R Observatory: Metrics for airr version 2.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

airr

2.0.0Package record

AIRR Data Representation Reference Library

3packages depend

24.8Kdownloads / year

67.3%test coverage

13/13flavors OK

Overview

About

Maintained by Jason Vander HeidenCRAN page ↗GitHub ↗Website ↗Issues ↗

Schema definitions and read, write and validation tools for data formatted in accordance with the AIRR Data Representation schemas defined by the AIRR Community https://docs.airr-community.org.

Changes in 2.0.0

Deprecation and Removal:

Completely removed read_alignment, write_alignment, and AlignmentSchema. Removed "Alignment" from the valid definitions list and AIRRSchema.

Tabular Data and Parsing:

Updated read_tabular to initially treat logical columns as character data to prevent silent NA conversions during parsing, then explicitly casting valid logical character values.
Updated validate_tabular to support character strings representing logical values (e.g., "TRUE", "T", "False", "F") when validating logical fields.

Validation:

Enhanced validate_entry to support comprehensive validation of arrays without reference schemas, including item type checking (string, integer, number, boolean) and enum constraints.

Show all changes in 2.0.0Hide the rest of the changes in 2.0.0

Added rigorous type and enum validation for individual fields within validate_entry, providing explicit warnings for unrecognized types.
Added an ontology validation check in validate_entry to ensure that an ontology field is structured as a list before performing recursive validation.

Data Model and Schema:

Updated AIRRSchema to replace the Acknowledgement schema with the new Contributor schema.
Added a safety check in extract_field_content to handle fields with null properties safely.

+

From NEWS.md in the release

Install

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

install.packages("airr", 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("airr-community/airr-standards")

Development version from airr-community/airr-standards. 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-airr

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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-airr

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-airr

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 2.2 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-10

Show 2 earlier changesHide 2 earlier changes

WARNING12 OK, 1 WARNING2026-05-09
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.0.0

READMEYes · 38 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 2.0.0Citation fileNoWebsiteYes

Help pages: 9
Examples that run: 100%8 run in a plain check
Exported functions with examples: 88%
Documented parameters: 100%
Return-value docs: 63%
Help pages citing references: 0%

Vignettes (1)

Usage Vignette

How these are measured

Downloads

24.8K

CRAN downloads in the past year

Rank #2,642 · ~68/day · ~2.1K/mo

Releases R versions

Daily download trend is not available in this view yet.

2K30 days

5.7K90 days

24.8K1 year

Compare downloads with other packages →

Also on563 r2u21 autocran4.2K conda_forge200 bioconda37 c2d4u

How downloads are counted

Repository

airr-community/airr-standards ↗Organization: airr-community

41Stars

24Forks

48Open issues

5Open PRs

14Releases

1,726Commits

28Commit identities

standardadaptiveimmunereceptors

License file reads as CC-BY-4.0 · 1,726 commits · Last activity 2026-09-17 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 86%
Median days to close, 50 most recently updated closed issues: 263
Median days to close, 50 most recently updated closed PRs: 32

Stars over time

2025-02-20 · 372026-07-07 · 41

How these are measured

PracticesBeta

7 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/airr-community/airr-standards on 2026-10-11.

Continuous integration (3)

GitHub ActionsR CMD check workflowTravis CI (config file)

The R CMD check workflow runs on Linux

Governance and community (1)

Contributing guide

Docs source (1)

GitHub Pages site last deployed 2023-04-17

Reproducibility and dev environment (1)

Makefile

Show all practicesHide 1 practice

Research and citation (1)

Zenodo

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Installing airr adds 27 packages (16 with compiled code, 19 MB of source tarballs). Heaviest: stringi 11 MB, jsonlite 1.0 MB, vctrs 1.0 MB.

Depends (1)

R >= 3.1.2

Imports (7)

jsonlitemethodsreadrstatsstringitoolsyaml

LinkingTo (0)

none

Suggests (4)

knitr rmarkdown tibble testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

3direct

8indirect

Imports 3

Depends, Imports or LinkingTo, most downloaded first

alakazam dowser immunarch

How these are counted

Code & Tests

Datasets

People & History

People (7)

Jason Vander Heiden

Author, Maintainer since 1.1.0 (2018)

Scott Christley

Author · added in 1.3.0

Gisela Gabernet

Author · added in 1.6.1

Katharina Imkeller

Author · added in 1.4.0

Susanna Marquez

Author

Ulrik Stervbo

Author · added in 1.4.0

AIRR Community

Copyright holder

Releases (8)

Pick two releases to compare their code metrics.

2.0.0Latest
record
2026-06-06 · current release · diff ↗ ·
removed 3 exports
AlignmentSchema, read_alignment, write_alignment
R
R 4.6.0 released · 2026-04-24
1.6.1
record
2026-02-18 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.5.0
record
2023-08-29 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.4.1
record
2022-08-28 · diff ↗
1.4.0
record
2022-08-27 · diff ↗ ·
added 10 exports
AIRRSchema, DataFileSchema, GenotypeSetSchema, GermlineSetSchema, InfoSchema, RepertoireSchema, read_tabular, validate_rearrangement, validate_tabular, write_tabular
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.3.0
record
2020-05-27 · diff ↗
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
1.2.0
record
2018-08-18 · diff ↗
1.1.0
record
2018-05-03

Show 1 earlier eventHide 1 earlier event

R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-05-03
Total releases: 8 / 8 yrs
License: CC BY 4.0
Minimum R: ≥ 3.1.2
Download size: 393 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("airr")

Format

Vander Heiden, J., AIRR Community, Christley, S., Gabernet, G., Imkeller, K., Marquez, S., & Stervbo, U. (2026). airr: AIRR Data Representation Reference Library (Version 2.0.0) [Computer software]. https://doi.org/10.32614/CRAN.package.airr

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 airr version 2.0.0 [Data set]. HJJB, LLC. Data release v2026-10-19. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →