R Observatory: Metrics for leiden version 0.4.3.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

leiden

0.4.3.1Package record

R Implementation of Leiden Clustering Algorithm

2packages dependsuggested by 1

59.8Kdownloads / year

4.7%test coverage

8/13flavors OK

Overview

About

Maintained by S. Thomas KellyCRAN page ↗GitHub ↗Issues ↗

Implements the 'Python leidenalg' module to be called in R. Enables clustering using the leiden algorithm for partition a graph into communities. See the 'Python' repository for more details: https://github.com/vtraag/leidenalg Traag et al (2018) From Louvain to Leiden: guaranteeing well-connected communities. arXiv:1810.08473.

Changes in 0.4.3.1

Bug fix to avoid archive when dependencies are updated.

corrects mismatched chunk delimiters in documentation

Resolves:

https://github.com/yihui/knitr/issues/2057

https://github.com/yihui/knitr/pull/2306

From NEWS.md in the release

Install

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

install.packages("leiden", 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("TomKellyGenetics/leiden")

Development version from TomKellyGenetics/leiden. 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-leiden

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-leiden

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-leiden

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

2WARNING3NOTE8OK

Check messages

WARNINGfor code/documentation mismatchesr-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

warning: Failed to inspect Python interpreter from search path at `/usr/sbin/pypy`
  cause: Can't use Python at `/usr/sbin/pypy`
  cause: Python executable does not support `-I` flag. Please use Python 3.6 or newer.
warning: Failed to inspect Python interpreter from search path at `/usr/sbin/pypy`
  cause: Can't use Python at `/usr/sbin/pypy`
  cause: Python executable does not support `-I` flag. Please use Python 3.6 or newer.
warning: Failed to inspect Python interpreter from search path at `/usr/sbin/pypy`
  cause: Can't use Python at `/usr/sbin/pypy`
  cause: Python executable does not support `-I` flag. Please use Python 3.6 or newer.

WARNINGfor missing documentation entriesr-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

warning: Failed to inspect Python interpreter from search path at `/usr/sbin/pypy`
  cause: Can't use Python at `/usr/sbin/pypy`
  cause: Python executable does not support `-I` flag. Please use Python 3.6 or newer.
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.

NOTER code for possible problemsr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64

Found calls to structure() using deprecated special names:
  leiden/tests/testthat/test_bipartite.R (.Names: 1)
  leiden/tests/testthat/test_multiplex.R (.Dim: 2, .Dimnames: 2, .Label: 1)
  leiden/tests/testthat/test_weighted.R (.Dim: 3, .Dimnames: 3)
  leiden/inst/doc/run_bipartite.R (.Names: 1)
  leiden/inst/doc/run_multiplex.R (.Label: 1)
'.Names' should be changed to 'names'.
'.Dim' should be changed to 'dim'.
'.Dimnames' should be changed to 'dimnames'.
'.Label' should be changed to 'levels'.

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘S. Thomas Kelly <tomkellygenetics@gmail.com>’

The Description field contains
  to Leiden: guaranteeing well-connected communities. <arXiv:1810.08473>.
Please refer to arXiv e-prints via their arXiv DOI <doi:10.48550/arXiv.YYMM.NNNNN>.

NOTEwhether startup messages can be suppressedr-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

warning: Failed to inspect Python interpreter from search path at `/usr/sbin/pypy`
  cause: Can't use Python at `/usr/sbin/pypy`
  cause: Python executable does not support `-I` flag. Please use Python 3.6 or newer.

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.

CRAN check page ↗

Slowest check: 20.3 min · r-release-windows-x86_64

Status changes

WARNING8 OK, 3 NOTE, 2 WARNINGNow
WARNING8 OK, 4 NOTE, 1 WARNING2026-09-10
NOTE9 OK, 5 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.4.3.1

README· In the repository, left out of the releaseVignettesYes · 5 · dynamicNEWSYes · 100% structured · mentions 0.4.3.1Citation fileYes · software entry onlyWebsitenot declared in DESCRIPTION

Help pages: 1
Examples that run: 100%1 run in a plain check
Exported functions with examples: 100%
Documented parameters: 67%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (5)

How these are measured

Downloads

59.8K

CRAN downloads in the past year

Rank #1,770 · ~164/day · ~5K/mo

Releases R versions

Daily download trend is not available in this view yet.

4.5K30 days

11.8K90 days

59.8K1 year

Compare downloads with other packages →

Also on1.2K r2u5 autocran36K conda_forge683 c2d4u

How downloads are counted

Repository

tomkellygenetics/leiden ↗Account: TomKellyGenetics

44Stars

9Forks

9Open issues

0Open PRs

21Releases

741Commits

2Commit identities

License file reads as GPL-3.0 · 741 commits · Last activity 2024-05-26 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 69
Median days to close, 50 most recently updated closed PRs: 21

Stars over time

2025-04-29 · 402026-10-20 · 44

How these are measured

PracticesBeta

7 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/tomkellygenetics/leiden on 2026-10-21.

Continuous integration (3)

Travis CI (config file)AppVeyorCircleCI

Coverage (1)

Coverage reporting (Codecov)

CRAN release process (1)

cran-comments.md

Research and citation (1)

CITATION.cff

Show all practicesHide 1 practice

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

19 external dependencies (excludes base and recommended)

Installing leiden adds 18 packages (12 with compiled code, 13 MB of source tarballs). Heaviest: igraph 4.8 MB, Rcpp 1.8 MB, reticulate 1.6 MB.

Depends (0)

none

Imports (4)

methodsreticulateMatrixigraph

LinkingTo (0)

none

Suggests (17)

bipartite covr data.table devtools graphsim knitr markdown multiplex multinet network qpdf RColorBrewer remotes rmarkdown spelling testthat tibble

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

1indirect

Imports 2

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

RaceID ClustAssess

Suggests, most downloaded first

FCPS

How these are counted

Code & Tests

People & History

People (2)

S. Thomas Kelly

Author, Maintainer, Translator · added in 0.3.0

Vincent A. Traag

Compiler · added in 0.3.0

Maintainer since 0.2.3 (2019)

Listed in earlier versions (1)

Tom Kelly

no longer listed · 0.2.3

Releases (15)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
0.4.3.1Latest
record
2023-11-17 · current release · diff ↗
R
R 4.3.0 released · 2023-04-21
0.4.3
record
2022-09-10 · diff ↗
0.4.2
record
2022-05-09 · diff ↗
0.3.10
record
2022-04-28 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.3.9
record
2021-07-27 · diff ↗
0.3.8
record
2021-05-24 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.3.7
record
2021-01-26 · diff ↗
0.3.6
record
2020-12-07 · diff ↗
0.3.5
record
2020-11-09 · diff ↗
0.3.4
record
2020-10-29 · diff ↗

Show 8 earlier eventsHide 8 earlier events

R
R 4.0.0 released · 2020-04-24
0.3.3
record
2020-02-04 · diff ↗
0.3.2
record
2020-01-18 · diff ↗
0.3.1
record
2019-07-23 · diff ↗
0.3.0
record
2019-07-15 · diff ↗
R
R 3.6.0 released · 2019-04-26
0.2.3
record
2019-02-11
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2019-02-11
Total releases: 15 / 7 yrs
License: GPL-3 | file LICENSE OSI
Download size: 2.7 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("leiden")

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

The repository also keeps a CITATION.cff.

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 leiden version 0.4.3.1 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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