R Observatory: Metrics for Cascade version 2.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

Cascade

2.4Package record

Selection, Reverse-Engineering and Prediction in Cascade Networks

1packages depend

5.6Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Frederic BertrandCRAN page ↗GitHub ↗Website ↗Issues ↗

A modeling tool allowing gene selection, reverse engineering, and prediction in cascade networks. Jung, N., Bertrand, F., Bahram, S., Vallat, L., and Maumy-Bertrand, M. (2014) doi:10.1093/bioinformatics/btt705.

Changes in 2.4

Fixed CRAN package load warning by removing the unused magic import.
Replaced broad igraph imports with selective namespace imports to reduce collision risk.
Replaced the remaining broad imports with selective imports or removed them when unused.
Removed the legacy inst/animation saveHTML output that vendored vulnerable jQuery assets.
Moved the E-MTAB-1475 re-analysis PDF out of the package vignettes and made it available through the pkgdown website only.

From NEWS.md in the release

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("Cascade", 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("fbertran/Cascade")

Development version from fbertran/Cascade. 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-cascade

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: 2.7 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-05-07
WARNING13 OK, 1 WARNING2026-03-29
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.4

READMEYes · 493 wordsVignettesYes · 2 · staticNEWSYes · 67% structured · mentions 2.4Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 27 (1 internal)includes a package overview page
Examples that run: 85%22 run in a plain check · 4 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 44%

Vignettes (2)

Cascade: Introduction to Cascade PDF
Cascade: Manual PDF

How these are measured

Downloads

5.6K

CRAN downloads in the past year

Rank #5,091 · ~15/day · ~463/mo

Releases R versions

Daily download trend is not available in this view yet.

76130 days

1.6K90 days

5.6K1 year

Compare downloads with other packages →

Also on181 r2u37 c2d4u

How downloads are counted

Repository

fbertran/cascade ↗Account: fbertran

1Stars

1Forks

1Open issues

1Open PRs

3Releases

54Commits

1Commit identities

54 commits · Last activity 2026-04-30 · 0% stars, 30d

Responsiveness

not measured

Stars over time

2014-04-04 · 12026-07-07 · 1

How these are measured

PracticesBeta

6 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/fbertran/cascade on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on macOS

Docs source (3)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-04-30

pkgdown site last built 2026-04-30

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Installing Cascade adds 18 packages (12 with compiled code, 18 MB of source tarballs). Heaviest: igraph 4.8 MB, magick 4.4 MB, Rcpp 1.8 MB. 1 more not on CRAN is not measured.

Depends (1)

R >= 3.5.0

Imports (13)

abind animationclusterigraph larslatticelimmamethodsnnlssplinesstats4tnet VGAM

LinkingTo (0)

none

Suggests (4)

R.rsp CascadeData knitr testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

3indirect

Imports 1

Depends, Imports or LinkingTo, most downloaded first

SelectBoost

How these are counted

Code & Tests

Datasets

People & History

People (4)

Frederic Bertrand

Maintainer since 1.7 (2019), Author

Myriam Maumy-Bertrand

Author

Nicolas Jung

Contributor

Laurent Vallat

Contributor

Releases (7)

Pick two releases to compare their code metrics.

2.4Latest
record
2026-04-30 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
2.3
record
2025-09-19 · diff ↗
2.2
record
2025-08-21 · diff ↗
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
2.1
record
2022-11-28 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
2.0
record
2021-03-19 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.8
record
2019-08-24 · diff ↗
R
R 3.6.0 released · 2019-04-26
1.7
record
2019-02-18
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2019-02-18
Total releases: 7 / 7 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.5.0
Bundled data: 132 KB / 6 files
Download size: 1.4 MB

Appears in task views

Network Analysis Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("Cascade")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

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 Cascade version 2.4 [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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