R Observatory: Metrics for adjclust version 0.6.11

Balamuta, James Joseph

adjclust

0.6.11

Adjacency-Constrained Clustering of a Block-Diagonal Similarity Matrix

3packages depend

6.1Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Pierre NeuvialFirst published 2017-10-1814 releasesCRAN page ↗GitHub ↗

Implements a constrained version of hierarchical agglomerative clustering, in which each observation is associated to a position, and only adjacent clusters can be merged. Typical application fields in bioinformatics include Genome-Wide Association Studies or Hi-C data analysis, where the similarity between items is a decreasing function of their genomic distance. Taking advantage of this feature, the implemented algorithm is time and memory efficient. This algorithm is described in Ambroise et al (2019) doi:10.1186/s13015-019-0157-4.

Install

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

install.packages("adjclust", 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("pneuvial/adjclust")

Development version from pneuvial/adjclust. 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-adjclust

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-adjclust

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-adjclust

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

Health

CRAN checks

13OK

Slowest check: 5.9 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.41

not tracked

Coverage

100%

Documentation · exports

12

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
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 1 earlier snapshots

NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 236 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 80%
Documented parameters: 94%
Return-value docs: 83%
References docs: 83%

Downloads

6.1K

CRAN downloads in the past year

Rank #8,346 · ~17/day · ~507/mo

Releases R versions

Daily download trend is not available in this view yet.

34230 days

1.2K90 days

6.1K1 year

Compare downloads with other packages →

Also on500 r2u8 autocran23 c2d4u

Repository

GitHub ↗ pneuvial/adjclust

16Stars

8Forks

5Open issues

0Open PRs

3Releases

739Commits

11Contributors

hierarchical-clusteringgwashi-clinkage-disequilibrium

739 commits · Last activity 2025-11-21

Stars over time

2023-01-18 · 162026-07-07 · 16

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/pneuvial/adjclust on 2026-08-03.

Continuous integration (1)

GitHub Actions

Docs source (1)

README.Rmd

Coverage (1)

Codecov

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

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.0.0

Imports (12)

statsgraphicsgrDevicesRcppMatrixsparseMatrixStatsmethodsutilscapushe ggplot2 dendextend rlang

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (7)

knitr testthat rmarkdown rioja HiTC snpStats BiocGenerics

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

3direct

0indirect

SISIR hicream treediff

Code & Tests

People & History

People (7)

Maintainer (1)

Pierre Neuvial

Author, Maintainer

Authors (7)

Author, Maintainer

Author

Author

Author

Author · added in 0.6.3

Guillem Rigaill

Author

Nathalie Vialaneix

Author · added in 0.5.7

Listed in earlier versions (2)

Michel Koskas

no longer listed · 0.5.2 to 0.5.9

Nathalie Villa-Vialaneix

no longer listed · 0.5.2 to 0.5.6

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
0.6.11Latest
2025-11-20 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
0.6.10
2024-10-08 · diff ↗
R
R 4.4.0 released · 2024-04-24
0.6.9
2024-02-08 · diff ↗
0.6.8
2024-01-13 · diff ↗
0.6.7
2023-04-27 · diff ↗
R
R 4.3.0 released · 2023-04-21
0.6.6
2022-09-15 · diff ↗
0.6.5
2022-08-18 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.6.4
2022-03-31 · diff ↗
0.6.3
2021-07-26 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.5.99
2020-06-18 · diff ↗

Show 10 earlier events

unarchivedReturned to CRAN
2020-06-18
archivedRemoved from CRAN
2020-06-15
check problems were not corrected in time
R
R 4.0.0 released · 2020-04-24
0.5.9
2019-12-10 · diff ↗
R
R 3.6.0 released · 2019-04-26
0.5.7
2018-09-26 · diff ↗
R
R 3.5.0 released · 2018-04-23
0.5.6
2018-02-08 · diff ↗
0.5.2
2017-10-18
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-10-18
Total releases: 14 / 9 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.0.0
Download size: 1.4 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Start here. This is the citation for the package itself.

citation("adjclust")

CRAN DOI

https://doi.org/10.32614/CRAN.package.adjclust

BibTeX, derived from DESCRIPTION

@Manual{adjclust,
  title  = {adjclust: Adjacency-Constrained Clustering of a Block-Diagonal Similarity
Matrix},
  author = {Neuvial, Pierre and Ambroise, Christophe and Chaturvedi, Shubham and Dehman, Alia and Hoffman, Gabriel and Rigaill, Guillem and Vialaneix, Nathalie},
  year   = {2025},
  note   = {R package version 0.6.11},
  doi    = {10.32614/CRAN.package.adjclust},
  url    = {https://CRAN.R-project.org/package=adjclust}
}

Derived from the package DESCRIPTION, not from a citation file the authors wrote. If they publish one later, prefer it.

This is the citation for the package. It is not a citation for the R Observatory.

Cite this page

Use this when the claim is about a measurement on this page.

BibTeX

@misc{robservatoryadjclust,
  author    = {Balamuta, James Joseph},
  title     = {{R} {Observatory}: Metrics for {adjclust} version 0.6.11},
  year      = {2026},
  publisher = {HJJB, LLC},
  url       = {https://r-observatory.thecoatlessprofessor.com/packages/adjclust},
  note      = {Data set. Data release v2026-08-05}
}

APA

Balamuta, J. J. (2026). R Observatory: Metrics for adjclust version 0.6.11 [Data set]. HJJB, LLC. Data release v2026-08-05. https://r-observatory.thecoatlessprofessor.com/packages/adjclust

RIS

TY  - DATA
AU  - Balamuta, James Joseph
TI  - R Observatory: Metrics for adjclust version 0.6.11
PY  - 2026
PB  - HJJB, LLC
N1  - Data release v2026-08-05
UR  - https://r-observatory.thecoatlessprofessor.com/packages/adjclust
ER  -

In prose

These package metrics were obtained from the R Observatory (Balamuta, 2026), data release v2026-08-05, https://r-observatory.thecoatlessprofessor.com/packages/adjclust.

Bound to data release v2026-08-05, which is what makes the numbers on this page reproducible. See how to cite.

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