CRAN Package Check Results for Package deeptime

Last updated on 2026-11-02 05:53:07 CET.

Flavor	Version	Tinstall	Tcheck	Ttotal	Status	Flags
r-devel-linux-x86_64-debian-clang	2.4.0	14.19	350.59	364.78	OK
r-devel-linux-x86_64-debian-gcc	2.4.0	9.76	242.32	252.08	OK
r-devel-linux-x86_64-fedora-clang	2.4.0			237.27	OK
r-devel-linux-x86_64-fedora-gcc	2.4.0	10.00	243.99	253.99	OK
r-devel-windows-x86_64	2.4.0	18.00	359.00	377.00	OK
r-patched-linux-x86_64	2.4.0	14.78	324.80	339.58	OK
r-release-linux-x86_64	2.4.0	13.55	263.37	276.92	ERROR
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	392.00	408.00	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	453.00	463.00	ERROR
r-oldrel-windows-x86_64	2.4.0	24.00	452.00	476.00	OK

Check Details

Version: 2.4.0
Check: tests
Result: ERROR Running ‘testthat.R’ [62s/91s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(deeptime) > > test_check("deeptime") viewport[GRID.VP.418] viewport[GRID.VP.569] Saving _problems/test-guides-194.R Saving _problems/test-guides-210.R NULL NULL NULL [ FAIL 2 | WARN 0 | SKIP 38 | PASS 134 ] ══ Skipped tests (38) ══════════════════════════════════════════════════════════ • On CRAN (27): 'test-coord_geo.R:67:1', 'test-coord_geo.R:92:3', 'test-coord_geo.R:133:1', 'test-coord_geo.R:148:1', 'test-coord_geo.R:163:1', 'test-coord_geo.R:184:1', 'test-coord_trans_flip.R:1:1', 'test-coord_trans_xy.R:1:1', 'test-disparity_through_time.R:1:1', 'test-facet_color.R:1:1', 'test-facet_color.R:78:1', 'test-facet_color.R:121:1', 'test-facet_color.R:167:1', 'test-get_scale_data.R:14:3', 'test-guides.R:1:1', 'test-guides.R:73:1', 'test-guides.R:88:1', 'test-guides.R:103:1', 'test-guides.R:125:1', 'test-patterns.R:42:1', 'test-patterns.R:55:1', 'test-patterns.R:76:1', 'test-phylomorpho.R:1:1', 'test-points_range.R:1:1', 'test-scales.R:1:1', 'test-scales.R:14:1', 'test-scales.R:27:1' • R.Version()$os != "mingw32" is TRUE (2): 'test-patterns.R:9:3', 'test-patterns.R:99:3' • {ggtree} is not installed (9): 'test-coord_geo.R:202:3', 'test-coord_geo.R:214:3', 'test-coord_geo_polar.R:1:1', 'test-coord_geo_radial.R:1:1', 'test-geom_text_phylo.R:3:3', 'test-geom_text_phylo.R:30:3', 'test-ggarrange2.R:25:3', 'test-guides.R:149:3', 'test-guides.R:163:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-guides.R:184:3'): guide_geo works with coord_geo_radial ──────── Error in `revts(ggtree(tree))`: could not find function "revts" ── Error ('test-guides.R:200:3'): ggtree scale works with only fossil taxa ───── Error in `ggtree(ceratopsianTreeRaia, position = position_nudge(x = -ceratopsianTreeRaia$root.time))`: could not find function "ggtree" [ FAIL 2 | WARN 0 | SKIP 38 | PASS 134 ] Deleting unused snapshots: 'coord_geo/scale-on-fossil-ggtree-new.svg', 'coord_geo/scale-on-ggtree-new.svg', 'coord_geo/scales-on-different-sides1-new.svg', 'coord_geo/scales-on-different-sides2-new.svg', 'coord_geo_polar/coord-geo-polar-grey-new.svg', 'coord_geo_polar/coord-geo-polar-new.svg', 'coord_geo_polar/coord-geo-polar-pos-new.svg', 'coord_geo_polar/scale-on-fossil-ggtree-new.svg', 'coord_geo_polar/scale-on-fossil-ggtree-with-labels-new.svg', 'coord_geo_polar/stacked-scales-new.svg', 'coord_geo_radial/coord-geo-radial-new.svg', 'coord_geo_radial/scale-on-fossil-ggtree-new.svg', 'coord_geo_radial/scale-on-fossil-ggtree-with-labels-new.svg', 'coord_geo_radial/stacked-scales-new.svg', 'geom_text_phylo/geom-text-phylo-new.svg', 'ggarrange2/double-ggarrange2-layout-new.svg', 'ggarrange2/double-ggarrange2-new.svg', 'ggarrange2/ggarrange2-no-dims-layout-new.svg', …, 'patterns/scale-fill-geopattern-na2-new.svg', and 'patterns/scale-fill-geopattern-new.svg' Error: ! Test failures. Execution halted Flavor: r-release-linux-x86_64

Version: 2.4.0
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘coord.Rmd’ using rmarkdown [WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead. --- finished re-building ‘coord.Rmd’ --- re-building ‘coord_geo.Rmd’ using rmarkdown [WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead. --- finished re-building ‘coord_geo.Rmd’ --- re-building ‘geo.Rmd’ using rmarkdown [WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead. --- finished re-building ‘geo.Rmd’ --- re-building ‘ggarrange2.Rmd’ using rmarkdown Quitting from ggarrange2.Rmd:14-23 [setup] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `library()`: ! there is no package called 'ggtree' --- Backtrace: ▆ 1. └─base::library(ggtree) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'ggarrange2.Rmd' failed with diagnostics: there is no package called 'ggtree' --- failed re-building ‘ggarrange2.Rmd’ --- re-building ‘phylogenies.Rmd’ using rmarkdown Quitting from phylogenies.Rmd:18-32 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `library()`: ! there is no package called 'ggtree' --- Backtrace: ▆ 1. └─base::library(ggtree) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'phylogenies.Rmd' failed with diagnostics: there is no package called 'ggtree' --- failed re-building ‘phylogenies.Rmd’ --- re-building ‘time.Rmd’ using rmarkdown [WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead. --- finished re-building ‘time.Rmd’ --- re-building ‘traits.Rmd’ using rmarkdown [WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead. --- finished re-building ‘traits.Rmd’ SUMMARY: processing the following files failed: ‘ggarrange2.Rmd’ ‘phylogenies.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-release-linux-x86_64

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