R Observatory: Metrics for rPDBapi version 3.0.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

rPDBapi

3.0.2

A Comprehensive Interface for Accessing the Protein Data Bank

0packages depend

3.9Kdownloads / year

75.2%test coverage

12/13checks pass

Overview

About

Maintained by Selcuk KorkmazFirst published 2024-01-1711 releasesCRAN page ↗

Provides an R interface to the 'RCSB' Protein Data Bank ('PDB') Search and Data APIs (https://www.rcsb.org/). Supports full-text, attribute, sequence, motif, structure, and chemical searches; retrieval of entry-, assembly-, polymer-entity-, and chemical-component-level metadata; and conversion of API responses into analysis-ready tables and typed R objects for reproducible structural bioinformatics workflows.

Install

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

install.packages("rPDBapi", 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-rpdbapi

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-rPDBapi

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

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

Health

CRAN checks

1ERROR12OK

Failing flavors

ERROR r-release-linux-x86_64

Slowest check: 5.2 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.44

75.2%

Coverage · measured lines

100%

Documentation · exports

8

Dependencies · direct

Check history

ERROR2026-08-12
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-02
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-07-24
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-07-23
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 8 earlier snapshots

ERROR2026-07-20
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-07-19
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-07-12
11 OK · 0 NOTE · 0 WARNING · 2 ERROR · 0 FAILURE
OK2026-06-15
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-14
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-08
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 1 FAILURE
ERROR2026-06-07
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 446 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 85%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

3.9K

CRAN downloads in the past year

Rank #8,535 · ~11/day · ~327/mo

Releases R versions

Daily download trend is not available in this view yet.

20530 days

1.1K90 days

3.9K1 year

Compare downloads with other packages →

Also on134 r2u

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (8)

dplyr purrr httr jsonlite xml2 bio3d magrittrmethods

LinkingTo (0)

none

Suggests (5)

knitr r3dmol rmarkdown shiny testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (2)

Maintainer (1)

Selcuk Korkmaz

Author, Maintainer

Authors (2)

Selcuk Korkmaz

Author, Maintainer

Bilge Eren Yamasan

Author

Package Timeline

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

3.0.2Latest
2026-08-21 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
3.0.1
2026-03-08 · diff ↗
3.0.0
2026-03-07 · diff ↗
2.1.2
2025-10-29 · diff ↗
R
R 4.5.0 released · 2025-04-11
2.1.1
2024-10-19 · diff ↗
2.1
2024-09-06 · diff ↗
2.0
2024-09-04 · diff ↗
unarchivedReturned to CRAN
2024-09-04
archivedRemoved from CRAN
2024-08-21
policy violation On Internet access
1.3
2024-06-06 · diff ↗
1.2
2024-05-16 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.1
2024-03-29 · diff ↗
1.0
2024-01-17

Show 1 earlier events

R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2024-01-17
Total releases: 11 / 2 yrs
License: MIT + file LICENSE OSI
Download size: 450 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("rPDBapi")

Format

Korkmaz, S., & Yamasan, B. E. (2026). rPDBapi: A Comprehensive Interface for Accessing the Protein Data Bank (Version 3.0.2) [Computer software]. https://doi.org/10.32614/CRAN.package.rPDBapi

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 rPDBapi version 3.0.2 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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