Running ‘testthat.R’ [0m/29m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # 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 '/Volumes/Temp/tmp/RtmprtDYYa/file5f9b398bff0d.rds' (1 entries).
  v Cache saved to '/Volumes/Temp/tmp/RtmprtDYYa/file5f9b18e789d.rds' (1 entries).
  v Cache loaded from '/Volumes/Temp/tmp/RtmprtDYYa/file5f9b18e789d.rds' (1 entries).
  v Cache saved to '/Volumes/Temp/tmp/RtmprtDYYa/file5f9b6f4ba5bb.rds' (2 entries).
  v Cache loaded from '/Volumes/Temp/tmp/RtmprtDYYa/file5f9b6f4ba5bb.rds' (2 entries).
  v Cache saved to '/Volumes/Temp/tmp/RtmprtDYYa/file5f9b2e705a9a.rds' (0 entries).
  v Cache saved to '/Volumes/Temp/tmp/RtmprtDYYa/file5f9b3e09d1ec.rds' (0 entries).
  v Cache loaded from '/Volumes/Temp/tmp/RtmprtDYYa/file5f9b3e09d1ec.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
  Saving _problems/test-distance-649.R
  i Searching Taxonomicon for Carnotaurus...
  ! Carnotaurus not found in Taxonomicon
  Saving _problems/test-distance-670.R
  i Searching Taxonomicon for Pterodactylus...
  
  
  ! Interrupting test: get_taxonomicon_id skips row matching both bio and astronomical keywords
  
  Execution halted