R Observatory: Metrics for AnnotationBustR version 2.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

AnnotationBustR

2.0Package record

Extract Subsequences from GenBank Annotations

0packages depend

5.3Kdownloads / year

–test coverage

12/13flavors OK

Overview

About

Maintained by Samuel R. BorsteinCRAN page ↗GitHub ↗Website ↗Issues ↗

Extraction of subsequences into FASTA files from GenBank annotations where gene names may vary among accessions. Borstein & O'Meara (2018) doi:10.7717/peerj.5179.

Install

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

install.packages("AnnotationBustR", 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("sborstein/AnnotationBustR")

Development version from sborstein/AnnotationBustR. 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-annotationbustr

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-AnnotationBustR

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-AnnotationBustR

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

1ERROR12OK

Check messages

ERRORpackage dependenciesr-oldrel-macos-x86_64

Packages required and available but unsuitable versions:
  'Biostrings', 'BSgenome', 'GenomicFeatures', 'GenomicRanges'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

CRAN check page ↗

Slowest check: 7.7 min · r-oldrel-windows-x86_64

Status changes

ERROR12 OK, 1 ERRORNow
ERROR10 OK, 2 NOTE, 1 ERROR2026-09-01
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.0

README· In the repository, left out of the releaseVignettesYes · 1 · dynamicNEWSYes · 33% structured · does not mention 2.0Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 8
Examples that run: 67%2 run in a plain check (1 of them under a condition) · 1 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 13%

Vignettes (1)

AnnotationBustR Tutorial

How these are measured

Downloads

5.3K

CRAN downloads in the past year

Rank #3,890 · ~14/day · ~440/mo

Releases R versions

Daily download trend is not available in this view yet.

1.4K30 days

2.4K90 days

5.3K1 year

Compare downloads with other packages →

Also on119 r2u41 autocran24 c2d4u

How downloads are counted

Repository

sborstein/annotationbustr ↗Account: sborstein

5Stars

3Forks

2Open issues

0Open PRs

5Releases

321Commits

2Commit identities

321 commits · Last activity 2026-09-06

Responsiveness

How these are sampled

PRs merged (all time): 0%
Median days to close, 50 most recently updated closed issues: 79
Median days to close, 50 most recently updated closed PRs: 1,335

Stars over time

2022-12-21 · 32026-07-07 · 5

How these are measured

PracticesBeta

6 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/sborstein/annotationbustr 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

Docs source (3)

pkgdown

GitHub Pages site last deployed 2026-09-08 · The repository has a site deploy workflow

pkgdown site last built 2026-09-08

CRAN release process (1)

cran-comments.md

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

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Installing AnnotationBustR adds 26 packages (17 with compiled code, 20 MB of source tarballs). Heaviest: stringi 11 MB, openssl 1.1 MB, jsonlite 1.0 MB. 4 more not on CRAN are not measured.

Depends (1)

R >= 4.5

Imports (8)

Biostrings BSgenome dplyr (>= 1.2.1)GenomicFeatures GenomicRanges magrittr rentrez stringr

LinkingTo (0)

none

Suggests (4)

knitr rmarkdown seqinr testthat

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)

Samuel R. Borstein

Author, Maintainer since 1.0 (2017)

Brian O'Meara

Author

Releases (5)

Pick two releases to compare their code metrics.

2.0Latest
record
2026-08-31 · current release · diff ↗
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
1.3.0
record
2020-09-24 · diff ↗
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
1.2
record
2018-04-10 · diff ↗
1.1
record
2017-09-01 · diff ↗
R
R 3.4.0 released · 2017-04-21
1.0
record
2017-03-02
R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2017-03-02
Total releases: 5 / 9 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.5
Bundled data: 6.0 KB / 4 files
Download size: 1.1 MB

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' entry:

citation("AnnotationBustR")

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

It points to 10.7717/peerj.5179.

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 AnnotationBustR version 2.0 [Data set]. HJJB, LLC. Data release v2026-10-17. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-17, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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