R Observatory: Metrics for phoenics version 0.6.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

phoenics

0.6.1

Pathways Longitudinal and Differential Analysis in Metabolomics

0packages depend

2.6Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Remi ServienFirst published 2024-05-227 releasesCRAN page ↗

Perform a differential analysis at pathway level based on metabolite quantifications and information on pathway metabolite composition. The method, described in Guilmineau et al (2025) doi:10.1186/s12859-025-06118-z is based on a Principal Component Analysis step and on a linear mixed model. Automatic query of metabolic pathways is also implemented.

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

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

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

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-phoenics

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

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-phoenics

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-phoenics

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 3.6 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

7

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 95%
Return-value docs: 100%
References docs: 83%

Downloads

2.6K

CRAN downloads in the past year

Rank #14,841 · ~7/day · ~213/mo

Releases R versions

Daily download trend is not available in this view yet.

16730 days

69990 days

2.6K1 year

Compare downloads with other packages →

Also on120 r2u

Repository

Repository ↗ panoramics/phoenics

Repository practices

Upstream repositoryBeta

Repository forge.inrae.fr/panoramics/phoenics is linked, but repository-practices checks have not run for it yet. Checks are GitHub-only for now.

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

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.0.0

Imports (7)

lme4 blme tibble FactoMineR factoextra tidyrstats

LinkingTo (0)

none

Suggests (2)

knitr KEGGREST

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (3)

Maintainer (1)

Remi Servien

Author, Maintainer

Authors (3)

Remi Servien

Author, Maintainer

Camille Guilmineau

Author

Nathalie Vialaneix

Author

Package Timeline

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

0.6.1Latest
2026-07-02 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
0.6
2025-08-19 · diff ↗
R
R 4.5.0 released · 2025-04-11
0.5
2025-01-29 · diff ↗
0.4
2024-12-12 · diff ↗
0.3
2024-07-22 · diff ↗
0.2
2024-06-27 · diff ↗
0.1
2024-05-22
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-05-22
Total releases: 7 / 2 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.0.0
Bundled data: 1.3 KB / 1 file
Download size: 319 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("phoenics")

Format

Servien, R., Guilmineau, C., & Vialaneix, N. (2026). phoenics: Pathways Longitudinal and Differential Analysis in Metabolomics (Version 0.6.1) [Computer software]. https://doi.org/10.32614/CRAN.package.phoenics

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 phoenics version 0.6.1 [Data set]. HJJB, LLC. Data release v2026-08-16. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-16, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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