R Observatory: Metrics for adjclust version 0.6.11

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

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: 5.7 min · r-devel-windows-x86_64

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 #7,114 · ~17/day · ~505/mo

Releases R versions

Daily download trend is not available in this view yet.

36430 days

1.2K90 days

6.1K1 year

Compare downloads with other packages →

Also on500 r2u39 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 2026-08-16.

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

Datasets

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

Run in R for the authors' preferred citation:

citation("adjclust")

Format

Neuvial, P., Ambroise, C., Chaturvedi, S., Dehman, A., Hoffman, G., Rigaill, G., & Vialaneix, N. (2025). adjclust: Adjacency-Constrained Clustering of a Block-Diagonal Similarity Matrix (Version 0.6.11) [Computer software]. https://doi.org/10.32614/CRAN.package.adjclust

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 adjclust version 0.6.11 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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