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S4Vectors

Bioc current

Foundation of vector-like and list-like containers in Bioconductor

v0.50.1 · software · Artistic-2.0
View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.0 · Oct 14, 2014

Current · Requires R 4.6

1.0 In 24 of 49 releases 3.23

Description

The S4Vectors package defines the Vector and List virtual classes and a set of generic functions that extend the semantic of ordinary vectors and lists in R. Package developers can easily implement vector-like or list-like objects as concrete subclasses of Vector or List. In addition, a few low-level concrete subclasses of general interest (e.g. DataFrame, Rle, Factor, and Hits) are implemented in the S4Vectors package itself (many more are implemented in the IRanges package and in other Bioconductor infrastructure packages).

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

831 125 exported

Complexity

3.4 avg / 26 max

Call network

831 nodes / 1084 edges

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

Call graph

Open call graph →
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Lowest coverage

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

Code

Structure

Lines of code

33,273

Files

143

Compiled share

33.1%

Has compiled src

Yes

Language breakdown

R 14,144 (42.5%)C/C++/src 11,028 (33.1%)Tests 2 (0%)Docs 7,218 (21.7%)Vignettes 881 (2.6%)

API

Exported functions

218

Internal functions

316

Recent export changes

v3.9+5 transform.DataTable, transform.Vector, mergeROWS +2 more
v3.8+3 rev.Vector, isSequence, bindROWS  −1 concatenateObjects

Testing & CI

Has tests

Yes

Test-to-code ratio

0.00

testthat edition

–

CI present

No

CI type

[]

PR gated

No

Docs

Roxygen coverage

99.1%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

83.3%

Unsafe pattern score

0

Dep constraint coverage

20%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

4.1.0

System requirements

–

C++ standard

–

License

Artistic-2.0

License flags

SPDX valid, OSI approved

History

Versions

24

First release

2014-10-13

Latest release

2026-05-03

Avg cadence

207 days

Cold removal rate

100%

Dep drift

0

LOC over versions

v3.0: 16,334 LOCv3.1: 18,546 LOCv3.2: 20,062 LOCv3.3: 22,948 LOCv3.4: 24,110 LOCv3.5: 26,795 LOCv3.6: 26,822 LOCv3.7: 27,880 LOCv3.8: 28,325 LOCv3.9: 28,980 LOCv3.10: 30,620 LOCv3.11: 31,220 LOCv3.12: 31,926 LOCv3.13: 32,423 LOCv3.14: 32,474 LOCv3.15: 32,704 LOCv3.16: 33,016 LOCv3.17: 33,047 LOCv3.18: 33,051 LOCv3.19: 33,032 LOCv3.20: 33,044 LOCv3.21: 33,068 LOCv3.22: 32,894 LOCv3.23: 33,273 LOC

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

Documentation

Documentation
READMEYes · 42 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo
Examples that run
100%
Documented parameters
59%
Return-value docs
45%
References docs
0%

Topics

Software › Infrastructure
Software › Infrastructure › DataRepresentation

Depended on by (1300)

Bioconductor (1245)

ADImpute adverSCarial affycoretools aggregateBioVar airpart alabaster.base alabaster.bumpy alabaster.files alabaster.mae alabaster.matrix alabaster.ranges alabaster.se alabaster.sfe alabaster.spatial alabaster.string alabaster.vcf ALDEx2 AllelicImbalance AlphaMissenseR AlpsNMR altcdfenvs amplican anansi ANCOMBC anglemania animalcules anndataR annoLinker AnnotationDbi AnnotationForge +1215 more

CRAN (55)

ActiveDriverWGS DESNP DR.SC LoopRig MetAlyzer NIPTeR PlasmaMutationDetector PopPsiSeqR RiskyCNV Signac TaxaNorm TmCalculator XYomics cpp11bigwig crispRdesignR driveR genBaRcode geno2proteo hicream imcExperiment karyotapR lisat microbial mikropml multimedia ocrRBBR oncoPredict restfulr revert rliger +25 more

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