R Observatory: Metrics for qtl2fst version 0.32

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

qtl2fst

0.32

Database Storage of Genotype Probabilities for QTL Mapping

1packages depend

3.4Kdownloads / year

64.6%test coverage

13/13checks pass

Overview

About

Maintained by Karl W BromanFirst published 2020-07-306 releasesCRAN page ↗GitHub ↗

Uses the 'fst' package to store genotype probabilities on disk for the 'qtl2' package. These genotype probabilities are a central data object for mapping quantitative trait loci (QTL), but they can be quite large. The facilities in this package enable the genotype probabilities to be stored on disk, leading to reduced memory usage with only a modest increase in computation time.

Install

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

install.packages("qtl2fst", 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/qtl2fst")

Development version from rqtl/qtl2fst. 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-qtl2fst

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-qtl2fst

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-qtl2fst

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

Health

CRAN checks

13OK

Slowest check: 2.2 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.46

64.6%

Coverage · measured lines

100%

Documentation · exports

2

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
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 109 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

3.4K

CRAN downloads in the past year

Rank #13,865 · ~9/day · ~280/mo

Releases R versions

Daily download trend is not available in this view yet.

18030 days

73890 days

3.4K1 year

Compare downloads with other packages →

Also on102 r2u28 autocran

Repository

GitHub ↗ rqtl/qtl2fst

2Stars

3Forks

0Open issues

0Open PRs

8Releases

115Commits

1Contributors

License GPL-3.0 · 115 commits · Last activity 2026-07-16

Stars over time

2020-08-25 · 22026-07-07 · 2

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/qtl2fst 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

5 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.1.0

Imports (2)

fst qtl2

LinkingTo (0)

none

Suggests (3)

testthat knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

qtl2pattern

Code & Tests

People & History

People (3)

Maintainer (1)

Karl W Broman

Author, Maintainer

Authors (3)

Karl W Broman

Author, Maintainer

Petr Simecek

Author

Brian S Yandell

Author

Package Timeline

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

0.32Latest
2026-07-16 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
0.30
2024-11-23 · diff ↗
0.28
2024-07-17 · diff ↗
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
0.26
2021-10-07 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.24
2021-04-29 · diff ↗
0.22-7
2020-07-30
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-07-30
Total releases: 6 / 6 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.1.0
Download size: 30 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("qtl2fst")

Format

Broman, K. W., Simecek, P., & Yandell, B. S. (2026). qtl2fst: Database Storage of Genotype Probabilities for QTL Mapping (Version 0.32) [Computer software]. https://doi.org/10.32614/CRAN.package.qtl2fst

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 qtl2fst version 0.32 [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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