R Observatory: Metrics for ogrdbstats version 0.5.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ogrdbstats

0.5.5Package record

Analysis of Adaptive Immune Receptor Repertoire Germ Line Statistics

0packages depend

2.9Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by William LeesCRAN page ↗GitHub ↗Issues ↗

Multiple tools are now available for inferring the personalised germ line set from an adaptive immune receptor repertoire. Output from these tools is converted to a single format and supplemented with rich data such as usage and characterisation of 'novel' germ line alleles. This data can be particularly useful when considering the validity of novel inferences. Use of the analysis provided is described in doi:10.3389/fimmu.2019.00435.

Changes in 0.5.5

Fix dependencies warning arising from changes in Bioconductor packages. This version of ogrdbstats requires R >= 4.4 and Bioconductor >= 3.19

Updated installation instructions in the documentation to reflect this.

From NEWS.md in the release

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("ogrdbstats", 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/ogrdbstats")

Development version from airr-community/ogrdbstats. 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-ogrdbstats

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

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 OK2026-07-28
NOTE12 OK, 1 NOTE2026-07-27
OK13 OK2026-06-09

Show 6 earlier changesHide 6 earlier changes

ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-10
ERROR12 OK, 1 ERROR2026-05-03
OK13 OK2026-05-02
ERROR10 OK, 3 WARNING, 1 ERROR2026-03-24
WARNING11 OK, 3 WARNING2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.5.5

README· In the repository, left out of the releaseVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 0.5.5Citation fileNo

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

Vignettes (1)

Using ogrdbstats

How these are measured

Downloads

2.9K

CRAN downloads in the past year

Rank #16,190 · ~8/day · ~241/mo

Releases R versions

Daily download trend is not available in this view yet.

31830 days

76590 days

2.9K1 year

Compare downloads with other packages →

Also on80 r2u

How downloads are counted

Repository

airr-community/ogrdbstats ↗Organization: airr-community

1Stars

0Forks

0Open issues

0Open PRs

1Releases

103Commits

1Commit identities

103 commits · Last activity 2026-08-03

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 296
Median days to close, 50 most recently updated closed PRs: not measured

Stars over time

2023-03-17 · 12026-07-07 · 1

How these are measured

PracticesBeta

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

Checks run against github.com/airr-community/ogrdbstats on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Docs source (2)

README.Rmd

GitHub Pages site last deployed 2026-08-03

Reproducibility and dev environment (1)

Dockerfile

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Show all practicesHide 1 practice

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

18 external dependencies (excludes base and recommended)

Installing ogrdbstats adds 82 packages (44 with compiled code, 80 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB. 5 more not on CRAN are not measured.

Depends (1)

R >= 4.4

Imports (16)

dplyr ggplot2 magrittr tigger (>= 0.4.0)alakazam stringr data.table gridExtra tidyr stringdist RColorBrewer pwalign argparser (>= 0.4)ComplexHeatmap bookdown scales

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (1)

William Lees

Author, Maintainer since 0.5.0 (2023)

Releases (4)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.5.5Latest
record
2026-03-23 · current release · diff ↗
0.5.4
record
2025-07-08 · diff ↗
R
R 4.5.0 released · 2025-04-11
0.5.2
record
2024-11-03 · diff ↗
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
0.5.0
record
2023-03-09
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2023-03-09
Total releases: 4 / 3 yrs
License: CC BY-SA 4.0
Additional repositories: bioconductor.org
Minimum R: ≥ 4.4
Bundled data: 12 KB / 1 file
Download size: 116 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("ogrdbstats")

Format

Lees, W. (2026). ogrdbstats: Analysis of Adaptive Immune Receptor Repertoire Germ Line Statistics (Version 0.5.5) [Computer software]. https://doi.org/10.32614/CRAN.package.ogrdbstats

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 ogrdbstats version 0.5.5 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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