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")
  v Cache saved to '/tmp/Rtmp5VbtnW/file3f27937261e4de.rds' (1 entries).
  v Cache saved to '/tmp/Rtmp5VbtnW/file3f2793461912b8.rds' (1 entries).
  v Cache loaded from '/tmp/Rtmp5VbtnW/file3f2793461912b8.rds' (1 entries).
  v Cache saved to '/tmp/Rtmp5VbtnW/file3f2793f1c41f1.rds' (2 entries).
  v Cache loaded from '/tmp/Rtmp5VbtnW/file3f2793f1c41f1.rds' (2 entries).
  v Cache saved to '/tmp/Rtmp5VbtnW/file3f27935c2099cb.rds' (0 entries).
  v Cache saved to '/tmp/Rtmp5VbtnW/file3f27937308e873.rds' (0 entries).
  v Cache loaded from '/tmp/Rtmp5VbtnW/file3f27937308e873.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...
  ! Pterodactylus not found in Taxonomicon
  Saving _problems/test-distance-691.R
  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 3 | WARN 0 | SKIP 26 | PASS 132 ]
  
  ══ 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'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-distance.R:649:3'): get_taxonomicon_id parses HTML and returns id ──
  Expected `result` to equal "12345".
  Differences:
  `actual` is NULL
  `expected` is a character vector ('12345')
  
  ── Failure ('test-distance.R:670:3'): get_taxonomicon_id skips astronomical entries ──
  Expected `result` to equal "12345".
  Differences:
  `actual` is NULL
  `expected` is a character vector ('12345')
  
  ── Failure ('test-distance.R:691:3'): 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 3 | WARN 0 | SKIP 26 | PASS 132 ]
  Error:
  ! Test failures.
  Execution halted