R Observatory: Metrics for MSclassifR version 0.5.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

MSclassifR

0.5.0Package record

Automated Classification of Mass Spectra

0packages depend

3.7Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Alexandre GodmerCRAN page ↗GitHub ↗Issues ↗

Functions to classify mass spectra in known categories and to determine discriminant mass-to-charge values (m/z). Includes easy-to-use preprocessing pipelines for Matrix Assisted Laser Desorption Ionisation - Time Of Flight Mass Spectrometry (MALDI-TOF) mass spectra, methods to select discriminant m/z from labelled libraries, and tools to predict categories (species, phenotypes, etc.) from selected features. Also provides utilities to build design matrices from peak intensities and labels. While this package was developed with the aim of identifying very similar species or phenotypes of bacteria from MALDI-TOF MS, the functions of this package can also be used to classify other categories associated to mass spectra; or from mass spectra obtained with other mass spectrometry techniques. Parallelized processing and optional C++-accelerated functions are available (notably to deal with large datasets) from version 0.5.0. If you use this package in your research, please cite the associated publication (doi:10.1016/j.eswa.2025.128796). For a comprehensive guide, additional applications, and detailed examples, see https://github.com/agodmer/MSclassifR_examples.

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("MSclassifR", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("agodmer/MSclassifR_examples")

Development version from agodmer/MSclassifR_examples. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-msclassifr

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 5.1 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-02

Show 6 earlier changesHide 6 earlier changes

ERROR11 OK, 1 ERROR2026-04-25
NOTE13 OK, 1 NOTE2026-04-22
ERROR12 OK, 1 NOTE, 1 ERROR2026-04-18
NOTE13 OK, 1 NOTE2026-04-08
ERROR12 OK, 1 NOTE, 1 ERROR2026-04-07
NOTE13 OK, 1 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.5.0

READMENoVignettesNoNEWSNoCitation fileNo

Help pages: 25 (3 internal)
Examples that run: 31%4 run in a plain check (2 of them under a condition) · 4 only when donttest examples are enabled (R CMD check --as-cran) · 5 never run
Exported functions with examples: 93%
Documented parameters: 96%
Return-value docs: 100%
Help pages citing references: 28%

How these are measured

Downloads

3.7K

CRAN downloads in the past year

Rank #7,476 · ~10/day · ~307/mo

Releases R versions

Daily download trend is not available in this view yet.

42230 days

1.2K90 days

3.7K1 year

Compare downloads with other packages →

Also on477 r2u

How downloads are counted

Repository

agodmer/msclassifr_examples ↗Account: agodmer

4Stars

1Forks

1Open issues

0Open PRs

0Releases

67Commits

2Commit identities

License file reads as GPL-3.0 · 67 commits · Last activity 2025-07-09 · Discussions: 2 posts

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: 0

How these are measured

PracticesBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/agodmer/msclassifr_examples on 2026-10-11.

Docs source (1)

GitHub Pages site last deployed 2025-07-09

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

29 external dependencies (excludes base and recommended)

Installing MSclassifR adds 150 packages (81 with compiled code, 128 MB of source tarballs). Heaviest: stringi 11 MB, ggformula 6.0 MB, ggplot2 6.0 MB. 3 more not on CRAN are not measured.

Depends (6)

R >= 4.0cp4p caret statmod MALDIquant MALDIrppa

Imports (9)

reshape2 ggplot2 dplyrstatslimma car RcppMatrixmethods

LinkingTo (1)

Rcpp

Suggests (18)

doParallel foreach ranger randomForest mixOmics VSURF vita Boruta glmnet e1071 xgboostnnetmclust mltools metap MALDIquantForeign matrixStats rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (3)

Alexandre Godmer

Author, Maintainer since 0.1.0 (2022)

Karen Druart

Author · added in 0.3.2

Quentin Giai Gianetto

Author

Releases (8)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.5.0Latest
record
2025-12-09 · current release · diff ↗ ·
removed 1 export
pattern:^[[:alpha:]]+

added 14 exports
PeakDetection, build_X_from_peaks_fast, build_XY_from_peaks, PredictLogReg, PredictFastClass, SelectionVar, SelectionVarStat, PlotSpectra, fast_mda, fast_cvpvi, LogReg, LogReg_rf_fast, SignalProcessing, smote_classif
unarchivedReturned to CRAN
2025-07-02
0.4.0
record
2025-07-02 · diff ↗
archivedRemoved from CRAN
2025-06-30
requires archived package 'UBL'
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
0.3.3
record
2023-08-09 · diff ↗
R
R 4.3.0 released · 2023-04-21
0.3.2
record
2023-03-28 · diff ↗
0.3.1
record
2022-09-29 · diff ↗
0.3.0
record
2022-08-13 · diff ↗
R
R 4.2.0 released · 2022-04-22
unarchivedReturned to CRAN
2022-02-25
archivedRemoved from CRAN
2022-02-25
check problems were not corrected in time
0.2.0
record
2022-02-25 · diff ↗

Show 2 earlier eventsHide 2 earlier events

0.1.0
record
2022-01-18
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2022-01-18
Total releases: 8 / 4 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.0
Bundled data: 2.3 MB / 2 files
Download size: 2.4 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("MSclassifR")

Format

Godmer, A., Druart, K., & Giai Gianetto, Q. (2025). MSclassifR: Automated Classification of Mass Spectra (Version 0.5.0) [Computer software]. https://doi.org/10.32614/CRAN.package.MSclassifR

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 MSclassifR version 0.5.0 [Data set]. HJJB, LLC. Data release v2026-10-19. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →