Last updated on 2026-05-07 09:53:19 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.2.0 | 2.46 | 54.51 | 56.97 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.3.0 | 2.56 | 41.95 | 44.51 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.3.0 | 88.27 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 0.3.0 | 100.96 | OK | |||
| r-devel-windows-x86_64 | 0.3.0 | 9.00 | 79.00 | 88.00 | OK | |
| r-patched-linux-x86_64 | 0.2.0 | 3.81 | 49.28 | 53.09 | ERROR | |
| r-release-linux-x86_64 | 0.2.0 | 2.86 | 49.33 | 52.19 | ERROR | |
| r-release-macos-arm64 | 0.3.0 | 1.00 | 47.00 | 48.00 | OK | |
| r-release-macos-x86_64 | 0.3.0 | 3.00 | 77.00 | 80.00 | OK | |
| r-release-windows-x86_64 | 0.3.0 | 7.00 | 78.00 | 85.00 | OK | |
| r-oldrel-macos-arm64 | 0.3.0 | 1.00 | 21.00 | 22.00 | OK | |
| r-oldrel-macos-x86_64 | 0.3.0 | 3.00 | 68.00 | 71.00 | OK | |
| r-oldrel-windows-x86_64 | 0.3.0 | 10.00 | 86.00 | 96.00 | OK |
Version: 0.2.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [0m/30m]
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 '/home/hornik/tmp/scratch/RtmppY1XBR/file599535d2f208.rds' (1 entries).
v Cache saved to '/home/hornik/tmp/scratch/RtmppY1XBR/file5995282fb22a.rds' (1 entries).
v Cache loaded from '/home/hornik/tmp/scratch/RtmppY1XBR/file5995282fb22a.rds' (1 entries).
v Cache saved to '/home/hornik/tmp/scratch/RtmppY1XBR/file59953c54474d.rds' (2 entries).
v Cache loaded from '/home/hornik/tmp/scratch/RtmppY1XBR/file59953c54474d.rds' (2 entries).
v Cache saved to '/home/hornik/tmp/scratch/RtmppY1XBR/file59956aabf0f9.rds' (0 entries).
v Cache saved to '/home/hornik/tmp/scratch/RtmppY1XBR/file599511821ee9.rds' (0 entries).
v Cache loaded from '/home/hornik/tmp/scratch/RtmppY1XBR/file599511821ee9.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
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.2.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [5s/8s]
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 '/home/hornik/tmp/scratch/RtmpyfpitN/filebba3f5221a548.rds' (1 entries).
v Cache saved to '/home/hornik/tmp/scratch/RtmpyfpitN/filebba3f73d17d84.rds' (1 entries).
v Cache loaded from '/home/hornik/tmp/scratch/RtmpyfpitN/filebba3f73d17d84.rds' (1 entries).
v Cache saved to '/home/hornik/tmp/scratch/RtmpyfpitN/filebba3f4d62f319.rds' (2 entries).
v Cache loaded from '/home/hornik/tmp/scratch/RtmpyfpitN/filebba3f4d62f319.rds' (2 entries).
v Cache saved to '/home/hornik/tmp/scratch/RtmpyfpitN/filebba3f3c022242.rds' (0 entries).
v Cache saved to '/home/hornik/tmp/scratch/RtmpyfpitN/filebba3f5006cc8b.rds' (0 entries).
v Cache loaded from '/home/hornik/tmp/scratch/RtmpyfpitN/filebba3f5006cc8b.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
Flavor: r-patched-linux-x86_64
Version: 0.2.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [6s/8s]
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 '/home/hornik/tmp/scratch/Rtmp3NUNye/file2878ba4f8581fa.rds' (1 entries).
v Cache saved to '/home/hornik/tmp/scratch/Rtmp3NUNye/file2878ba5eb6ece9.rds' (1 entries).
v Cache loaded from '/home/hornik/tmp/scratch/Rtmp3NUNye/file2878ba5eb6ece9.rds' (1 entries).
v Cache saved to '/home/hornik/tmp/scratch/Rtmp3NUNye/file2878ba2fac5eb0.rds' (2 entries).
v Cache loaded from '/home/hornik/tmp/scratch/Rtmp3NUNye/file2878ba2fac5eb0.rds' (2 entries).
v Cache saved to '/home/hornik/tmp/scratch/Rtmp3NUNye/file2878ba48fc80cf.rds' (0 entries).
v Cache saved to '/home/hornik/tmp/scratch/Rtmp3NUNye/file2878ba1055f7d8.rds' (0 entries).
v Cache loaded from '/home/hornik/tmp/scratch/Rtmp3NUNye/file2878ba1055f7d8.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
Flavor: r-release-linux-x86_64