R Observatory: Metrics for bio3d version 2.4-5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

bio3d

2.4-5

Biological Structure Analysis

9packages depend

56.4Kdownloads / year

31.6%test coverage

13/13checks pass

Overview

About

Maintained by Barry GrantFirst published 2014-10-1518 releasesCRAN page ↗Bitbucket ↗

Utilities to process, organize and explore protein structure, sequence and dynamics data. Features include the ability to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. In addition, various utility functions are provided to enable the statistical and graphical power of the R environment to work with biological sequence and structural data. Please refer to the URLs below for more information.

Install

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

install.packages("bio3d", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

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-bio3d

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-bio3d

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

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

Health

CRAN checks

13OK

Slowest check: 7.1 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.12

31.6%

Coverage · measured lines

7

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 1 earlier snapshots

NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 285 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 52%
Documented parameters: not tracked
Return-value docs: not tracked
References docs: 87%

Downloads

56.4K

CRAN downloads in the past year

Rank #2,709 · ~154/day · ~4.7K/mo

Releases R versions

Daily download trend is not available in this view yet.

2.1K30 days

6.2K90 days

56.4K1 year

Compare downloads with other packages →

Also on586 r2u5.5K conda_forge535 bioconda54 c2d4u

Repository

Bitbucket ↗ grantlab/bio3d

Repository practices

Upstream repositoryBeta

Repository bitbucket.org/grantlab/bio3d is linked, but repository-practices checks have not run for it yet. Checks are GitHub-only for now.

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

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.1.0

Imports (7)

RcppparallelgridgraphicsgrDevicesstatsutils

LinkingTo (1)

Rcpp

Suggests (12)

XML RCurllatticencdf4 igraph bigmemory knitr rmarkdown testthat httr msa Biostrings

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

9direct

1indirect

Bios2cor EnvNJ SOMMD compas orthGS ptm r3dmol rPDBapi AntibodyForests

Code & Tests

Datasets

People & History

People (4)

Maintainer (1)

Barry Grant

Author, Maintainer

Authors (4)

Author, Maintainer

Author

Author

Author

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
2.4-5Latest
2024-10-30 · current release · diff ↗
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
2.4-4
2022-10-27 · diff ↗
R
R 4.2.0 released · 2022-04-22
2.4-3
2022-03-10 · diff ↗
R
R 4.1.0 released · 2021-05-18
2.4-2
2021-05-11 · diff ↗
R
R 4.0.0 released · 2020-04-24
2.4-1
2020-01-21 · diff ↗
2.4-0
2019-11-26 · diff ↗
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
2.3-4
2018-04-03 · diff ↗

Show 15 earlier events

2.3-3
2017-07-31 · diff ↗
2.3-2
2017-06-15 · diff ↗
R
R 3.4.0 released · 2017-04-21
2.3-1
2016-11-12 · diff ↗
2.3-0
2016-09-30 · diff ↗
R
R 3.3.0 released · 2016-05-03
2.2-4
2015-12-12 · diff ↗
2.2-3
2015-09-04 · diff ↗
R
R 3.2.0 released · 2015-04-16
2.2-2
2015-03-03 · diff ↗
2.2-1
2015-02-27 · diff ↗
2.1-3
2014-10-27 · diff ↗
2.1-2
2014-10-21 · diff ↗
2.1-1
2014-10-15
R
R 3.1.0 released · 2014-04-10

Package metadata

First published: 2014-10-15
Total releases: 18 / 12 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.1.0
Bundled data: 768 KB / 8 files
Download size: 1.5 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("bio3d")

Format

Grant, B., Ide, J., Skjaerven, L., & Yao, X. (2024). bio3d: Biological Structure Analysis (Version 2.4-5) [Computer software]. https://doi.org/10.32614/CRAN.package.bio3d

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 bio3d version 2.4-5 [Data set]. HJJB, LLC. Data release v2026-08-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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