R Observatory: Metrics for biobouncer version 0.1.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

biobouncer

0.1.4Package record

Validate Biological Identifiers and Inputs

0packages depend

457downloads / year

81.5%test coverage

13/13flavors OK

Overview

About

Maintained by Samuel BhartiCRAN page ↗GitHub ↗Website ↗Issues ↗

Gene symbols, ontology terms, variant formats, and database accessions are validated through one small application programming interface (API), either offline against identifier patterns and bundled snapshots or live against a source web service. Results are designed to match those of the companion 'Python' package for the same inputs. Input order and length are preserved, and errors are reported explicitly rather than as a silent failure. Identifier patterns follow the registry and nomenclature described in Hoyt et al. (2022) doi:10.1038/s41597-022-01807-3 and den Dunnen et al. (2016) doi:10.1002/humu.22981.

Changes in 0.1.4

Two new pattern sources for model-organism identifiers. mgi validates an MGI accession, such as MGI:97306, and rgd validates an RGD identifier, such as RGD:3059. Both require the prefix, since the bare number the registries record would accept any digits, and both repair a bare id or a lowercase prefix to the canonical form.
Two new pattern sources for genomic variant coordinates. gnomad validates a gnomAD-style chrom-pos-ref-alt string, such as 1-55516888-G-A, with an optional chr prefix. spdi validates NCBI SPDI notation, such as NC_000001.11:55516887:G:A. Both check the coordinate shape offline in pattern mode, so an empty allele or a malformed field is rejected rather than passed through as valid.
Documentation changes requested by CRAN on the first submission. The Description field now cites the Bioregistry and HGVS nomenclature references the identifier patterns follow, and the id_predicate() examples no longer carry commented-out code. The assertr, validate and pointblank integrations are still shown in the "Examples" article. There is no change to behavior.

From NEWS.md in the release

Install

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

install.packages("biobouncer", 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("samuelbharti/biobouncer")

Development version from samuelbharti/biobouncer. 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-biobouncer

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-biobouncer

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-biobouncer

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: 2.7 min · r-oldrel-windows-x86_64

Status changes

OK13 OKNow
OK7 OK2026-09-04

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.4

READMEYes · 142 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 0.1.4Citation fileYes · computed when R runs itWebsiteYes

Help pages: 16 (1 internal)includes a package overview page
Examples that run: 93%14 run in a plain check · 1 never run
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

Getting started with biobouncer HTML

How these are measured

Downloads

457

CRAN downloads in the past year

Rank #24,673 · ~1/day · ~38/mo

Releases R versions

Daily download trend is not available in this view yet.

24330 days

45790 days

4571 year

Compare downloads with other packages →

Also on7 r2u24 autocran

How downloads are counted

Repository

samuelbharti/biobouncer ↗Account: samuelbharti

4Stars

0Forks

1Open issues

2Open PRs

5Releases

360Commits

2Commit identities

bioinformaticsdatabase-toolsjspythonrshinyvalidate

License file reads as MIT · 360 commits · Last activity 2026-09-16 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 98%
Median days to close, 50 most recently updated closed issues: 6
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2026-09-04 · 22026-09-14 · 4

How these are measured

PracticesBeta

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

Checks run against github.com/samuelbharti/biobouncer on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Governance and community (6)

Code of conductContributing guideIssue templatesPR templateSecurity policyCODEOWNERS

Docs source (2)

GitHub Pages site last deployed 2026-09-16 · The repository has a site deploy workflow

Research and citation (1)

CITATION.cff

Show all practicesHide 3 practices

Automation and maintenance (2)

Dependabotpre-commit

Lint, format, editor (3)

lintrLint workflowAir

Git structural (1)

.gitattributes

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

AI coding toolsBeta

This repository shows signs of AI coding tools.

Claude Codefirst seen 2026-07-09
Seen in the repository: CLAUDE.md

How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Installing biobouncer adds 15 packages (12 with compiled code, 6.1 MB of source tarballs). Heaviest: jsonlite 1.0 MB, vctrs 1.0 MB, rlang 766 KB.

Depends (1)

R >= 4.0

Imports (8)

checkmate cli curl jsonlite tibbletoolsutilsyaml

LinkingTo (0)

none

Suggests (4)

knitr rmarkdown testthat withr

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)

Samuel Bharti

Releases (1)

0.1.4Latest
record
2026-09-03 · current release
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-09-03
Total releases: 1 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.0
Download size: 785 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("biobouncer")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

The repository also keeps a CITATION.cff.

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 biobouncer version 0.1.4 [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.

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