R Observatory: Metrics for rPDBapi version 3.0.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

rPDBapi

3.0.2Package record

A Comprehensive Interface for Accessing the Protein Data Bank

0packages depend

4.2Kdownloads / year

75.2%test coverage

13/13flavors OK

Overview

About

Maintained by Selcuk KorkmazCRAN 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.

Changes in 3.0.2

Made all help examples that contact RCSB services interactive-only, so package checks no longer depend on network availability or remote-service response times.
Made live API calls in the structural-bioinformatics vignette opt-in through RPDBAPI_RUN_LIVE=true; offline and CRAN vignette builds now retain the code while skipping external requests.
Kept live API tests opt-in and verified the package with networking disabled, including examples, \donttest{} code, tests, and vignette rebuilding.
Corrected source-build exclusions so the prebuilt vignette index is retained in release tarballs and recognized by CRAN incoming checks.

From NEWS.md in the release

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. 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-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

13OK

CRAN check page ↗

Slowest check: 2.1 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-23
ERROR12 OK, 1 ERROR2026-08-12
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-02
ERROR12 OK, 1 ERROR2026-07-24

Show 9 earlier changesHide 9 earlier changes

OK13 OK2026-07-23
ERROR12 OK, 1 ERROR2026-07-20
OK13 OK2026-07-19
ERROR11 OK, 2 ERROR2026-07-12
OK13 OK2026-06-15
ERROR12 OK, 1 ERROR2026-06-14
OK12 OK, 1 FAILURE2026-06-08
ERROR12 OK, 1 ERROR2026-06-07
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 3.0.2

READMEYes · 446 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 3.0.2Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 62 (1 internal)includes a package overview page
Examples that run: 85%23 run in a plain check (8 of them under a condition) · 3 only when donttest examples are enabled (R CMD check --as-cran) · 1 never run
Exported functions with examples: 46%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

Accessing and Analyzing RCSB PDB Data with rPDBapi

How these are measured

Downloads

4.2K

CRAN downloads in the past year

Rank #12,318 · ~12/day · ~352/mo

Releases R versions

Daily download trend is not available in this view yet.

35130 days

88890 days

4.2K1 year

Compare downloads with other packages →

Also on116 r2u

How downloads are counted

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Installing rPDBapi adds 26 packages (19 with compiled code, 12 MB of source tarballs). Heaviest: Rcpp 1.8 MB, bio3d 1.5 MB, openssl 1.1 MB.

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.

How these are counted

Code & Tests

People & History

People (2)

Selcuk Korkmaz

Author, Maintainer since 1.0 (2024)

Bilge Eren Yamasan

Author

Releases (11)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
3.0.2Latest
record
2026-03-08 · current release · diff ↗
3.0.1
record
2026-03-08 · diff ↗ ·
added 1 export
fetch_data
3.0.0
record
2026-03-07 · diff ↗ ·
added 23 exports
as_rpdb_assembly, as_rpdb_chemical_component, as_rpdb_entry, as_rpdb_polymer_entity, as_rpdb_structure, build_assembly_id, build_entity_id, build_entry_id, build_instance_id, cache_info, clear_rpdbapi_cache, data_fetcher_batch, extract_calpha_coordinates, extract_ligand_table, extract_taxonomy_table, infer_id_type, join_structure_sequence, list_rcsb_fields, parse_rcsb_id, search_rcsb_fields, summarize_assemblies, summarize_entries, validate_properties
2.1.2
record
2025-10-29 · diff ↗
R
R 4.5.0 released · 2025-04-11
2.1.1
record
2024-10-19 · diff ↗
2.1
record
2024-09-06 · diff ↗ ·
added 4 exports
get_pdb_api_url, handle_api_errors, parse_response, send_api_request
unarchivedReturned to CRAN
2024-09-04
2.0
record
2024-09-04 · diff ↗ ·
removed 2 exports
FastaSequence, parse_fasta_text_to_list

added 2 exports
ChemicalOperator, return_data_as_dataframe
archivedRemoved from CRAN
2024-08-21
policy violation On Internet access
1.3
record
2024-06-06 · diff ↗
1.2
record
2024-05-16 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.1
record
2024-03-29 · diff ↗ ·
removed 3 exports
fetch_data, return_data_as_dataframe, walk_nested_dict
1.0
record
2024-01-17

Show 1 earlier eventHide 1 earlier event

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 · relicensed from GPL (>= 2) in 3.0.0
Download size: 450 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("rPDBapi")

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 rPDBapi version 3.0.2 [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.

Report a problem with this page →