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alabaster.base

Bioc current

Save Bioconductor Objects to File

v1.12.1 · software · MIT + file LICENSE
View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.17 · Apr 26, 2023

Current · Requires R 4.6

1.0 In 7 of 49 releases 3.23

Description

Save Bioconductor data structures into file artifacts, and load them back into memory. This is a more robust and portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

Code

Structure

Lines of code

13,113

Files

138

Compiled share

12.4%

Has compiled src

Yes

Language breakdown

R 5,609 (42.8%)C/C++/src 1,622 (12.4%)Tests 3,377 (25.8%)Docs 2,207 (16.8%)Vignettes 298 (2.3%)

API

Exported functions

107

Internal functions

80

Recent export changes

v3.23+1 cloneFile
v3.21+13 absolutizePath, addObjectToDedupSession, checkObjectInDedupSession +10 more

Testing & CI

Has tests

Yes

Test-to-code ratio

0.60

testthat edition

–

CI present

Yes

CI type

["github-actions"]

PR gated

Yes

Docs

Return-value doc rate

94.4%

\dontrun example ratio

0%

Roxygen coverage

100%

Has pkgdown

No

NEWS present

No

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

71.4%

Unsafe pattern score

6

Dep constraint coverage

12.5%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

–

System requirements

2

C++ standard

–

License

MIT + file LICENSE

License flags

SPDX valid, OSI approved

History

Versions

7

First release

2023-04-25

Latest release

2026-06-30

Avg cadence

201 days

Cold removal rate

–

Dep drift

0

LOC over versions

v3.17: 5,875 LOCv3.18: 8,372 LOCv3.19: 10,274 LOCv3.20: 10,746 LOCv3.21: 12,844 LOCv3.22: 12,879 LOCv3.23: 13,113 LOC

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

Topics

Software › Infrastructure › DataRepresentation
Software › Infrastructure › DataImport

Depended on by (16)

Bioconductor (16)

alabaster alabaster.bumpy alabaster.files alabaster.mae alabaster.matrix alabaster.ranges alabaster.sce alabaster.se alabaster.sfe alabaster.spatial alabaster.string alabaster.vcf chevreulShiny celldex scRNAseq augere.core

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