R Observatory: Metrics for specmine version 3.1.8

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

specmine

3.1.8

Metabolomics and Spectral Data Analysis and Mining

0packages depend

327downloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Pedro FontãoFirst published 2026-08-0512 releasesCRAN page ↗GitHub ↗

Provides methods for metabolomics and spectral data analysis, including data import, preprocessing, visualization, univariate and multivariate analysis, machine learning, feature selection, and pathway analysis. The package supports analytical workflows for different data types used in metabolomics and spectroscopy. Some optional functionality uses the suggested packages 'cyjShiny' and 'specmine.datasets'. The package 'specmine.datasets' is maintained separately at https://github.com/PedroFontao/specmine.datasets.

Install

R (CRAN)pak (dev)

install.packages("specmine", 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("PedroFontao/specmine")

Development version from PedroFontao/specmine. Installs pak first if it is not already available.

Health

CRAN checks

13OK

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

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

22

Dependencies · direct

Check history

OK2026-08-06
6 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 59%
Documented parameters: 97%
Return-value docs: 100%
References docs: 1%

Downloads

327

CRAN downloads in the past year

Rank #24,246 · ~1/day · ~27/mo

specmine Releases R versions

Daily download trend is not available in this view yet.

32030 days

32290 days

3271 year

Compare downloads with other packages →

Repository

GitHub ↗ pedrofontao/specmine

1Stars

0Forks

1Open issues

0Open PRs

0Releases

5Commits

1Contributors

5 commits · Last activity 2026-07-27

Repository practices

Upstream repositoryBeta

5 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/pedrofontao/specmine on 2026-08-16.

Continuous integration (1)

GitHub Actions

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

40 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.0.0

Imports (22)

baseline caret compare ellipse genefilter GGally ggplot2grDevicesgraphicsimpute imputeTSMASSmethodsMetrics narray pcaPP plotly pls RColorBrewer readJDXstatsutils

LinkingTo (0)

none

Suggests (24)

clusterCrit curl dbscan fastICA ggdendro KEGGgraph KEGGREST knitr MAIT mclust pins qdap qpdf RCurl cyjShiny reticulate rgl Rtsne rmarkdown scatterplot3d specmine.datasets uwot randomForest xcms

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (9)

Maintainer (1)

Pedro Fontão

Author, Maintainer · added in 3.1.8

Authors (7)

Pedro Fontão

Author, Maintainer · added in 3.1.8

Telma Afonso

Author · added in 2.0.2

Sara Cardoso

Author · added in 2.0.2

Christopher Costa

Author

Marcelo Maraschin

Author

Bruno Pereira

Author · added in 3.0.3

Miguel Rocha

Author

Copyright holders (2)

C. Beleites

Copyright holder · added in 2.0.2

Jie Hao

Copyright holder · added in 2.0.2

Listed in earlier versions (1)

Daniel Jacob

no longer listed · 2.0.2 to 2.0.3

Package Timeline

12 releases. Pick two to compare their code metrics. R releases are shown for context.

3.1.8Latest
2026-08-05 · current release · diff ↗
unarchivedReturned to CRAN
2026-08-05
R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
archivedRemoved from CRAN
2022-04-04
require archived package 'specmine.datasets'
3.1.6
2021-09-21 · diff ↗
R
R 4.1.0 released · 2021-05-18
3.1.5
2021-05-16 · diff ↗
3.1.4
2021-03-04 · diff ↗
3.1.3
2021-02-20 · diff ↗
unarchivedReturned to CRAN
2020-12-18
3.0.3
2020-12-17 · diff ↗
archivedRemoved from CRAN
2020-11-29
requires archived package 'hyperSpec'

Show 18 earlier events

3.0.2
2020-09-18 · diff ↗
3.0.1
2020-07-10 · diff ↗
3.0.0
2020-07-10 · diff ↗
unarchivedReturned to CRAN
2020-07-10
R
R 4.0.0 released · 2020-04-24
archivedRemoved from CRAN
2019-06-02
requires non-portable package 'mzR' from BioC
R
R 3.6.0 released · 2019-04-26
2.0.3
2018-05-15 · diff ↗
unarchivedReturned to CRAN
2018-05-15
archivedRemoved from CRAN
2018-05-13
it installed a package from an untrusted source
2.0.2
2018-05-11 · diff ↗
unarchivedReturned to CRAN
2018-05-11
R
R 3.5.0 released · 2018-04-23
archivedRemoved from CRAN
2018-01-27
check problems were not corrected despite reminders
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
1.0
2015-11-10
R
R 3.2.0 released · 2015-04-16

Package metadata

First published: 2026-08-05
Total releases: 12 / 1 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 4.0.0
Bundled data: 15 KB / 1 file
Download size: 4.6 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("specmine")

Format

Fontão, P., Afonso, T., Beleites, C., Cardoso, S., Costa, C., Hao, J., Maraschin, M., Pereira, B., & Rocha, M. (2026). specmine: Metabolomics and Spectral Data Analysis and Mining (Version 3.1.8) [Computer software]. https://doi.org/10.32614/CRAN.package.specmine

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 specmine version 3.1.8 [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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