R Observatory: Metrics for CALANGO version 1.0.20

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

CALANGO

1.0.20

Comparative Analysis with Annotation-Based Genomic Components

0packages depend

3.3Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Felipe CampeloFirst published 2021-07-077 releasesCRAN page ↗GitHub ↗

A first-principle, phylogeny-aware comparative genomics tool for investigating associations between terms used to annotate genomic components (e.g., Pfam IDs, Gene Ontology terms,) with quantitative or rank variables such as number of cell types, genome size, or density of specific genomic elements. See the project website for more information, documentation and examples, and doi:10.1016/j.patter.2023.100728 for the full paper.

Install

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

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

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

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("fcampelo/CALANGO")

Development version from fcampelo/CALANGO. Installs pak first if it is not already available.

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-calango

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-CALANGO

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-CALANGO

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

Health

CRAN checks

13OK

Slowest check: 1.8 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

15

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
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 1,578 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

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

Downloads

3.3K

CRAN downloads in the past year

Rank #11,596 · ~9/day · ~278/mo

Releases R versions

Daily download trend is not available in this view yet.

24430 days

84690 days

3.3K1 year

Compare downloads with other packages →

Also on113 r2u34 autocran15 c2d4u

Repository

GitHub ↗ fcampelo/calango

2Stars

2Forks

0Open issues

0Open PRs

0Releases

354Commits

6Contributors

License GPL-2.0 · 354 commits · Last activity 2024-09-05

Stars over time

2024-08-01 · 22026-07-07 · 2

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/fcampelo/calango on 2026-08-16.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.6.0

Imports (15)

assertthat pbmcapply ape rmarkdownnlmeBiocManager (>= 1.30.10)dendextend heatmaply ggplot2 plotly DT htmltools (>= 0.5.0)htmlwidgets pkgdown knitr (>= 1.28)

LinkingTo (0)

none

Suggests (3)

AnnotationDbi KEGGREST GO.db

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (5)

Maintainer (1)

Felipe Campelo

Author, Maintainer

Authors (4)

Felipe Campelo

Author, Maintainer

Jorge Augusto Hongo

Author

Francisco Lobo

Author

Giovanni Marques de Castro

Author

Other (1)

Gabriel Almeida

sad, dnc

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
1.0.20Latest
2024-09-05 · current release · diff ↗
R
R 4.4.0 released · 2024-04-24
1.0.16
2023-04-26 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.0.12
2022-09-18 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.0.10
2022-03-12 · diff ↗
1.0.8
2021-12-13 · diff ↗
1.0.5
2021-09-02 · diff ↗
1.0.2
2021-07-07
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-07-07
Total releases: 7 / 5 yrs
License: GPL-2 OSI
Minimum R: ≥ 3.6.0
Download size: 750 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Phylogenetics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("CALANGO")

Format

Campelo, F., Almeida, G., Hongo, J. A., Lobo, F., & Marques de Castro, G. (2024). CALANGO: Comparative Analysis with Annotation-Based Genomic Components (Version 1.0.20) [Computer software]. https://doi.org/10.32614/CRAN.package.CALANGO

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 CALANGO version 1.0.20 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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