Running ‘testthat.R’ [4s/6s]
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")
  
  -- 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...
  ! Pterodactylus not found in Taxonomicon
  Saving _problems/test-distance-547.R
  i Searching Taxonomicon for Quercus...
  ! Quercus not found in Taxonomicon
  [ FAIL 1 | WARN 0 | SKIP 26 | PASS 90 ]
  
  ══ Skipped tests (26) ══════════════════════════════════════════════════════════
  • On CRAN (26): 'test-distance.R:604:3', 'test-distance.R:615:3',
    'test-distance.R:624:3', 'test-distance.R:633:3', 'test-distance.R:641:3',
    'test-distance.R:649:3', 'test-distance.R:655:3', 'test-distance.R:665:3',
    'test-distance.R:672:3', 'test-distance.R:680:3', 'test-distance.R:688:3',
    'test-distance.R:694:3', 'test-distance.R:700:3', 'test-distance.R:706:3',
    'test-distance.R:714:3', 'test-distance.R:721:3', 'test-distance.R:727:3',
    'test-distance.R:736:3', 'test-distance.R:746:3', 'test-distance.R:756:3',
    'test-distance.R:764:3', 'test-distance.R:770:3', 'test-distance.R:782:3',
    'test-distance.R:789:3', 'test-distance.R:795:3', 'test-distance.R:801:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-distance.R:547:3'): get_taxonomicon_id skips row matching both bio and astronomical keywords ──
  Expected `result` to equal "42042".
  Differences:
  `actual` is NULL
  `expected` is a character vector ('42042')
  
  
  [ FAIL 1 | WARN 0 | SKIP 26 | PASS 90 ]
  Error:
  ! Test failures.
  Execution halted