R version 4.6.0 beta (2026-04-16 r89899 ucrt) -- "Because it was There" Copyright (C) 2026 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # 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(clootl) Loading required package: ape To cite package 'clootl' in publications use: Miller E, McTavish E, Sanchez-Reyes L (2025). "clootl: Fetch and Explore the Cornell Lab of Ornithology Open Tree of Life Avian Phylogeny." . McTavish E, Gerbracht J, Holder M, Iliff M, Lepage D, Rasmussen P, Redelings B, Sanchez-Reyes L, Miller E (2025). "A complete and dynamic tree of birds." _Proceedings of the National Academy of Sciences_. To see these entries in BibTeX format, use 'format(, bibtex=TRUE)', or 'toBibtex(.)'. The current version of the Aves tree is v1.6.2025. Please specify the tree and taxonomy version used when citing this R package. When possible, cite all the original studies supporting your tree: These citations are acessible using getCitations(your_tree) > > test_check("clootl") This extracted tree is from version 1.6 and taxonomy year 2025. Please cite the version, clootl, and the contributing studies using getCitations(tree, version). This extracted tree is from version 1.6 and taxonomy year 2025. Please cite the version, clootl, and the contributing studies using getCitations(tree, version). This extracted tree is from version 1.6 and taxonomy year 2025. Please cite the version, clootl, and the contributing studies using getCitations(tree, version). Some of your provided species codes do not match with codes in the requested year's eBird taxonomy: 1 codes did not match. 4 codes did match These codes did not match: error Some of your provided species names do not match with names in the requested year's eBird taxonomy: 1 names did not match. 4 names did match These names did not match: error Argument force=TRUE, returning a tree for the species that match. This extracted tree is from version 1.6 and taxonomy year 2025. Please cite the version, clootl, and the contributing studies using getCitations(tree, version). Some of your provided species names do not match with names in the requested year's eBird taxonomy: 1 names did not match. 3 names did match These names did not match: Error badspecies Some of your provided species names do not match with names in the requested year's eBird taxonomy: 1 names did not match. 3 names did match These names did not match: Error badspecies Argument force=TRUE, returning a tree for the species that match. This extracted tree is from version 1.6 and taxonomy year 2025. Please cite the version, clootl, and the contributing studies using getCitations(tree, version). This extracted tree is from version 1.6 and taxonomy year 2025. Please cite the version, clootl, and the contributing studies using getCitations(tree, version). AVESDATA_PATH set to: use set_avesdata_repo_path to change path. Downloading AvesDataLite repo from github (holds key files from large McTavishLab/AvesData repo). This may take several minutes depending on your connection. trying URL 'https://github.com/McTavishLab/AvesDataLite/archive/refs/heads/main.zip?raw=TRUE' downloaded 309.9 MB AVESDATA_PATH set to D:/temp/2026_04_17_13_55_17_12759/RtmpY56JOm/AvesDataLite-main AvesDataLite repo downloaded and upzipped to:D:/temp/2026_04_17_13_55_17_12759/RtmpY56JOm/AvesDataLite-main AVESDATA_PATH set to: D:/temp/2026_04_17_13_55_17_12759/RtmpY56JOm/AvesDataLite-main use set_avesdata_repo_path to change path. Using data download for tree in D:/temp/2026_04_17_13_55_17_12759/RtmpY56JOm/AvesDataLite-main/Tree_versions/Aves_1.5/Clements2022/summary_dated_clements.nex This extracted tree is from version 1.5 and taxonomy year 2022. Please cite the version, clootl, and the contributing studies using getCitations(tree, version). Using data download for annotations in D:/temp/2026_04_17_13_55_17_12759/RtmpY56JOm/AvesDataLite-main/Tree_versions/Aves_1.5/OpenTreeSynth/annotated_supertree/annotations.json Using data download for tree in D:/temp/2026_04_17_13_55_17_12759/RtmpY56JOm/AvesDataLite-main/Tree_versions/Aves_1.5/Clements2022/summary_dated_clements.nex This extracted tree is from version 1.5 and taxonomy year 2022. Please cite the version, clootl, and the contributing studies using getCitations(tree, version). Using data download for tree in D:/temp/2026_04_17_13_55_17_12759/RtmpY56JOm/AvesDataLite-main/Tree_versions/Aves_1.4/Clements2022/summary_dated_clements.nex Using data download for taxonomy in D:/temp/2026_04_17_13_55_17_12759/RtmpY56JOm/AvesDataLite-main/Taxonomy_versions/Clements2021/OTT_crosswalk_2021.csv Sampling trees from: D:/temp/2026_04_17_13_55_17_12759/RtmpY56JOm/AvesDataLite-main/Tree_versions/Aves_1.6/Clements2025/dated_rand_sample_clements.tre [ FAIL 0 | WARN 0 | SKIP 0 | PASS 31 ] > > proc.time() user system elapsed 58.06 13.17 121.07