Last updated on 2026-11-02 07:53:30 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 | 235.70 | 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 | 11.00 | 532.00 | 543.00 | ERROR | |
| r-oldrel-windows-x86_64 | 2.4.0 | 24.00 | 452.00 | 476.00 | OK |
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