R Observatory: Metrics for refdb version 0.1.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

refdb

0.1.3Package record

A DNA Reference Library Manager

0packages depend

2.8Kdownloads / year

75.5%test coverage

13/13flavors OK

Overview

About

Maintained by Francois KeckCRAN page ↗GitHub ↗Website ↗Issues ↗

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. 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-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). 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: 2.7 min · r-oldrel-macos-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.3

READMEYes · 126 wordsVignettesYes · 2 · dynamicNEWSNoCitation fileNoWebsiteYes · pkgdown

Help pages: 52 (1 internal)includes a package overview page
Examples that run: 95%39 run in a plain check · 2 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 98%
Documented parameters: 97%
Return-value docs: 100%
Help pages citing references: 2%

Vignettes (2)

How these are measured

Downloads

2.8K

CRAN downloads in the past year

Rank #13,349 · ~8/day · ~230/mo

Releases R versions

Daily download trend is not available in this view yet.

33530 days

86390 days

2.8K1 year

Compare downloads with other packages →

Also on108 r2u2 autocran

How downloads are counted

Repository

fkeck/refdb ↗Account: fkeck

13Stars

0Forks

5Open issues

0Open PRs

0Releases

194Commits

1Commit identities

194 commits · Last activity 2026-02-27

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 6
Median days to close, 50 most recently updated closed PRs: not measured

Stars over time

2025-07-08 · 132026-07-07 · 13

How these are measured

PracticesBeta

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

Checks run against github.com/fkeck/refdb on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Docs source (2)

pkgdown

GitHub Pages site last deployed 2026-02-27

Coverage (1)

Coverage reporting (Codecov)

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

22 external dependencies (excludes base and recommended)

Installing refdb adds 121 packages (72 with compiled code, 111 MB of source tarballs). Heaviest: stringi 11 MB, sf 9.3 MB, ggplot2 6.0 MB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (1)

Francois Keck

Releases (4)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
unarchivedReturned to CRAN
2026-02-27
0.1.3Latest
record
2026-02-27 · current release · diff ↗
archivedRemoved from CRAN
2026-02-08
requires archived package 'taxize'
unarchivedReturned to CRAN
2025-12-19
0.1.2
record
2025-12-19 · diff ↗ ·
removed 1 export
refdb_import_BOLD

added 1 export
refdb_export_utax
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
record
2022-09-22 · diff ↗
0.1.0
record
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

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("refdb")

Format

Keck, F. (2026). refdb: A DNA Reference Library Manager (Version 0.1.3) [Computer software]. https://doi.org/10.32614/CRAN.package.refdb

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 refdb version 0.1.3 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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