R Observatory: Metrics for adegenet version 2.1.11

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

adegenet

2.1.11Package record

Exploratory Analysis of Genetic and Genomic Data

23packages dependsuggested by 13

205Kdownloads / year

28.7%test coverage

8/13flavors OK

Overview

About

Maintained by Zhian N. KamvarCRAN page ↗GitHub ↗

Toolset for the exploration of genetic and genomic data. Adegenet provides formal (S4) classes for storing and handling various genetic data, including genetic markers with varying ploidy and hierarchical population structure ('genind' class), alleles counts by populations ('genpop'), and genome-wide SNP data ('genlight'). It also implements original multivariate methods (DAPC, sPCA), graphics, statistical tests, simulation tools, distance and similarity measures, and several spatial methods. A range of both empirical and simulated datasets is also provided to illustrate various methods.

Install

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

install.packages("adegenet", 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("thibautjombart/adegenet")

Development version from thibautjombart/adegenet. 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-adegenet

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-adegenet

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-adegenet

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

1FAILURE4NOTE8OK

Check messages

FAILUREfor hidden files and directoriesr-devel-linux-x86_64-fedora-clang

WARNINGif this is a source packager-devel-linux-x86_64-fedora-clang

Subdirectory ‘adegenet/src’ contains apparent object files/libraries
  GLfunctions.o adegenet.so adesub.o init.o monmonier-utils.o
  sharedAll.o snpbin.o
Object files/libraries should not be included in a source package.

Subdirectory ‘src’ contains:
  symbols.rds
These are unlikely file names for src files.

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

Found calls to structure() using deprecated special names:
  adegenet/tests/testthat/test-prop.R (.Dim: 1, .Dimnames: 1)
'.Dim' should be changed to 'dim'.
'.Dimnames' should be changed to 'dimnames'.

CRAN check page ↗

Slowest check: 6.0 min · r-release-windows-x86_64

Status changes

FAILURE8 OK, 4 NOTE, 1 FAILURENow
NOTE8 OK, 5 NOTE2026-09-08
ERROR8 OK, 4 NOTE, 1 ERROR2026-09-07
NOTE11 OK, 2 NOTE2026-07-16
OK12 OK2026-04-25
NOTE13 OK, 1 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.1.11

READMEYes · 90 wordsVignettesNoNEWSNoCitation fileYes · cites a publication

Help pages: 94includes a package overview page
Examples that run: 35%27 run in a plain check · 50 never run
Exported functions with examples: 74%
Documented parameters: 99%
Return-value docs: 65%
Help pages citing references: 29%

How these are measured

Downloads

205K

CRAN downloads in the past year

Rank #717 · ~562/day · ~17.1K/mo

Releases R versions

Daily download trend is not available in this view yet.

27.5K30 days

72.3K90 days

205K1 year

Compare downloads with other packages →

Also on2.1K r2u108 autocran12.6K conda_forge260 bioconda243 c2d4u

How downloads are counted

Repository

thibautjombart/adegenet ↗Account: thibautjombart

203Stars

67Forks

67Open issues

9Open PRs

10Releases

947Commits

21Commit identities

947 commits · Last activity 2025-02-07 · +1% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 94%
Median days to close, 50 most recently updated closed issues: 12
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2025-10-02 · 1952026-10-21 · 203

How these are measured

PracticesBeta

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

Checks run against github.com/thibautjombart/adegenet on 2026-10-21.

Continuous integration (4)

GitHub ActionsR CMD check workflowTravis CI (config file)AppVeyor

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Docs source (1)

GitHub Pages site last deployed 2017-06-19

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

18 external dependencies (excludes base and recommended)

Installing adegenet adds 62 packages (37 with compiled code, 71 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, bslib 5.6 MB.

Depends (3)

R >= 2.14methodsade4

Imports (14)

utilsstatsgrDevicesMASSigraph ape shiny ggplot2 seqinrparallelbootreshape2 dplyr vegan

LinkingTo (0)

none

Suggests (9)

adespatial pegas hierfstat maps spdep interp splancs poppr testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

23direct

10indirect

Depends 5 · Imports 18

Suggested by 13

Show all 36 packagesHide all 36 packages

Depends, Imports or LinkingTo, most downloaded first

Suggests, most downloaded first

pegas vcfR polysat sequoia RAINBOWR polyRAD tidypopgen outbreaker2 wingen memgene quiddich VCFArrow corridoR

How these are counted

Code & Tests

Datasets

People & History

People (22)

Zhian N. Kamvar

Author, Maintainer since 2.1.2 (2020) · added in 2.0.0

Thibaut Jombart

Author

Ismail Ahmed

Contributor · added in 1.3-6

Marie-Pauline Beugin

Contributor · added in 2.1.3

Federico Calboli

Contributor · added in 3.0.1

Lindsay V. Clark

Contributor · added in 2.1.6

Caitlin Collins

Contributor · added in 1.4-0

Anne Cori

Contributor · added in 1.3-6

Max Coulter

Contributor · added in 2.1.11

Alexandre Courtiol

Contributor · added in 2.1.3

Show 12 more contributorsHide 12 contributors

Rebecca DeCamp

Contributor · added in 2.1.2

Pavel Dimens

Contributor · added in 2.1.6

RJ Ewing

Contributor · added in 2.1.0

Brian J. Knaus

Contributor · added in 2.1.0

Ivan Krylov

Contributor · added in 2.1.11

Roman Lustrik

Contributor · added in 2.0.0

Tiago Maié

Contributor · added in 2.1.0

Frédéric Michaud

Contributor · added in 2.1.2

Vladimir Mikryukov

Contributor · added in 2.1.0

Libor Morkovsky

Contributor · added in 2.1.0

Klaus Schliep

Contributor · added in 2.0.0

Peter Solymos

Contributor · added in 2.13.1

Previously maintained by Thibaut Jombart (1.0-0 to 2.1.1).

Listed in earlier versions (11)

Show 8 of 11 peopleHide 8 people

with contributions from Peter Solymos

no longer listed · 1.1-0 to 1.2-3

Francois Balloux