Check results for 'taxodist'

using R version 4.6.0 (2026-04-24)
using platform: x86_64-apple-darwin20
R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0
running under: macOS Ventura 13.3.1
using session charset: UTF-8 * current time: 2026-04-28 21:55:46 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 ... [3s/4s] OK See the install log for details.
checking installed package size ... OK
checking package directory ... 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 ... [0s/1s] 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 ... [3s/4s] OK
checking Rd files ... [0s/0s] OK
checking Rd metadata ... 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 ... [0m/29m] ERROR 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
checking for unstated dependencies in vignettes ... OK
checking package vignettes ...* using check arguments '--no-clean-on-error '