R Observatory: Metrics for rentrez version 1.2.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

rentrez

1.2.4Package record

'Entrez' in R

18packages dependsuggested by 5

521Kdownloads / year

59.2%test coverage

13/13flavors OK

Overview

About

Maintained by David WinterCRAN page ↗GitHub ↗Issues ↗

Provides an R interface to the NCBI's 'EUtils' API, allowing users to search databases like 'GenBank' https://www.ncbi.nlm.nih.gov/genbank/ and 'PubMed' https://pubmed.ncbi.nlm.nih.gov/, process the results of those searches and pull data into their R sessions.

Changes in 1.2.4

Bug fix to tweak documentation and meet CRAN requirements

From NEWS.md in the release

Install

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

install.packages("rentrez", 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("ropensci/rentrez")

Development version from ropensci/rentrez. 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-rentrez

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-rentrez

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-rentrez

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 1.4 min · r-release-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.2.4

README· In the repository, left out of the releaseVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 1.2.4Citation fileYes · cites a publication

Help pages: 17 (1 internal)includes a package overview page
Examples that run: 0%1 only when donttest examples are enabled (R CMD check --as-cran) · 12 never run
Exported functions with examples: 81%
Documented parameters: 99%
Return-value docs: 94%
Help pages citing references: 29%

Vignettes (1)

Rentrez Tutorial

How these are measured

Downloads

521K

CRAN downloads in the past year

Rank #465 · ~1.4K/day · ~43.4K/mo

Releases R versions

Daily download trend is not available in this view yet.

50.9K30 days

169.2K90 days

521K1 year

Compare downloads with other packages →

Also on5.3K r2u94 autocran15.5K conda_forge129 bioconda123 c2d4u

How downloads are counted

Repository

ropensci/rentrez ↗Organization: ropensci

221Stars

41Forks

54Open issues

3Open PRs

8Releases

504Commits

15Commit identities

rrstatsr-package

504 commits · Last activity 2026-10-10 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 83%
Median days to close, 50 most recently updated closed issues: 25
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2025-09-08 · 2072026-09-04 · 221

How these are measured

PracticesBeta

10 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/ropensci/rentrez on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Governance and community (4)

Code of conductContributing guideIssue templatesPR template

Docs source (3)

README.Rmdpkgdown

GitHub Pages site

Automation and maintenance (1)

pre-commit

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Installing rentrez adds 9 packages (7 with compiled code, 3.9 MB of source tarballs). Heaviest: openssl 1.1 MB, jsonlite 1.0 MB, XML 937 KB.

Depends (1)

R >= 2.6.0

Imports (3)

XML httr jsonlite

LinkingTo (0)

none

Suggests (3)

testthat knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

18direct

9indirect

Depends 1 · Imports 17

Suggested by 5

Show all 23 packagesHide all 23 packages

Depends, Imports or LinkingTo, most downloaded first

pubmedR rotl AnnotationBustR fanyi covid19.analytics MACER DeSciDe read.gb biolink refdb Map2NCBI refseqR puremoe vDiveR geneHummus restez ORscraper LBDiscover

Suggests, most downloaded first

openalexR idiogramFISH BoSSA PACVr searchAnalyzeR

How these are counted

Code & Tests

People & History

People (3)

David Winter

Author, Maintainer since 0.1.1 (2013)

Scott Chamberlain

Contributor · added in 0.3

Han Guangchun

Contributor · added in 1.0.0

Releases (19)

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
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
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
R
R 3.2.0 released · 2015-04-16
R
R 3.1.0 released · 2014-04-10
R
R 3.0.0 released · 2013-04-03
R
R 2.15.0 released · 2012-03-30
2.14.1Latest
record
2011-11-22 · current release · diff ↗ ·
added 8 exports
entrez_email, entrez_fetch, entrez_global_query, entrez_link, entrez_post, entrez_search, entrez_summary, parse_pubmed_xml

Show 19 earlier eventsHide 19 earlier events

1.2.4
record
2025-06-11 · diff ↗
1.2.3
record
2020-11-10 · diff ↗
1.2.2
record
2019-05-02 · diff ↗
1.2.1
record
2018-03-05 · diff ↗
1.2.0
record
2018-02-12 · diff ↗ ·
added 1 export
set_entrez_key
1.1.0
record
2017-06-01 · diff ↗
1.0.4
record
2016-10-26 · diff ↗
1.0.2
record
2016-04-21 · diff ↗
1.0.1
record
2016-02-29 · diff ↗
1.0.0
record
2015-09-23 · diff ↗ ·
added 2 exports
extract_from_esummary, linkout_urls
0.4.2
record
2015-06-26 · diff ↗
0.4.1
record
2015-03-03 · diff ↗
0.4
record
2015-02-09 · diff ↗ ·
removed 1 export
entrez_email

added 6 exports
entrez_citmatch, entrez_db_links, entrez_db_searchable, entrez_db_summary, entrez_dbs, entrez_info
0.3.1
record
2014-09-24 · diff ↗
0.3
record
2014-09-23 · diff ↗
0.2.4
record
2014-05-15 · diff ↗
0.2.3
record
2014-03-05 · diff ↗
0.1.1
record
2013-08-20
R
R 2.14.0 released · 2011-10-31

Package metadata

First published: 2011-11-22
Total releases: 19 / 15 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 2.6.0
Download size: 66 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("rentrez")

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 rentrez version 1.2.4 [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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