R Observatory: Metrics for qtl2 version 0.46

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

qtl2

0.46

Quantitative Trait Locus Mapping in Experimental Crosses

6packages depend

20.3Kdownloads / year

61.0%test coverage

13/13checks pass

Overview

About

Maintained by Karl W BromanFirst published 2020-06-2613 releasesCRAN page ↗GitHub ↗

Provides a set of tools to perform quantitative trait locus (QTL) analysis in experimental crosses. It is a reimplementation of the 'R/qtl' package to better handle high-dimensional data and complex cross designs. Broman et al. (2019) doi:10.1534/genetics.118.301595.

Install

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

install.packages("qtl2", 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("rqtl/qtl2")

Development version from rqtl/qtl2. 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-qtl2

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-qtl2

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-qtl2

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

Health

CRAN checks

13OK

Slowest check: 19.2 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.92

61.0%

Coverage · measured lines

100%

Documentation · exports

10

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
OK2026-07-25
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-07-16
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 5 earlier snapshots

ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 225 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 82%
Documented parameters: 99%
Return-value docs: 99%
References docs: 6%

Downloads

20.3K

CRAN downloads in the past year

Rank #3,529 · ~56/day · ~1.7K/mo

Releases R versions

Daily download trend is not available in this view yet.

76530 days

2.8K90 days

20.3K1 year

Compare downloads with other packages →

Also on591 r2u35 autocran5.7K conda_forge206 bioconda

Repository

GitHub ↗ rqtl/qtl2

40Stars

26Forks

19Open issues

0Open PRs

16Releases

2,693Commits

3Contributors

License GPL-3.0 · 2,693 commits · Last activity 2026-07-22 · 0% stars, 30d

Stars over time

2023-11-20 · 342026-07-10 · 40

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/rqtl/qtl2 on 2026-08-16.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

Makefile

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

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.1.0

Imports (10)

Rcpp yaml jsonlite data.tableparallelstatsutilsgraphicsgrDevicesRSQLite

LinkingTo (2)

Rcpp RcppEigen

Suggests (5)

testthat devtools roxygen2 vdiffr qtl

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

6direct

0indirect

qtl2convert qtl2fst qtl2ggplot qtl2pattern mmconvert qtl2pleio

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

Karl W Broman

Author, Maintainer

Authors (1)

Karl W Broman

Author, Maintainer

Contributors (1)

R Core Team

Contributor

Package Timeline

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

0.46Latest
2026-07-21 · current release · diff ↗
0.44
2026-07-06 · diff ↗
0.42
2026-06-09 · diff ↗
0.40
2026-05-05 · diff ↗
R
R 4.6.0 released · 2026-04-24
0.38
2025-06-02 · diff ↗
R
R 4.5.0 released · 2025-04-11
0.36
2024-05-13 · diff ↗
R
R 4.4.0 released · 2024-04-24
0.34
2023-11-28 · diff ↗
0.32
2023-04-22 · diff ↗
R
R 4.3.0 released · 2023-04-21
0.30
2022-12-02 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.28
2021-10-17 · diff ↗
R
R 4.1.0 released · 2021-05-18

Show 4 earlier events

0.24
2020-12-18 · diff ↗
0.22-11
2020-07-10 · diff ↗
0.22-8
2020-06-26
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-06-26
Total releases: 13 / 6 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.1.0
Bundled data: 0.5 KB / 3 files
Download size: 1.5 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("qtl2")

Format

Broman, K. W., & R Core Team. (2026). qtl2: Quantitative Trait Locus Mapping in Experimental Crosses (Version 0.46) [Computer software]. https://doi.org/10.32614/CRAN.package.qtl2

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 qtl2 version 0.46 [Data set]. HJJB, LLC. Data release v2026-08-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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