* using log directory 'd:/Rcompile/CRANpkg/local/4.5/clootl.Rcheck' * using R version 4.5.3 (2026-03-11 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 14.3.0 GNU Fortran (GCC) 14.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'clootl/DESCRIPTION' ... OK * this is package 'clootl' version '0.1.4' * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'clootl' can be installed ... OK * checking installed package size ... OK * checking package 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 ... [2s] OK * checking whether the package can be loaded with stated dependencies ... [2s] OK * checking whether the package can be unloaded cleanly ... [2s] OK * checking whether the namespace can be loaded with stated dependencies ... [2s] OK * checking whether the namespace can be unloaded cleanly ... [2s] OK * checking loading without being on the library search path ... [2s] OK * checking whether startup messages can be suppressed ... [2s] 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 ... [6s] OK * checking Rd files ... [1s] 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 contents of 'data' directory ... OK * checking data for non-ASCII characters ... [8s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking examples ... [7s] OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... [48s] ERROR Running 'testthat.R' [48s] 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(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). 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' Saving _problems/test_basics-161.R [ FAIL 1 | WARN 1 | SKIP 0 | PASS 27 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_basics.R:161:3'): several data download requiring tests (skip on cran) ── Error in `utils::download.file(url, destfile = zipfilepath, mode = "wb")`: cannot open URL 'https://github.com/McTavishLab/AvesDataLite/archive/refs/heads/main.zip?raw=TRUE' Backtrace: ▆ 1. └─clootl::get_avesdata_repo(tmpdir_path, overwrite = TRUE) at test_basics.R:161:3 2. └─utils::download.file(url, destfile = zipfilepath, mode = "wb") [ FAIL 1 | WARN 1 | SKIP 0 | PASS 27 ] Error: ! Test failures. Execution halted * checking PDF version of manual ... [21s] OK * checking HTML version of manual ... [2s] OK * DONE Status: 1 ERROR