R Observatory: Metrics for HoloFoodR version 1.6.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

HoloFoodR

Bioc current

R interface to EBI HoloFood resource

v1.6.0 · software · Artistic-2.0 | file LICENSE

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.20 · Oct 30, 2024

Current · Requires R 4.6

1.0 In 4 of 49 releases 3.23

Description

Utility package to facilitate integration and analysis of EBI HoloFood data in R. This package streamlines access to the resource, allowing for direct loading of data into formats optimized for downstream analytics.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

52 5 exported

Complexity

4.3 avg / 53 max

Call network

52 nodes / 72 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

4,186

Files

43

Compiled share

0%

Has compiled src

No

Language breakdown

R 2,299 (54.9%)Tests 244 (5.8%)Docs 454 (10.8%)Vignettes 1,189 (28.4%)

API

Exported functions

6

Internal functions

47

Recent export changes

v3.21+1 addMGnify

v3.20+5 doQuery, getData, getMetaboLights +2 more

Testing & CI

Has tests

Yes

Test-to-code ratio

0.11

testthat edition

–

CI present

Yes

CI type

["github-actions"]

PR gated

Yes

Docs

Roxygen coverage

100%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

0%

Unsafe pattern score

0

Dep constraint coverage

0%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

4.4.0

System requirements

–

C++ standard

–

License

Artistic-2.0 | file LICENSE

License flags

SPDX valid, not OSI

History

Versions

4

First release

2024-10-29

Latest release

2026-04-28

Avg cadence

181 days

Cold removal rate

–

Dep drift

2

LOC over versions

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

Documentation

READMEYes · 483 wordsVignettesYes · dynamicpkgdown siteYesNEWSYes · 33% structuredCode of conductNoContributing guideNo

Examples that run: 80%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Topics

Software

Software › Infrastructure

Software › Infrastructure › DataImport

Software › Technology › Sequencing › Microbiome

ExperimentData › TechnologyData › SequencingData › MicrobiomeData

People

Tuomas Borman author maintainer
Leo Lahti author
Artur Sannikov author

At a glance

Version: 1.6.0
Category: software
License: Artistic-2.0 | file LICENSE
Requires R: ≥ 4.6
Maintainer: Tuomas Borman
Entered: 3.20 · Oct 30, 2024
Current: 3.23 · Apr 29, 2026

Available on

CRAN r2u Bioconductor autoCRAN COPR

Dependencies

Depends

R(>= 4.4.0)MultiAssayExperimentBiocTreeSummarizedExperimentBioc

Imports

dplyr httr2 jsonliteS4VectorsBiocstringistatsSummarizedExperimentBiocutils

Suggests

BiocStyleBiocDT ggh4x ggsignif knitrMGnifyRBiocmiaBiocmiaVizBiocMOFA2Biocpatchwork reticulate rmarkdownscaterBiocshadowtext testthat UpSetR

Source & history

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("HoloFoodR")

Format

Borman, T., Lahti, L., & Sannikov, A. (2026). HoloFoodR: R interface to EBI HoloFood resource (Version 1.6.0) [Computer software]. https://bioconductor.org/packages/HoloFoodR

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 HoloFoodR version 1.6.0 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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