Last updated on 2026-10-27 17:54:41 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.4 | 16.89 | 112.12 | 129.01 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.1.4 | 14.42 | 107.29 | 121.71 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.1.5 | 17.00 | 92.24 | 109.24 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 0.1.5 | 15.00 | 91.39 | 106.39 | OK | |
| r-devel-windows-x86_64 | 0.1.4 | 21.00 | 210.00 | 231.00 | OK | |
| r-patched-linux-x86_64 | 0.1.4 | 15.35 | 135.19 | 150.54 | OK | |
| r-release-linux-x86_64 | 0.1.4 | 16.46 | 134.50 | 150.96 | OK | |
| r-release-macos-arm64 | 0.1.5 | 6.00 | 93.00 | 99.00 | OK | |
| r-release-macos-x86_64 | 0.1.5 | 14.00 | 360.00 | 374.00 | OK | |
| r-release-windows-x86_64 | 0.1.4 | 21.00 | 176.00 | 197.00 | ERROR | |
| r-oldrel-macos-arm64 | 0.1.5 | 7.00 | 106.00 | 113.00 | OK | |
| r-oldrel-macos-x86_64 | 0.1.5 | 14.00 | 340.00 | 354.00 | OK | |
| r-oldrel-windows-x86_64 | 0.1.4 | 27.00 | 240.00 | 267.00 | OK |
Version: 0.1.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [44s/95s]
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." <https://github.com/eliotmiller/clootl>.
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(<citation>,
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'
downloaded 309.9 MB
AVESDATA_PATH set to /home/hornik/tmp/scratch/Rtmp21s4kp/AvesDataLite-main
AvesDataLite repo downloaded and upzipped to:/home/hornik/tmp/scratch/Rtmp21s4kp/AvesDataLite-main
AVESDATA_PATH set to: /home/hornik/tmp/scratch/Rtmp21s4kp/AvesDataLite-main use set_avesdata_repo_path to change path.
Using data download for tree in
/home/hornik/tmp/scratch/Rtmp21s4kp/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
/home/hornik/tmp/scratch/Rtmp21s4kp/AvesDataLite-main/Tree_versions/Aves_1.5/OpenTreeSynth/annotated_supertree/annotations.json
Using data download for tree in
/home/hornik/tmp/scratch/Rtmp21s4kp/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
/home/hornik/tmp/scratch/Rtmp21s4kp/AvesDataLite-main/Tree_versions/Aves_1.4/Clements2022/summary_dated_clements.nex
Using data download for taxonomy in
/home/hornik/tmp/scratch/Rtmp21s4kp/AvesDataLite-main/Taxonomy_versions/Clements2021/OTT_crosswalk_2021.csv
Sampling trees from:
/home/hornik/tmp/scratch/Rtmp21s4kp/AvesDataLite-main/Tree_versions/Aves_1.6/Clements2025/dated_rand_sample_clements.tre
Saving _problems/test_basics-207.R
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 33 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_basics.R:202:3'): several data download requiring tests (skip on cran) ──
Error in `sampleTrees(species = test_spp, label_type = "scientific", taxonomy_year = "2025", version = "1.6", count = 100, data_path = path)`: Tree set file:/home/hornik/tmp/scratch/Rtmp21s4kp/AvesDataLite-main/Tree_versions/Aves_1.6/Clements2025/dated_rand_sample_clements.tre is not found. This version may not be available for this taxonomy year or you may need to update your AvesData repo using get_avesdata_repo(overwrite=TRUE)
Backtrace:
▆
1. └─clootl::sampleTrees(...) at test_basics.R:202:3
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 33 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.1.4
Check: tests
Result: ERROR
Running 'testthat.R' [93s]
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." <https://github.com/eliotmiller/clootl>.
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(<citation>,
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'
downloaded 309.9 MB
AVESDATA_PATH set to D:/temp/2026_10_26_01_50_00_20015/RtmpszDkVp/AvesDataLite-main
AvesDataLite repo downloaded and upzipped to:D:/temp/2026_10_26_01_50_00_20015/RtmpszDkVp/AvesDataLite-main
AVESDATA_PATH set to: D:/temp/2026_10_26_01_50_00_20015/RtmpszDkVp/AvesDataLite-main use set_avesdata_repo_path to change path.
Using data download for tree in
D:/temp/2026_10_26_01_50_00_20015/RtmpszDkVp/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_10_26_01_50_00_20015/RtmpszDkVp/AvesDataLite-main/Tree_versions/Aves_1.5/OpenTreeSynth/annotated_supertree/annotations.json
Using data download for tree in
D:/temp/2026_10_26_01_50_00_20015/RtmpszDkVp/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_10_26_01_50_00_20015/RtmpszDkVp/AvesDataLite-main/Tree_versions/Aves_1.4/Clements2022/summary_dated_clements.nex
Using data download for taxonomy in
D:/temp/2026_10_26_01_50_00_20015/RtmpszDkVp/AvesDataLite-main/Taxonomy_versions/Clements2021/OTT_crosswalk_2021.csv
Sampling trees from:
D:/temp/2026_10_26_01_50_00_20015/RtmpszDkVp/AvesDataLite-main/Tree_versions/Aves_1.6/Clements2025/dated_rand_sample_clements.tre
Saving _problems/test_basics-207.R
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 33 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_basics.R:202:3'): several data download requiring tests (skip on cran) ──
Error in `sampleTrees(species = test_spp, label_type = "scientific", taxonomy_year = "2025", version = "1.6", count = 100, data_path = path)`: Tree set file:D:/temp/2026_10_26_01_50_00_20015/RtmpszDkVp/AvesDataLite-main/Tree_versions/Aves_1.6/Clements2025/dated_rand_sample_clements.tre is not found. This version may not be available for this taxonomy year or you may need to update your AvesData repo using get_avesdata_repo(overwrite=TRUE)
Backtrace:
▆
1. └─clootl::sampleTrees(...) at test_basics.R:202:3
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 33 ]
Error:
! Test failures.
Execution halted
Flavor: r-release-windows-x86_64