R Observatory: Metrics for gbifdb version 1.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

gbifdb

1.0.0Package record

High Performance Interface to 'GBIF'

0packages depend

3Kdownloads / year

66.3%test coverage

11/13flavors OK

Overview

About

Maintained by Carl BoettigerCRAN page ↗GitHub ↗Website ↗Issues ↗

A high performance interface to the Global Biodiversity Information Facility, 'GBIF'. In contrast to 'rgbif', which can access small subsets of 'GBIF' data through web-based queries to a central server, 'gbifdb' provides enhanced performance for R users performing large-scale analyses on servers and cloud computing providers, providing full support for arbitrary 'SQL' or 'dplyr' operations on the complete 'GBIF' data tables (now over 1 billion records, and over a terabyte in size). 'gbifdb' accesses a copy of the 'GBIF' data in 'parquet' format, which is already readily available in commercial computing clouds such as the Amazon Open Data portal and the Microsoft Planetary Computer, or can be accessed directly without downloading, or downloaded to any server with suitable bandwidth and storage space. The high-performance techniques for local and remote access are described in https://duckdb.org/why_duckdb and https://arrow.apache.org/docs/r/articles/fs.html respectively.

Changes in 1.0.0

gbif_download() now uses minioclient as a backend, offering dramatically (100x+) better performance, especially on multi-core machines with high bandwidth network connections.
gbif_local() now defaults to duckdb backend, and utilizes duckdbfs to streamline the interface. The latest performance of duckdb is substantially better than alternatives.

Breaking changes

gbif_conn() is deprecated

From NEWS.md in the release

Install

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

install.packages("gbifdb", 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("ropensci/gbifdb")

Development version from ropensci/gbifdb. 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-gbifdb

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-gbifdb

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-gbifdb

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

2NOTE11OK

Check messages

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Carl Boettiger <cboettig@gmail.com>’

The BugReports field in DESCRIPTION has
  https://github.com/ropensci/gbifdb
which should likely be
  https://github.com/ropensci/gbifdb/issues
instead.

CRAN check page ↗

Slowest check: 1.4 min · r-release-macos-x86_64

Status changes

NOTE11 OK, 2 NOTE2026-09-29
ERROR10 OK, 2 NOTE, 1 ERROR2026-09-04
NOTE11 OK, 2 NOTE2026-05-24
ERROR10 OK, 2 NOTE, 1 ERROR2026-05-17
NOTE11 OK, 2 NOTE2026-05-15

Show 2 earlier changesHide 2 earlier changes

ERROR11 OK, 1 NOTE, 1 ERROR2026-05-13
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.0

READMEYes · 831 wordsVignettesYes · 1 · staticNEWSYes · 100% structured · mentions 1.0.0Citation fileNoWebsiteYes · pkgdown

Help pages: 7 (1 internal)includes a package overview page
Examples that run: 100%6 run in a plain check (4 of them under a condition)
Exported functions with examples: 100%
Documented parameters: 88%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

Intro to gbifdb HTML

How these are measured

Downloads

3K

CRAN downloads in the past year

Rank #12,469 · ~8/day · ~247/mo

Releases R versions

Daily download trend is not available in this view yet.

31130 days

90190 days

3K1 year

Compare downloads with other packages →

Also on66 r2u6 autocran

How downloads are counted

Repository

ropensci/gbifdb ↗Organization: ropensci

40Stars

5Forks

0Open issues

0Open PRs

0Releases

89Commits

4Commit identities

89 commits · Last activity 2025-09-14 · 0% stars, 30d · Default branch at 1.0.0.99, ahead of CRAN 1.0.0 (checked 2026-10-21)

Responsiveness

How these are sampled

PRs merged (all time): 78%
Median days to close, 50 most recently updated closed issues: 3
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2025-10-05 · 402026-07-07 · 40

How these are measured

PracticesBeta

11 development-tooling and community-health practices detected across 8 families in the upstream repository

Checks run against github.com/ropensci/gbifdb 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

Governance and community (2)

Code of conduct (inherited from ropensci)Contributing guide

Docs source (2)

README.Rmd

GitHub Pages site last deployed 2022-03-15

Coverage (1)

Coverage reporting (Codecov)

Show all practicesHide 4 practices

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Research and citation (1)

codemeta.json

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Installing gbifdb adds 30 packages (17 with compiled code, 33 MB of source tarballs). Heaviest: stringi 11 MB, duckdb 7.9 MB, arrow 4.2 MB.

Depends (1)

R >= 4.0

Imports (3)

arrow dplyr duckdbfs

LinkingTo (0)

none

Suggests (7)

spelling dbplyr testthat covr knitr rmarkdown minioclient

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (1)

Carl Boettiger

Author, Maintainer since 0.1.2 (2022)

Releases (2)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.0.0Latest
record
2023-10-19 · current release · diff ↗ ·
removed 1 export
gbif_conn
R
R 4.3.0 released · 2023-04-21
0.1.2
record
2022-05-21
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-05-21
Total releases: 2 / 4 yrs
License: Apache License (>= 2)
Minimum R: ≥ 4.0
Download size: 293 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("gbifdb")

Format

Boettiger, C. (2023). gbifdb: High Performance Interface to 'GBIF' (Version 1.0.0) [Computer software]. https://doi.org/10.32614/CRAN.package.gbifdb

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 gbifdb version 1.0.0 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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