refdb

0.1.3

A DNA Reference Library Manager

0packages depend

2.1Kdownloads / year

75.5%test coverage

12/13checks pass

Overview

About

Maintained by Francois KeckFirst published 2022-09-194 releasesCRAN page ↗GitHub ↗

Reference database manager offering a set of functions to import, organize, clean, filter, audit and export reference genetic data. Provide functions to download sequence data from NCBI GenBank https://www.ncbi.nlm.nih.gov/genbank/. Designed as an environment for semi-automatic and assisted construction of reference databases and to improve standardization and repeatability in barcoding and metabarcoding studies.

Install

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

install.packages("refdb", 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("fkeck/refdb")

Development version from fkeck/refdb. 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-refdb

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-refdb

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-refdb

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

Health

CRAN checks

1NOTE12OK

Failing flavors

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

Slowest check: 2.7 min · r-oldrel-macos-x86_64

Code health

Yes

Tests · ratio 0.58

75.5%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 126 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 95%
Documented parameters: 97%
Return-value docs: 100%
References docs: 2%

Downloads

2.1K

CRAN downloads in the past year

Rank #14,120 · ~6/day · ~174/mo

Releases R versions

Daily download trend is not available in this view yet.

18930 days

73390 days

2.1K1 year

Compare downloads with other packages →

Also on117 r2u5 autocran

Repository

GitHub ↗ fkeck/refdb

13Stars

0Forks

5Open issues

0Open PRs

0Releases

194Commits

1Contributors

194 commits · Last activity 2026-02-27 · 0% stars, 30d

Stars over time

2025-07-08 · 132026-07-07 · 13

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/fkeck/refdb on 2026-07-31.

Continuous integration (1)

GitHub Actions

Lint, format, editor (1)

RStudio project

Coverage (1)

Codecov

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

Dependencies

Declared dependencies

22 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.1.0

Imports (17)

tibble readr dplyr stringr tidyr rentrez taxize xml2 bioseq ape igraph ggplot2 ggraph yaml rlang rmarkdown leaflet

LinkingTo (0)

none

Suggests (5)

testthat covr DT knitr forcats

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Maintainer (1)

Francois Keck

Author, Maintainer, Copyright holder

Authors (1)

Francois Keck

Author, Maintainer, Copyright holder

Francois Keck

Author, Maintainer, Copyright holder

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
0.1.3Latest
2026-02-27 · current release · diff ↗
unarchivedReturned to CRAN
2026-02-27
archivedRemoved from CRAN
2026-02-08
requires archived package 'taxize'
0.1.2
2025-12-19 · diff ↗
unarchivedReturned to CRAN
2025-12-19
R
R 4.5.0 released · 2025-04-11
archivedRemoved from CRAN
2024-08-25
issues were not corrected in time Dependence on failing package 'bold', deadline 2024-08-19
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
0.1.1
2022-09-22 · diff ↗
0.1.0
2022-09-19
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-09-19
Total releases: 4 / 4 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.1.0
Download size: 576 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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