• using R version 4.6.0 Patched (2026-05-05 r90004)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-15 (Debian 15.2.0-17) 15.2.0     GNU Fortran (Debian 15.2.0-17) 15.2.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8 * current time: 2026-05-06 19:59:41 UTC
• checking for file ‘taxodist/DESCRIPTION’ ... OK
• this is package ‘taxodist’ version ‘0.2.0’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘taxodist’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... [1s/1s] OK
• checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
• checking whether the package can be unloaded cleanly ... [1s/1s] OK
• checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
• checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
• checking loading without being on the library search path ... [1s/1s] OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [7s/10s] OK
• checking Rd files ... [0s/1s] OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [1s/1s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [6s/8s] 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
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [4s/6s] OK
• checking PDF version of manual ... [6s/8s] OK
• checking HTML version of manual ... [3s/4s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR