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RMassBank

Bioc current

Workflow to process tandem MS files and build MassBank records

v3.22.0 · 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.

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

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Lowest coverage

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

Code

Structure

Lines of code

20,968

Files

186

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 & CI

Has tests

Yes

Test-to-code ratio

0.00

testthat edition

–

CI present

Yes

CI type

["github-actions","travis"]

PR gated

Yes

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

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

v2.11: 7,976 LOCv2.12: 8,156 LOCv2.13: 10,461 LOCv2.14: 11,653 LOCv3.0: 11,630 LOCv3.1: 13,090 LOCv3.2: 13,090 LOCv3.3: 16,551 LOCv3.4: 16,551 LOCv3.5: 16,551 LOCv3.6: 16,559 LOCv3.7: 16,559 LOCv3.8: 16,573 LOCv3.9: 16,564 LOCv3.10: 16,568 LOCv3.11: 17,267 LOCv3.12: 19,036 LOCv3.13: 19,036 LOCv3.14: 19,286 LOCv3.15: 19,944 LOCv3.16: 19,944 LOCv3.17: 19,944 LOCv3.18: 20,319 LOCv3.19: 20,319 LOCv3.20: 20,968 LOCv3.21: 20,968 LOCv3.22: 20,968 LOCv3.23: 20,968 LOC

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

Documentation

Documentation
READMEYes · 181 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo
Examples that run
44%
Documented parameters
99%
Return-value docs
86%
References docs
16%

Topics

Software › ResearchField › Immunology › ImmunoOncology
Bioinformatics
Software › Technology › MassSpectrometry
Software › ResearchField › Metabolomics
Software

Depended on by (1)

Bioconductor (1)

RMassBankData

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