R Observatory: Metrics for jointseg version 1.0.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

jointseg

1.0.3Package record

Joint Segmentation of Multivariate (Copy Number) Signals

2packages dependsuggested by 1

5.9Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Morgane Pierre-JeanCRAN page ↗GitHub ↗Issues ↗

Methods for fast segmentation of multivariate signals into piecewise constant profiles and for generating realistic copy-number profiles. A typical application is the joint segmentation of total DNA copy numbers and allelic ratios obtained from Single Nucleotide Polymorphism (SNP) microarrays in cancer studies. The methods are described in Pierre-Jean, Rigaill and Neuvial (2015) doi:10.1093/bib/bbu026.

Changes in 1.0.3

Bug fixed url

From NEWS.md in the release

Install

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

install.packages("jointseg", 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("mpierrejean/jointseg")

Development version from mpierrejean/jointseg. 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-jointseg

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: 3.2 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-10-20
ERROR12 OK, 1 ERROR2026-10-19
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.3

READMEYes · 194 wordsVignettesYes · 2 · dynamicNEWSYes · 100% structured · mentions 1.0.3Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 30 (9 internal)
Examples that run: 96%24 run in a plain check · 1 never run
Exported functions with examples: 100%
Documented parameters: 97%
Return-value docs: 76%
Help pages citing references: 60%

Vignettes (2)

Generating realistic data HTML
PSSeg HTML

How these are measured

Downloads

5.9K

CRAN downloads in the past year

Rank #7,537 · ~16/day · ~489/mo

Releases R versions

Daily download trend is not available in this view yet.

34430 days

1.2K90 days

5.9K1 year

Compare downloads with other packages →

Also on416 r2u

How downloads are counted

Repository

mpierrejean/jointseg ↗Account: mpierrejean

7Stars

1Forks

5Open issues

0Open PRs

0Releases

235Commits

8Commit identities

235 commits · Last activity 2019-01-07 · 0% stars, 30d · The default branch showed an older version (1.0.2) than CRAN on 2026-10-21

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 22
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2023-11-05 · 62026-07-07 · 7

How these are measured

PracticesBeta

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

Checks run against github.com/mpierrejean/jointseg on 2026-10-21.

Continuous integration (2)

Travis CI (config file)AppVeyor

Docs source (1)

pkgdown

CRAN release process (1)

cran-comments.md

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Installing jointseg adds 2 packages (1 with compiled code, 2.9 MB of source tarballs). Heaviest: acnr 2.7 MB, matrixStats 207 KB. 1 more not on CRAN is not measured.

Depends (1)

R >= 3.1.0

Imports (3)

acnr matrixStats DNAcopy

LinkingTo (0)

none

Suggests (7)

PSCBS R.cache digest changepoint knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

0indirect

Depends 1 · Imports 1

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

CNVScope SegCorr

Suggests, most downloaded first

penaltyLearning

How these are counted

Code & Tests

People & History

People (3)

Morgane Pierre-Jean

Author, Maintainer since 1.0.0 (2017)

Pierre Neuvial

Author

Guillem Rigaill

Author

Releases (4)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.0.3Latest
record
2025-05-14 · current release · 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
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
1.0.2
record
2019-01-11 · diff ↗
R
R 3.5.0 released · 2018-04-23
1.0.1
record
2017-11-28 · diff ↗
1.0.0
record
2017-11-27
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-11-27
Total releases: 4 / 9 yrs
License: LGPL (>= 2.1)
Minimum R: ≥ 3.1.0
Download size: 939 KB

Appears in task views

Time Series Analysis

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("jointseg")

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 jointseg version 1.0.3 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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