Rduckhts

1.5.1-0.1.3

'DuckDB' High Throughput Sequencing File Formats Reader Extension

0packages depend

2Kdownloads / year

56.9%test coverage

12/13checks pass

Overview

About

Maintained by Sounkou Mahamane ToureFirst published 2026-02-239 releasesCRAN page ↗GitHub ↗

Bundles the 'duckhts' 'DuckDB' extension for reading High Throughput Sequencing file formats with 'DuckDB'. The 'DuckDB' C extension API https://duckdb.org/docs/stable/clients/c/api and its 'htslib' dependency are compiled from vendored sources during package installation. James K Bonfield and co-authors (2021) doi:10.1093/gigascience/giab007. VariantKey / RegionKey support follows Nicola Asuni (2018) doi:10.1101/473744.

Install

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

install.packages("Rduckhts", 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("RGenomicsETL/duckhts")

Development version from RGenomicsETL/duckhts. 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-rduckhts

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-Rduckhts

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

Health

CRAN checks

1NOTE12OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 6.7 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.00

56.9%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
WARNING2026-07-29
12 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-07-26
8 OK · 0 NOTE · 4 WARNING · 1 ERROR · 0 FAILURE
WARNING2026-07-16
12 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE
OK2026-05-24
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 5 earlier snapshots

ERROR2026-05-17
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-15
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-05-13
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 71%
Documented parameters: 99%
Return-value docs: 100%
References docs: 2%

Downloads

CRAN downloads in the past year

Rank #9,796 · ~5/day · ~165/mo

Releases R versions

Daily download trend is not available in this view yet.

31130 days

1.1K90 days

2K1 year

Compare downloads with other packages →

Also on112 r2u

Repository

GitHub ↗ rgenomicsetl/duckhts

16Stars

2Forks

16Open issues

0Open PRs

7Releases

895Commits

10Contributors

bamduckdb-extensionfastqhtslibrstatsvcf

895 commits · Last activity 2026-07-28 · 0% stars, 30d

Stars over time

2026-02-21 · 12026-07-07 · 16

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/rgenomicsetl/duckhts on 2026-07-30.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

Makefile

Docs source (1)

README.Rmd

Git structural (2)

.gitattributesSubmodules

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

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.4.0

Imports (4)

DBI duckdbmethodsutils

LinkingTo (0)

none

Suggests (2)

Rtinycc tinytest

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (7)

Maintainer (1)

Sounkou Mahamane Toure

Author, Maintainer

Authors (1)

Sounkou Mahamane Toure

Author, Maintainer

Contributors (2)

DuckDB C Extension API Authors

Contributor

James K Bonfield, John Marshall,Petr Danecek ,Heng Li , Valeriu Ohan, Andrew Whitwham,Thomas Keane , Robert M Davies

Contributor

Package Timeline

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

1.5.1-0.1.3Latest
2026-07-28 · current release · diff ↗
1.5.0-0.1.0
2026-07-24 · diff ↗
1.4.0-0.1.0
2026-07-10 · diff ↗
1.3.0-0.1.0
2026-05-30 · diff ↗
1.2.1-0.1.0
2026-05-08 · diff ↗
R
R 4.6.0 released · 2026-04-24
1.1.6-0.0.2
2026-04-09 · diff ↗
1.1.4-0.0.1
2026-03-31 · diff ↗
0.1.3-0.0.2
2026-02-24 · diff ↗
0.1.2-0.1.4
2026-02-23
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2026-02-23
Total releases: 9 / 1 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.4.0
Download size: 1.6 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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