R Observatory: Metrics for phoenics version 0.6.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

phoenics

0.6.1Package record

Pathways Longitudinal and Differential Analysis in Metabolomics

0packages depend

2.9Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Remi ServienCRAN page ↗Repository ↗Issues ↗

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. 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

# 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). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 3.6 min · r-oldrel-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
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.6.1

READMENoVignettesYes · 1 · dynamicNEWSYes · 100% structured · does not mention 0.6.1Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 6
Examples that run: 100%6 run in a plain check (1 of them under a condition)
Exported functions with examples: 100%
Documented parameters: 95%
Return-value docs: 100%
Help pages citing references: 83%

Vignettes (1)

Introduction to phoenics

How these are measured

Downloads

2.9K

CRAN downloads in the past year

Rank #10,168 · ~8/day · ~245/mo

Releases R versions

Daily download trend is not available in this view yet.

42530 days

98190 days

2.9K1 year

Compare downloads with other packages →

Also on90 r2u5 autocran

How downloads are counted

Repository

forge.inrae.fr/panoramics/phoenics ↗

Responsiveness

not measured

How these are measured

PracticesBeta

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 v3 (2026-09-26)

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Installing phoenics adds 113 packages (54 with compiled code, 106 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, bslib 5.6 MB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (3)

Remi Servien

Author, Maintainer since 0.6 (2025)

Camille Guilmineau

Author

Nathalie Vialaneix

Author

Previously maintained by Camille Guilmineau (0.1 to 0.5).

Releases (7)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.6.1Latest
record
2025-08-19 · current release · diff ↗
0.6
record
2025-08-19 · diff ↗
R
R 4.5.0 released · 2025-04-11
0.5
record
2025-01-29 · diff ↗ ·
removed 1 export
head
0.4
record
2024-12-12 · diff ↗
0.3
record
2024-07-22 · diff ↗
0.2
record
2024-06-27 · diff ↗
0.1
record
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

Cite

Cite this package

Run in R for the authors' entry:

citation("phoenics")

The package provides a citation file, so citation() returns the authors' own entry.

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 v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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