R Observatory: Metrics for specmine version 4.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

specmine

4.0.1Package record

Metabolomics and Spectral Data Analysis and Mining

0packages depend

1.6Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Pedro FontãoCRAN page ↗GitHub ↗Issues ↗

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)Ubuntu (r2u)

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.

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-specmine

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: 6.5 min · r-oldrel-windows-x86_64

Status changes

OK13 OKNow
OK6 OK2026-08-06

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 4.0.1

README· In the repository, left out of the releaseVignettesYes · 1 · staticNEWSYes · 100% structured · does not mention 4.0.1Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 121 (11 internal)includes a package overview page
Examples that run: 69%83 run in a plain check (20 of them under a condition) · 15 only when donttest examples are enabled (R CMD check --as-cran) · 23 never run
Exported functions with examples: 100%
Documented parameters: 96%
Return-value docs: 100%
Help pages citing references: 2%

Vignettes (1)

User guide to analyze 2D-NMR metabolomics' experiments using *specmine* package HTML

How these are measured

Downloads

1.6K

CRAN downloads in the past year

Rank #5,093 · ~4/day · ~134/mo

Releases R versions

Daily download trend is not available in this view yet.

73530 days

1.6K90 days

1.6K1 year

Compare downloads with other packages →

Also on23 r2u

How downloads are counted

Repository

pedrofontao/specmine ↗Account: PedroFontao

1Stars

0Forks

1Open issues

0Open PRs

0Releases

8Commits

1Commit identities

8 commits · Last activity 2026-09-28 · The default branch showed an older version (4.0.0) than CRAN on 2026-10-18

Responsiveness

not measured

Commits over time

2026-08-09 · 52026-10-04 · 8

How these are measured

PracticesBeta

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

Checks run against github.com/pedrofontao/specmine on 2026-10-18.

Continuous integration (1)

GitHub Actions

Docs source (1)

README.Rmd

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

40 external dependencies (excludes base and recommended)

Installing specmine adds 130 packages (69 with compiled code, 99 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB. 2 more not on CRAN are not measured.

Depends (1)

R >= 4.0.0

Imports (23)

baseline caret compare ellipse genefilter GGally ggplot2grDevicesgraphicsimpute imputeTSMASSMatrixmethodsMetrics 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.

How these are counted

Code & Tests

Datasets

People & History

People (10)

Pedro Fontão

Author, Maintainer since 3.1.8 (2026) · 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

Rafael Moreira

Author · added in 4.0.1

Bruno Pereira

Author · added in 3.0.3

Miguel Rocha

Author

C. Beleites

Copyright holder · added in 2.0.2

Jie Hao

Copyright holder · added in 2.0.2

Previously maintained by Miguel Rocha (2.0.2 to 3.1.6) and Christopher Costa (1.0).

Listed in earlier versions (1)

Daniel Jacob

no longer listed · 2.0.2 to 2.0.3

Releases (14)

Pick two releases to compare their code metrics.

4.0.1Latest
record
2026-09-28 · current release · diff ↗
4.0.0
record
2026-09-08 · diff ↗ ·
added 33 exports
airPLS_fast_dataset, ica_analysis_dataset, ica_kmeans_plot2D, ica_kmeans_plot3D, ica_loadingsplot, ica_pairs_kmeans_plot, ica_pairs_plot, ica_scoresplot2D, ica_scoresplot3D, pca_importance, raman_align_peaks, raman_crop_spectra, raman_despike, raman_find_peaks, raman_normalize, raman_normalize_peak_features, raman_sgolay_derivative, raman_transform_fourier, raman_transform_wavelet, tsne_analysis_dataset, tsne_kmeans_plot2D, tsne_kmeans_plot3D, tsne_pairs_kmeans_plot, tsne_pairs_plot, tsne_scoresplot2D, tsne_scoresplot3D, umap_analysis_dataset, umap_kmeans_plot2D, umap_kmeans_plot3D, umap_pairs_kmeans_plot and 3 more
unarchivedReturned to CRAN
2026-08-05
3.1.8
record
2026-08-05 · diff ↗ ·
removed 119 exports
create_2d_dataset, check_dataset, check_2d_dataset, sum_dataset, sum_2d_dataset, get_data, get_data_as_df, get_metadata, get_metadata_var, get_sample_names, get_sample_2d_data, get_x_values_as_num, get_value_label, get_type, get_data_value, get_metadata_value, get_data_values, num_samples, num_x_values, is_spectra, x_values_to_indexes, xvalue_interval_to_indexes, indexes_to_xvalue_interval, variables_as_metadata, metadata_as_variables, set_metadata, set_x_values, set_x_label, set_value_label, set_sample_names and 89 more

added 5 exports
aov_one_var, convert_keggpathway_2_reactiongraph, create_pathway_with_reactions, get_MetabolitePath, read_spc_nosubhdr
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
record
2021-09-21 · diff ↗
R
R 4.1.0 released · 2021-05-18
3.1.5
record
2021-05-16 · diff ↗
3.1.4
record
2021-03-04 · diff ↗
3.1.3
record
2021-02-20 · diff ↗ ·
added 8 exports
create_2d_dataset, check_2d_dataset, sum_2d_dataset, get_sample_2d_data, peak_detection2d, plot_2d_spectra, read_varian_2dspectra_raw, read_Bruker_files_2d
unarchivedReturned to CRAN
2020-12-18

Show 20 earlier eventsHide 20 earlier events

3.0.3
record
2020-12-17 · diff ↗ ·
removed 2 exports
convert_from_hyperspec, convert_to_hyperspec
archivedRemoved from CRAN
2020-11-29
requires archived package 'hyperSpec'
3.0.2
record
2020-09-18 · diff ↗
unarchivedReturned to CRAN
2020-07-10
3.0.1
record
2020-07-10 · diff ↗
3.0.0
record
2020-07-10 · diff ↗ ·
removed 3 exports
choose_nmr_references, get_hmdbs_with_specs_id, get_metabolights_study_list

added 7 exports
convert_chebi_to_kegg, convert_multiple_spcmnm_to_kegg, metabolights_studies_list, get_files_list_per_assay, get_metabolights_study_samples_files, get_metabolights_study_files_assay, get_metabolights_study_metadata_assay
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
unarchivedReturned to CRAN
2018-05-15
2.0.3
record
2018-05-15 · diff ↗
archivedRemoved from CRAN
2018-05-13
it installed a package from an untrusted source
unarchivedReturned to CRAN
2018-05-11
2.0.2
record
2018-05-11 · diff ↗ ·
added 15 exports
choose_nmr_references, get_hmdbs_with_specs_id, nmr_identification, get_cpd_names, convert_hmdb_to_kegg, get_OrganismsCodes, get_metabPaths_org, get_paths_with_cpds_org, pathway_analysis, get_metabolights_study_list, get_metabolights_study, read_varian_spectra_raw, read_Bruker_files, detect_nmr_peaks_from_dataset, plot_peaks
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
record
2015-11-10
R
R 3.2.0 released · 2015-04-16

Package metadata

First published: 2015-11-10
Total releases: 14 / 11 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 4.0.0
Bundled data: 15 KB / 1 file
Download size: 4.6 MB

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., Moreira, R., Pereira, B., & Rocha, M. (2026). specmine: Metabolomics and Spectral Data Analysis and Mining (Version 4.0.1) [Computer software]. https://doi.org/10.32614/CRAN.package.specmine

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 specmine version 4.0.1 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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