R Observatory: Metrics for bio3d version 2.4-5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

bio3d

2.4-5Package record

Biological Structure Analysis

9packages dependsuggested by 1

43.3Kdownloads / year

31.6%test coverage

13/13flavors OK

Overview

About

Maintained by Barry GrantCRAN page ↗Bitbucket ↗Website ↗

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. 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-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

CRAN check page ↗

Slowest check: 6.3 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK12 OK2026-04-25

Show 3 earlier changesHide 3 earlier changes

NOTE12 OK, 2 NOTE2026-04-22
ERROR11 OK, 2 NOTE, 1 ERROR2026-04-18
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.4-5

READMEYes · 285 wordsVignettesYes · 1 · staticNEWSYes · 100% structured · does not mention 2.4-5Citation fileYes · cites a publicationWebsiteYes

Help pages: 185includes a package overview page
Examples that run: 43%75 run in a plain check (6 of them under a condition) · 42 only when donttest examples are enabled (R CMD check --as-cran) · 55 never run · 2 hold no code
Exported functions with examples: 94%
Documented parameters: not tracked
Return-value docs: not tracked
Help pages citing references: 87%

Also includes 4 demo scripts (run with demo())

Vignettes (1)

bio3d Vignettes HTML

How these are measured

Downloads

43.3K

CRAN downloads in the past year

Rank #2,365 · ~119/day · ~3.6K/mo

Releases R versions

Daily download trend is not available in this view yet.

2.5K30 days

7K90 days

43.3K1 year

Compare downloads with other packages →

Also on778 r2u5.8K conda_forge558 bioconda104 c2d4u

How downloads are counted

Repository

bitbucket.org/grantlab/bio3d ↗

Responsiveness

not measured

How these are measured

PracticesBeta

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 v3 (2026-09-26)

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Installing bio3d adds 1 package (1 with compiled code, 1.8 MB of source tarballs). Heaviest: Rcpp 1.8 MB.

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

Depends 1 · Imports 8

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

MDaRes r3dmol Bios2cor ptm orthGS rPDBapi EnvNJ compas SOMMD

Suggests, most downloaded first

AntibodyForests

How these are counted

Code & Tests

Datasets

People & History

People (4)

Barry Grant

Author, Maintainer since 2.1-1 (2014)

Julien Ide

Author

Lars Skjaerven

Author

Xin-Qiu Yao

Author

Releases (18)

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
2.4-5Latest
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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
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2022-10-27 · diff ↗
R
R 4.2.0 released · 2022-04-22
2.4-3
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2022-03-10 · diff ↗
R
R 4.1.0 released · 2021-05-18
2.4-2
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2021-05-11 · diff ↗
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R 4.0.0 released · 2020-04-24
2.4-1
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2020-01-21 · diff ↗
2.4-0
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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
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2018-04-03 · diff ↗

Show 15 earlier eventsHide 15 earlier events

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

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' entry:

citation("bio3d")

The package provides a citation file, so citation() returns the authors' own entry.

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 v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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