcdVvh’ ‘~/tmp/scratch/xvfb-run.XbEZkQ’ ‘~/tmp/scratch/xvfb-run.YGPeGd’ ‘~/tmp/scratch/xvfb-run.YHDEfY’ ‘~/tmp/scratch/xvfb-run.YvGFk6’ ‘~/tmp/scratch/xvfb-run.a3GBp8’ ‘~/tmp/scratch/xvfb-run.awdPcY’ ‘~/tmp/scratch/xvfb-run.bHAFf4’ ‘~/tmp/scratch/xvfb-run.biHpJk’ ‘~/tmp/scratch/xvfb-run.c0hlLy’ ‘~/tmp/scratch/xvfb-run.dEOjhS’ ‘~/tmp/scratch/xvfb-run.dzsPog’ ‘~/tmp/scratch/xvfb-run.e2aQCt’ ‘~/tmp/scratch/xvfb-run.ewEJvy’ ‘~/tmp/scratch/xvfb-run.ezGetx’ ‘~/tmp/scratch/xvfb-run.f7bMk8’ ‘~/tmp/scratch/xvfb-run.f8xmj3’ ‘~/tmp/scratch/xvfb-run.fsLyNc’ ‘~/tmp/scratch/xvfb-run.gq4FwR’ ‘~/tmp/scratch/xvfb-run.hEDWvJ’ ‘~/tmp/scratch/xvfb-run.hG3RYf’ ‘~/tmp/scratch/xvfb-run.hGkfRv’ ‘~/tmp/scratch/xvfb-run.jeR02o’ ‘~/tmp/scratch/xvfb-run.lIHmXb’ ‘~/tmp/scratch/xvfb-run.lQLJIa’ ‘~/tmp/scratch/xvfb-run.mUL4hV’ ‘~/tmp/scratch/xvfb-run.nIlhCu’ ‘~/tmp/scratch/xvfb-run.qvQLKw’ ‘~/tmp/scratch/xvfb-run.sDQs0A’ ‘~/tmp/scratch/xvfb-run.t7e8qE’ ‘~/tmp/scratch/xvfb-run.umdWN7’ ‘~/tmp/scratch/xvfb-run.urorIo’ ‘~/tmp/scratch/xvfb-run.yEV88n’ ‘~/tmp/scratch/xvfb-run.zCKmOD’ ‘~/tmp/scratch/xvfb-run.zbX3Ot’ 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