R Observatory: Metrics for restez version 2.1.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

restez

2.1.5Package record

Create and Query a Local Copy of 'GenBank' in R

0packages depend

4.4Kdownloads / year

81.0%test coverage

13/13flavors OK

Overview

About

Maintained by Joel H. NittaCRAN page ↗GitHub ↗Website ↗Issues ↗

Download large sections of 'GenBank' https://www.ncbi.nlm.nih.gov/genbank/ and generate a local SQL-based database. A user can then query this database using 'restez' functions or through 'rentrez' https://CRAN.R-project.org/package=rentrez wrappers.

Changes in 2.1.5

BUG FIXES

gb_sequence_get() now ensures that accessions are returned in same order as

query (https://github.com/ropensci/restez/issues/64), thanks @krlmlr

tests no longer use with_mock()

(https://github.com/ropensci/restez/issues/63), thanks @hadley

Fix bug where a very long sequence record crashed db_create() (#60), thanks @btupper

From NEWS.md in the release

Install

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

install.packages("restez", 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/restez")

Development version from ropensci/restez. 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-restez

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-restez

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-restez

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: 3.9 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-09-30
ERROR12 OK, 1 ERROR2026-09-04
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-08

Show 6 earlier changesHide 6 earlier changes

WARNING12 OK, 1 WARNING2026-06-07
OK13 OK2026-05-24
ERROR12 OK, 1 ERROR2026-05-17
OK13 OK2026-05-15
ERROR12 OK, 1 ERROR2026-05-13
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.1.5

READMEYes · 426 wordsVignettes· In the repository, left out of the releaseNEWSYes · 33% structured · mentions 2.1.5Citation fileYes · cites a publicationWebsiteYes · pkgdown

Cites a JOSS paper

Help pages: 90 (1 internal)includes a package overview page
Examples that run: 81%17 run in a plain check · 4 never run
Exported functions with examples: 87%
Documented parameters: 97%
Return-value docs: 70%
Help pages citing references: 1%

How these are measured

Downloads

4.4K

CRAN downloads in the past year

Rank #12,272 · ~12/day · ~367/mo

Releases R versions

Daily download trend is not available in this view yet.

32230 days

90490 days

4.4K1 year

Compare downloads with other packages →

Also on66 r2u6 autocran

How downloads are counted

Repository

ropensci/restez ↗Organization: ropensci

28Stars

5Forks

9Open issues

0Open PRs

9Releases

362Commits

6Commit identities

genbankdnasequenceentrezrr-packagerstats

362 commits · Last activity 2025-03-06 · 0% stars, 30d · Default branch at 2.1.5.9000, ahead of CRAN 2.1.5 (checked 2026-10-18)

Responsiveness

How these are sampled

PRs merged (all time): 95%
Median days to close, 50 most recently updated closed issues: 16
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-05-01 · 272026-07-07 · 28

How these are measured

PracticesBeta

14 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/ropensci/restez on 2026-10-18.

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 conduct (inherited from ropensci)Contributing guideIssue templatesPR template

Docs source (3)

README.Rmdpkgdown

GitHub Pages site last deployed 2020-01-14

CRAN release process (3)

cran-comments.mdrevdep/CRAN-SUBMISSION

Show all practicesHide 2 practices

Research and citation (1)

codemeta.json

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Installing restez adds 20 packages (14 with compiled code, 26 MB of source tarballs). Heaviest: stringi 11 MB, duckdb 4.6 MB, Rcpp 1.8 MB.

Depends (1)

R >= 3.3.0

Imports (11)

utilsrentrez DBI curl cli crayon stringi duckdb fs assertthat ape

LinkingTo (0)

none

Suggests (6)

sessioninfo testthat knitr R.utils rmarkdown mockery

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (2)

Joel H. Nitta

Author, Maintainer · added in 2.1.3

Dom Bennett

Author

Maintainer since 2.1.2 (2022), previously Dom Bennett (1.0.0)

Listed in earlier versions (1)

Joel Nitta

no longer listed · 2.1.2

Releases (5)

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
2.1.5Latest
record
2025-03-07 · current release · diff ↗
R
R 4.4.0 released · 2024-04-24
2.1.4
record
2023-10-25 · diff ↗
R
R 4.3.0 released · 2023-04-21
2.1.3
record
2022-11-11 · diff ↗
unarchivedReturned to CRAN
2022-09-05
2.1.2
record
2022-09-05 · diff ↗ ·
added 1 export
ncbi_acc_get
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
archivedRemoved from CRAN
2019-04-18
requested by the maintainer
1.0.0
record
2018-11-26
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-11-26
Total releases: 5 / 8 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.3.0
Bundled data: 2.0 KB / 1 file
Download size: 1.3 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("restez")

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

It points to 10.21105/joss.01102.

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 restez version 2.1.5 [Data set]. HJJB, LLC. Data release v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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