R Observatory: Metrics for biocViews version 1.80.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

biocViews

Bioc current

Categorized views of R package repositories

v1.80.0 · software · Artistic-2.0

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 1.7 · Oct 14, 2005

Current · Requires R 4.6

1.0 In 42 of 49 releases 3.23

Description

Infrastructure to support 'views' used to classify Bioconductor packages. 'biocViews' are directed acyclic graphs of terms from a controlled vocabulary. There are three major classifications, corresponding to 'software', 'annotation', and 'experiment data' packages.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

87 30 exported

Complexity

3.4 avg / 24 max

Call network

87 nodes / 76 edges

Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.

Call graph

Open call graph →

Loading call graph…

Lowest coverage

Per-function coverage is not measured for this package yet.

Code

Structure

Lines of code

4,811

Files

76

Compiled share

0%

Has compiled src

No

Language breakdown

R 2,995 (62.3%)Tests 1 (0%)Docs 1,520 (31.6%)Vignettes 295 (6.1%)

API

Exported functions

30

Internal functions

55

Recent export changes

v3.7+1 guessPackageType

Testing & CI

Has tests

Yes

Test-to-code ratio

0.00

testthat edition

–

CI present

No

CI type

[]

PR gated

No

Docs

Roxygen coverage

100%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

35.3%

Unsafe pattern score

0

Dep constraint coverage

20%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

3.6.0

System requirements

–

C++ standard

–

License

Artistic-2.0

License flags

SPDX valid, OSI approved

History

Versions

42

First release

2005-10-12

Latest release

2026-04-28

Avg cadence

182 days

Cold removal rate

100%

Dep drift

12

LOC over versions

Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.

Documentation

READMEYes · 43 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 0% structuredCode of conductNoContributing guideNo

Examples that run: 92%
Documented parameters: 100%
Return-value docs: 44%
References docs: 0%

Topics

Software › Infrastructure

Depended on by (13)

Bioconductor (11)

AnnotationHubData BiocCheck BiocPkgTools BioGA monocle packFinder plasmut ReducedExperiment sigFeature RforProteomics Risa

CRAN (2)

genetic.algo.optimizeR rworkflows

People

Bioconductor Package Maintainer maintainer
Sonali Arora author
Vincent Carey author
Seth Falcon author
Benjamin Harshfield author
Lori Shepherd author

At a glance

Version: 1.80.0
Category: software
License: Artistic-2.0
Requires R: ≥ 4.6
Maintainer: Bioconductor Package Maintainer
Entered: 1.7 · Oct 14, 2005
Current: 3.23 · Apr 29, 2026

Available on

CRAN r2u Bioconductor autoCRAN COPR

Dependencies

Depends

R (>= 3.6.0)

Imports

BiobaseBiocgraph (>= 1.9.26)methodsRBGL (>= 1.13.5)toolsutilsXML RCurl RUnit BiocManager

Suggests

BiocGenericsBiocBiocPkgToolsBiocknitr commonmarkBiocStyleBioc

Source & history

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("biocViews")

Format

Maintainer, B. P., Arora, S., Carey, V., Falcon, S., Harshfield, B., & Shepherd, L. (2026). biocViews: Categorized views of R package repositories (Version 1.80.0) [Computer software]. https://bioconductor.org/packages/biocViews

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 biocViews version 1.80.0 [Data set]. HJJB, LLC. Data release v2026-08-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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