R Observatory: Metrics for refseqR version 1.1.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

refseqR

1.1.5

Common Computational Operations Working with RefSeq Entries (GenBank)

0packages depend

6Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Jose V. DieFirst published 2024-04-015 releasesCRAN page ↗GitHub ↗

Fetches NCBI data (RefSeq https://www.ncbi.nlm.nih.gov/refseq/ database) and provides an environment to extract information at the level of gene, mRNA or protein accessions.

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("refseqR", 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("jdieramon/refseqR")

Development version from jdieramon/refseqR. 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-refseqr

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

Health

CRAN checks

13OK

Slowest check: 3.2 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

4

Dependencies · direct

Check history

OK2026-08-14
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-08-13
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-25
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 2 earlier snapshots

ERROR2026-03-22
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 42%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

6K

CRAN downloads in the past year

Rank #7,663 · ~16/day · ~501/mo

Releases R versions

Daily download trend is not available in this view yet.

19830 days

1.1K90 days

6K1 year

Compare downloads with other packages →

Also on90 r2u

Repository

GitHub ↗ jdieramon/refseqr

4Stars

1Forks

0Open issues

0Open PRs

4Releases

157Commits

2Contributors

157 commits · Last activity 2024-12-25

Stars over time

2024-11-29 · 42026-07-07 · 4

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/jdieramon/refseqr on 2026-08-16.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

cran-comments.md

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

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (4)

IRanges rentrez tibble Biostrings

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (2)

Maintainer (1)

Jose V. Die

Author, Maintainer

Authors (1)

Jose V. Die

Author, Maintainer

Contributors (1)

Lluís Revilla Sancho

Contributor

Package Timeline

5 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
1.1.5Latest
2024-10-30 · current release · diff ↗
1.1.4
2024-08-18 · diff ↗
1.1.2
2024-07-15 · diff ↗
1.0.2
2024-05-22 · diff ↗
unarchivedReturned to CRAN
2024-05-22
archivedRemoved from CRAN
2024-04-30
policy violation On Internet access. Also other errors
R
R 4.4.0 released · 2024-04-24
1.0.1
2024-04-01
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2024-04-01
Total releases: 5 / 2 yrs
License: MIT + file LICENSE OSI
Download size: 20 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("refseqR")

Format

Die, J. V., & Revilla Sancho, L. (2024). refseqR: Common Computational Operations Working with RefSeq Entries (GenBank) (Version 1.1.5) [Computer software]. https://doi.org/10.32614/CRAN.package.refseqR

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 refseqR version 1.1.5 [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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