R Observatory: Metrics for cliqueMS version 0.3.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2019-06-02. Its history is shown below.

Reason: requires non-portable package. 'mzR' from BioC via 'xcms'

Details below reflect version 0.3.1, its last release before removal.

cliqueMS

0.3.1

Annotation of Isotopes, Adducts and Fragmentation Adducts for in-Source LC/MS Metabolomics Data

0packages depend

–downloads / year

–test coverage

–checks pass

Overview

About

Maintained by Oriol Senan Campos5 releasesCRAN page ↗GitHub ↗

Annotates data from liquid chromatography coupled to mass spectrometry (LC/MS) metabolomics experiments. Based on a network algorithm (O.Senan, A. Aguilar- Mogas, M. Navarro, O. Yanes, R.Guimerà and M. Sales-Pardo, Metabolomics Conference (2016), Dublin), 'CliqueMS' builds a weighted similarity network where nodes are features and edges are weighted according to the similarity of this features. Then it searches for the most plausible division of the similarity network into cliques (fully connected components). Finally it annotates metabolites within each clique, obtaining for each annotated metabolite the neutral mass and their features, corresponding to isotopes, ionization adducts and fragmentation adducts of that metabolite.

Install

BioconductorR (source archive)pak (dev)Ubuntu (r2u)

BiocManager::install("cliqueMS")

Installs the current Bioconductor release. Requires the BiocManager package.

url <- "https://cran.r-project.org/src/contrib/Archive/cliqueMS/cliqueMS_0.3.1.tar.gz"
pkgFile <- "cliqueMS_0.3.1.tar.gz"
download.file(url, pkgFile)
install.packages(pkgFile, type = "source", repos = NULL)

This package is no longer on CRAN, so install.packages() cannot fetch it by name. This downloads the last archived source (0.3.1) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

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

Development version from osenan/cliqueMS. 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-cliquems

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

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

Health

CRAN checks

CRAN check results are not tracked yet.

Code health

Yes

Tests · ratio 0.06

not tracked

Coverage

100%

Documentation · exports

7

Dependencies · direct

Documentation

READMEYes · 75 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 20%
Documented parameters: 100%
Return-value docs: 71%
References docs: 0%

Downloads

Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on347 r2u1.9K bioconda

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.4.0

Imports (7)

Rcpp xcms MSnbase igraph qlcMatrixMatrixmethods

LinkingTo (3)

Rcpp BH RcppArmadillo

Suggests (4)

knitr rmarkdown testthat CAMERA

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (7)

Maintainer (1)

Oriol Senan Campos

Author, Maintainer

Authors (7)

Author, Maintainer

Author

Author

Author

Author

Author

Author

Package Timeline

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

R
R 4.0.0 released · 2020-04-24
archivedRemoved from CRAN
2019-06-02
requires non-portable package 'mzR' from BioC via 'xcms'
R
R 3.6.0 released · 2019-04-26
0.3.1
2019-04-25 · diff ↗
0.3.0
2019-01-30 · diff ↗
0.2.4
2019-01-10 · diff ↗
0.2.3
2018-11-15 · diff ↗
0.2.1
2018-05-14
R
R 3.5.0 released · 2018-04-23

Package metadata

Total releases: 5
License: GPL (>= 2) OSI
Minimum R: ≥ 3.4.0
Bundled data: 86 KB / 3 files
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("cliqueMS")

Format

Senan Campos, O., Aguilar-Mogas, A., Capellades, J., Navarro, M., Yanes, O., Guimerà, R., & Sales-Pardo, M. (n.d.). cliqueMS: Annotation of Isotopes, Adducts and Fragmentation Adducts for in-Source LC/MS Metabolomics Data (Version 0.3.1) [Computer software]. Retrieved August 13, 2026, from https://CRAN.R-project.org/package=cliqueMS

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 cliqueMS version 0.3.1 [Data set]. HJJB, LLC. Data release v2026-08-13. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-13, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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