R Observatory: Metrics for r3dmol version 0.1.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

r3dmol

0.1.2

Create Interactive 3D Visualizations of Molecular Data

3packages depend

8.8Kdownloads / year

41.0%test coverage

13/13checks pass

Overview

About

Maintained by Wei SuFirst published 2020-10-263 releasesCRAN page ↗GitHub ↗

Create rich and fully interactive 3D visualizations of molecular data. Visualizations can be included in Shiny apps and R markdown documents, or viewed from the R console and 'RStudio' Viewer. 'r3dmol' includes an extensive API to manipulate the visualization after creation, and supports getting data out of the visualization into R. Based on the '3dmol.js' and the 'htmlwidgets' R package.

Install

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

install.packages("r3dmol", 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("swsoyee/r3dmol")

Development version from swsoyee/r3dmol. 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-r3dmol

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-r3dmol

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-r3dmol

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

Health

CRAN checks

13OK

Slowest check: 2.3 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.15

41.0%

Coverage · measured lines

99%

Documentation · exports

4

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
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 1 earlier snapshots

NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 201 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 98%
Documented parameters: 98%
Return-value docs: 71%
References docs: 0%

Downloads

8.8K

CRAN downloads in the past year

Rank #5,337 · ~24/day · ~730/mo

Releases R versions

Daily download trend is not available in this view yet.

49030 days

1.5K90 days

8.8K1 year

Compare downloads with other packages →

Also on113 r2u20 autocran

Repository

GitHub ↗ swsoyee/r3dmol

99Stars

6Forks

11Open issues

0Open PRs

3Releases

359Commits

3Contributors

proteinprotein-structure3drhtmlwidgetsvisualizationmolecular-graphicsmolecular-modeling

359 commits · Last activity 2023-10-25 · 0% stars, 30d

Stars over time

2024-12-23 · 892026-07-07 · 99

Repository practices

Upstream repositoryBeta

10 development-tooling and community-health practices detected across 7 families in the upstream repository

Checks run against github.com/swsoyee/r3dmol on 2026-08-16.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (2)

renvdata-raw/

Docs source (1)

README.Rmd

Lint, format, editor (2)

lintrRStudio project

Show all practices

Coverage (1)

Codecov

Governance and community (2)

Issue templatesFunding

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.10

Imports (4)

htmlwidgets magrittrmethodsbio3d

LinkingTo (0)

none

Suggests (6)

knitr rmarkdown shiny colourpicker covr testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

3direct

0indirect

HaDeX2 protti rPDBapi

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

Wei Su

Author, Maintainer

Authors (2)

Wei Su

Author, Maintainer

Brady Johnston

Author · added in 0.1.1

Package Timeline

3 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
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
0.1.2Latest
2021-03-14 · current release · diff ↗
0.1.1
2021-02-15 · diff ↗
0.1.0
2020-10-26
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-10-26
Total releases: 3 / 6 yrs
License: BSD_3_clause + file LICENSE OSI
Minimum R: ≥ 2.10
Bundled data: 643 KB / 6 files
Download size: 3.5 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("r3dmol")

Format

Su, W., & Johnston, B. (2021). r3dmol: Create Interactive 3D Visualizations of Molecular Data (Version 0.1.2) [Computer software]. https://doi.org/10.32614/CRAN.package.r3dmol

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 r3dmol version 0.1.2 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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