R Observatory: Metrics for detectRUNS version 0.9.6

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

detectRUNS

0.9.6Package record

Detect Runs of Homozygosity and Runs of Heterozygosity in Diploid Genomes

0packages dependsuggested by 1

5.4Kdownloads / year

45.0%test coverage

13/13flavors OK

Overview

About

Maintained by Filippo BiscariniCRAN page ↗GitHub ↗Issues ↗

Detection of runs of homozygosity and of heterozygosity in diploid genomes using two methods: sliding windows (Purcell et al (2007) doi:10.1086/519795) and consecutive runs (Marras et al (2015) doi:10.1111/age.12259).

Install

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

install.packages("detectRUNS", 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("bioinformatics-ptp/detectRUNS")

Development version from bioinformatics-ptp/detectRUNS. 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-detectruns

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-detectRUNS

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-detectRUNS

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

13OK

CRAN check page ↗

Slowest check: 4.0 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK12 OK2026-04-25
NOTE11 OK, 3 NOTE2026-04-22
ERROR10 OK, 3 NOTE, 1 ERROR2026-04-18

Show 1 earlier changeHide 1 earlier change

NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.9.6

READMEYes · 165 wordsVignettesYes · 1 · dynamicNEWSYes · 67% structured · does not mention 0.9.6Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 37 (4 internal)
Examples that run: 94%15 run in a plain check · 1 never run
Exported functions with examples: 94%
Documented parameters: 97%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

detectRUNS: an R package to detect runs of homozygosity and heterozygosity in diploid genomes

How these are measured

Downloads

5.4K

CRAN downloads in the past year

Rank #6,152 · ~15/day · ~452/mo

Releases R versions

Daily download trend is not available in this view yet.

50230 days

1.3K90 days

5.4K1 year

Compare downloads with other packages →

Also on359 r2u4 autocran

How downloads are counted

Repository

bioinformatics-ptp/detectruns ↗Organization: bioinformatics-ptp

15Stars

4Forks

16Open issues

0Open PRs

0Releases

338Commits

8Commit identities

338 commits · Last activity 2026-06-10 · 0% stars, 30d · Discussions: 1 post

Responsiveness

How these are sampled

PRs merged (all time): 89%
Median days to close, 50 most recently updated closed issues: 883
Median days to close, 50 most recently updated closed PRs: 5

Stars over time

2025-03-18 · 102026-08-04 · 15

How these are measured

PracticesBeta

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

Checks run against github.com/bioinformatics-ptp/detectruns on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Governance and community (2)

Issue templatesPR template

Coverage (1)

Coverage reporting

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Installing detectRUNS adds 27 packages (13 with compiled code, 34 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (1)

R >= 3.0.0

Imports (8)

plyr iterators itertools ggplot2 reshape2 Rcpp gridExtra data.table

LinkingTo (1)

Rcpp

Suggests (4)

testthat knitr rmarkdown prettydoc

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Suggested by 1

Suggests, most downloaded first

tidypopgen

How these are counted

Code & Tests

Datasets

People & History

People (4)

Filippo Biscarini

Author, Maintainer since 0.9.5 (2018)

Paolo Cozzi

Author

Giustino Gaspa

Author

Gabriele Marras

Author

Releases (2)

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
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
0.9.6Latest
record
2019-10-24 · current release · diff ↗
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
0.9.5
record
2018-02-06
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2018-02-06
Total releases: 2 / 8 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.0.0
Download size: 892 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("detectRUNS")

Format

Biscarini, F., Cozzi, P., Gaspa, G., & Marras, G. (2019). detectRUNS: Detect Runs of Homozygosity and Runs of Heterozygosity in Diploid Genomes (Version 0.9.6) [Computer software]. https://doi.org/10.32614/CRAN.package.detectRUNS

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 detectRUNS version 0.9.6 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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