R Observatory: Metrics for bedrockbio version 2.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

bedrockbio

2.0.0

Open-Access Computational Biology Datasets

0packages depend

654downloads / year

98.3%test coverage

10/10checks pass

Overview

About

Maintained by Liam AbbottFirst published 2026-04-294 releasesCRAN page ↗GitHub ↗

Efficiently access the 'Bedrock Bio' library of open-access computational biology datasets. Lazily query datasets backed by 'DuckDB' and 'Apache Iceberg', with support for predicate pushdown and column projection to the cloud storage backend. This enables quick, iterative access to otherwise massive, unwieldy datasets without downloading them in full. See https://bedrock.bio for available datasets and documentation.

Install

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

install.packages("bedrockbio", 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("bedrock-bio/bedrock-bio-client")

Development version from bedrock-bio/bedrock-bio-client. 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-bedrockbio

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-bedrockbio

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-bedrockbio

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

Health

CRAN checks

10OK

Slowest check: 50 s · r-devel-linux-x86_64-debian-clang

Code health

Yes

Tests · ratio 1.71

98.3%

Coverage · measured lines

100%

Documentation · exports

6

Dependencies · direct

Check history

OK2026-08-05
10 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
9 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
10 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
9 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-24
10 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 4 earlier snapshots

ERROR2026-05-17
9 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-15
10 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-05-13
9 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-29
4 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 260 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

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

Downloads

654

CRAN downloads in the past year

Rank #21,401 · ~2/day · ~55/mo

Releases R versions

Daily download trend is not available in this view yet.

10030 days

51590 days

6541 year

Compare downloads with other packages →

Also on44 r2u6 autocran

Repository

GitHub ↗ bedrock-bio/bedrock-bio-client

1Stars

0Forks

0Open issues

1Open PRs

8Releases

166Commits

3Contributors

License GPL-3.0 · 166 commits · Last activity 2026-07-27 · 0% stars, 30d

Stars over time

2026-02-07 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/bedrock-bio/bedrock-bio-client on 2026-08-09.

Continuous integration (1)

GitHub Actions

Automation and maintenance (1)

Dependabot

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

Development tooling

AI-assisted toolingBeta

Uses AI-assisted development tooling (declared in repo)

Earliest detected marker: claude on 2026-05-20

claude

Most recent: claude on 2026-05-20

Evidence

claude: on 2026-05-20 · evidence B, D

How this is detected·Detection ruleset v2 (updated 2026-07-29)

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.2

Imports (6)

curl DBI dbplyr dplyr duckdb jsonlite

LinkingTo (0)

none

Suggests (2)

testthat withr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Maintainer (1)

Liam Abbott

Author, Maintainer, Copyright holder

Authors (1)

Liam Abbott

Author, Maintainer, Copyright holder

Copyright holders (1)

Liam Abbott

Author, Maintainer, Copyright holder

Package Timeline

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

2.0.0Latest
2026-07-02 · current release · diff ↗
1.4.0
2026-05-28 · diff ↗
1.3.1
2026-05-18 · diff ↗
1.3.0
2026-04-29
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-04-29
Total releases: 4 / 1 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.2
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("bedrockbio")

Format

Abbott, L. (2026). bedrockbio: Open-Access Computational Biology Datasets (Version 2.0.0) [Computer software]. https://doi.org/10.32614/CRAN.package.bedrockbio

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 bedrockbio version 2.0.0 [Data set]. HJJB, LLC. Data release v2026-08-15. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-15, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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