R Observatory: Metrics for itol.toolkit version 1.1.12

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

itol.toolkit

1.1.12

Helper Functions for 'Interactive Tree Of Life'

0packages depend

7.4Kdownloads / year

24.9%test coverage

13/13checks pass

Overview

About

Maintained by Tong ZhouFirst published 2023-01-265 releasesCRAN page ↗

The 'Interactive Tree Of Life' https://itol.embl.de/ online server can edit and annotate trees interactively. The 'itol.toolkit' package can support all types of annotation templates.

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("itol.toolkit", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-itol.toolkit

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-itol.toolkit

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-itol.toolkit

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 3.1 min · r-oldrel-macos-x86_64

Code health

Yes

Tests · ratio 0.05

24.9%

Coverage · measured lines

100%

Documentation · exports

19

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 1,149 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 96%
References docs: 0%

Downloads

7.4K

CRAN downloads in the past year

Rank #6,891 · ~20/day · ~618/mo

Releases R versions

Daily download trend is not available in this view yet.

23530 days

1.3K90 days

7.4K1 year

Compare downloads with other packages →

Also on110 r2u15 autocran

Repository

GitHub ↗ tongzhou2017/itol.toolkit

185Stars

17Forks

1Open issues

0Open PRs

20Releases

68Commits

4Contributors

bioinformaticsitolvisualization

68 commits · Last activity 2025-11-02 · +0.5% stars, 30d

Stars over time

2026-07-14 · 1832026-07-25 · 185

Repository practices

Upstream repositoryBeta

3 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/tongzhou2017/itol.toolkit on 2026-08-09.

Reproducibility and dev environment (1)

renv

Lint, format, editor (1)

RStudio project

Governance and community (1)

Issue templates

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

19 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.10

Imports (19)

dplyr stringrstatsseqinrutilsmethodstidyr ape data.table purrr wesanderson miniUI shiny rstudioapi colourpicker ggsci RColorBrewer stringdist magrittr

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

Tong Zhou

Author, Maintainer

Authors (1)

Tong Zhou

Author, Maintainer

Package Timeline

5 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.1.12Latest
2025-09-10 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.1.7
2023-11-18 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.1.5
2023-04-20 · diff ↗
1.1.0
2023-02-12 · diff ↗
1.0.0
2023-01-26
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2023-01-26
Total releases: 5 / 3 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 2.10
Bundled data: 4.5 KB / 3 files
Download size: 654 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("itol.toolkit")

Format

Zhou, T. (2025). itol.toolkit: Helper Functions for 'Interactive Tree Of Life' (Version 1.1.12) [Computer software]. https://doi.org/10.32614/CRAN.package.itol.toolkit

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for itol.toolkit version 1.1.12 [Data set]. HJJB, LLC. Data release v2026-08-15. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-15, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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