R version 4.6.0 RC (2026-04-20 r89921 ucrt) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(taxodist)
> 
> test_check("taxodist")
v Cache saved to 'D:\temp\2026_04_22_00_30_17_20577\RtmpK8jHb9\file96f819cb3cc3.rds' (1 entries).
v Cache saved to 'D:\temp\2026_04_22_00_30_17_20577\RtmpK8jHb9\file96f85b287743.rds' (1 entries).
v Cache loaded from 'D:\temp\2026_04_22_00_30_17_20577\RtmpK8jHb9\file96f85b287743.rds' (1 entries).
v Cache saved to 'D:\temp\2026_04_22_00_30_17_20577\RtmpK8jHb9\file96f864ff13bc.rds' (2 entries).
v Cache loaded from 'D:\temp\2026_04_22_00_30_17_20577\RtmpK8jHb9\file96f864ff13bc.rds' (2 entries).
v Cache saved to 'D:\temp\2026_04_22_00_30_17_20577\RtmpK8jHb9\file96f845ad1ecd.rds' (0 entries).
v Cache saved to 'D:\temp\2026_04_22_00_30_17_20577\RtmpK8jHb9\file96f85cf633ce.rds' (0 entries).
v Cache loaded from 'D:\temp\2026_04_22_00_30_17_20577\RtmpK8jHb9\file96f85cf633ce.rds' (0 entries).
x Could not retrieve lineage for Fakeosaurus
x Could not retrieve lineage for Fakeosaurus

-- Taxonomic Path: Tyrannosaurus → Triceratops --

  Dinosauria (depth 2) ↑
  Animalia (depth 1) ↑
* Dinosauria (MRCA, depth 3)
  Ornithischia (depth 1) ↓
  Triceratops (depth 2) ↓

-- Taxonomic Path: Tyrannosaurus → Triceratops --

  Dinosauria (depth 2) ↑
  Animalia (depth 1) ↑
* Dinosauria (MRCA, depth 3)
  Ornithischia (depth 1) ↓
  Triceratops (depth 2) ↓

-- Lineage Comparison --

MRCA: Dinosauria at depth 3

Shared lineage (3 nodes):
  Biota
  Animalia
  Dinosauria

Tyrannosaurus only (2 nodes):
> Theropoda
> Tyrannosaurus

Triceratops only (2 nodes):
> Ornithischia
> Triceratops
x Could not retrieve lineage for Fakeosaurus
x Could not retrieve lineage for Fakeosaurus
x Could not retrieve lineage for Fakeosaurus
i Fetching 3 lineages...
v Lineages fetched.
i Using cached ID for Carnotaurus
i Searching Taxonomicon for Drosophila...
! Could not reach Taxonomicon for Drosophila
i Searching Taxonomicon for Drosophila...
! Could not reach Taxonomicon for Drosophila
i Using cached lineage for ID 99999
! Could not retrieve lineage for ID 00000
! Could not retrieve lineage for ID 99999
i Using cached lineage for ID 50841

-- Taxonomic Distance --

* Carnotaurus vs Triceratops
  Distance : 0.333333333333333
  MRCA : Dinosauria (depth 3)
  Depth A : 6
  Depth B : 5

-- Taxonomic Distance --

* Carnotaurus vs Triceratops
  Distance : 0.333333333333333
  MRCA : Dinosauria (depth 3)
  Depth A : 6
  Depth B : 5
x Could not retrieve one or both lineages

-- Lineage Comparison --

MRCA: NA at depth 0


Drosophila only (5 nodes):
> Biota
> Animalia
> Arthropoda
> Insecta
> Drosophila

Saccharomyces only (3 nodes):
> Fungi
> Ascomycota
> Saccharomyces

-- Lineage Comparison --

MRCA: Dinosauria at depth 3

Shared lineage (3 nodes):
  Biota
  Animalia
  Dinosauria

Dinosauria only (0 nodes):

Carnotaurus only (2 nodes):
> Theropoda
> Carnotaurus
i Searching Taxonomicon for Carnotaurus...
v Found Carnotaurus with ID 12345
i Searching Taxonomicon for Pterodactylus...
v Found Pterodactylus with ID 42042
i Searching Taxonomicon for Quercus...
! Quercus not found in Taxonomicon

-- Taxonomic Ordination Summary (PCoA) --

Goodness-of-Fit (GOF): 95%


-- Taxonomic Ordination Summary (PCoA) --

Goodness-of-Fit (GOF): 95%

[ FAIL 0 | WARN 0 | SKIP 26 | PASS 135 ]

══ Skipped tests (26) ══════════════════════════════════════════════════════════
• On CRAN (26): 'test-distance.R:765:3', 'test-distance.R:776:3',
  'test-distance.R:785:3', 'test-distance.R:794:3', 'test-distance.R:802:3',
  'test-distance.R:810:3', 'test-distance.R:816:3', 'test-distance.R:826:3',
  'test-distance.R:833:3', 'test-distance.R:841:3', 'test-distance.R:849:3',
  'test-distance.R:855:3', 'test-distance.R:861:3', 'test-distance.R:867:3',
  'test-distance.R:875:3', 'test-distance.R:882:3', 'test-distance.R:888:3',
  'test-distance.R:897:3', 'test-distance.R:907:3', 'test-distance.R:917:3',
  'test-distance.R:925:3', 'test-distance.R:931:3', 'test-distance.R:943:3',
  'test-distance.R:950:3', 'test-distance.R:956:3', 'test-distance.R:962:3'

[ FAIL 0 | WARN 0 | SKIP 26 | PASS 135 ]
> 
> proc.time()
   user  system elapsed 
   3.75    0.54    4.67