R Observatory: Metrics for RMassBank version 3.22.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

RMassBank

Bioc current

Workflow to process tandem MS files and build MassBank records

v3.22.0 · Package record · software · Artistic-2.0

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 2.11 · Oct 3, 2012

Current · Requires R 4.6

1.0 In 28 of 49 releases 3.23

Description

Workflow to process tandem MS files and build MassBank records. Functions include automated extraction of tandem MS spectra, formula assignment to tandem MS fragments, recalibration of tandem MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet databases, and export to MassBank records.

Advisories

None published for Bioconductor

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

210 125 exported

Complexity

5.2 avg / 51 max

Call network

210 nodes / 301 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.

How coverage is measured·How the call graph is built

Code

Structure

Lines of code

20,968

Files

184

Compiled share

0%

Has compiled src

No

Language breakdown

R 14,323 (68.3%)Tests 24 (0.1%)Docs 5,538 (26.4%)Vignettes 1,083 (5.2%)

API

Exported functions

141

Internal functions

85

Testing

Has tests

Yes

Test-to-code ratio

0.00

testthat edition

–

Docs

Roxygen coverage

100%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

10.5%

Unsafe pattern score

0

Dep constraint coverage

0%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

–

System requirements

1 externalOpenBabel

C++ standard

–

License

Artistic-2.0

License flags

SPDX valid, OSI approved

History

Versions

28

First release

2012-10-01

Latest release

2026-04-28

Avg cadence

182 days

Cold removal rate

100%

Dep drift

27

LOC over versions

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

Documentation

In the Bioconductor 3.23 release

READMEYes · 181 wordsVignettesYes · 2 · dynamicNEWSYes · 100% structuredCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 126
Examples that run: 25%18 run in a plain check · 54 never run
Exported functions with examples: 64%
Documented parameters: 99%
Return-value docs: 86%
Help pages citing references: 16%

Vignettes (2)

How these are measured

Repository practices

Bioconductor git repository

Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.

3 practices detected in the Bioconductor git repository

Continuous integration (3)

GitHub ActionsTravis CI (config file)PR checks

How this is detected

Topics

Software › ResearchField › Immunology › ImmunoOncology

Bioinformatics

Software › Technology › MassSpectrometry

Software › ResearchField › Metabolomics

Software

Maintainer: RMassBank at Eawag

Available on

CRANr2uBioconductorautoCRANCOPR

Suggested by (1)

RMassBankData

People

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("RMassBank")

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

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 RMassBank version 3.22.0 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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