R Observatory: Metrics for bioseq version 0.1.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

bioseq

0.1.5Package record

A Toolbox for Manipulating Biological Sequences

1packages dependsuggested by 1

7.4Kdownloads / year

95.3%test coverage

13/13flavors OK

Overview

About

Maintained by Francois KeckCRAN page ↗GitHub ↗Website ↗Issues ↗

Classes and functions to work with biological sequences (DNA, RNA and amino acid sequences). Implements S3 infrastructure to work with biological sequences as described in Keck (2020) doi:10.1111/2041-210X.13490. Provides a collection of functions to perform biological conversion among classes (transcription, translation) and basic operations on sequences (detection, selection and replacement based on positions or patterns). The package also provides functions to import and export sequences from and to other package formats.

Changes in 0.1.5

Fix issue with upcoming release of stringr.

From NEWS.md in the release

Install

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

install.packages("bioseq", 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("fkeck/bioseq")

Development version from fkeck/bioseq. 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-bioseq

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-bioseq

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-bioseq

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: 2.0 min · r-oldrel-macos-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-28

Show 2 earlier changesHide 2 earlier changes

ERROR12 OK, 1 ERROR2026-05-22
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.5

READMEYes · 135 wordsVignettesYes · 2 · dynamicNEWSYes · 100% structured · mentions 0.1.5Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 58 (6 internal)includes a package overview page
Examples that run: 100%31 run in a plain check
Exported functions with examples: 61%
Documented parameters: 98%
Return-value docs: 80%
Help pages citing references: 7%

Vignettes (2)

How these are measured

Downloads

7.4K

CRAN downloads in the past year

Rank #5,557 · ~20/day · ~618/mo

Releases R versions

Daily download trend is not available in this view yet.

45430 days

1.5K90 days

7.4K1 year

Compare downloads with other packages →

Also on1.5K r2u20 autocran769 conda_forge43 c2d4u

How downloads are counted

Repository

fkeck/bioseq ↗Account: fkeck

26Stars

3Forks

8Open issues

0Open PRs

5Releases

126Commits

3Commit identities

License file reads as GPL-3.0 · 126 commits · Last activity 2025-09-29 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 8
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2025-09-26 · 262026-07-07 · 26

How these are measured

PracticesBeta

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

Checks run against github.com/fkeck/bioseq on 2026-10-21.

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 (2)

pkgdown

GitHub Pages site last deployed 2025-09-29

Coverage (1)

Coverage reporting (Codecov)

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Installing bioseq adds 32 packages (19 with compiled code, 23 MB of source tarballs). Heaviest: stringi 11 MB, Rcpp 1.8 MB, ape 1.4 MB.

Depends (1)

R >= 3.1.0

Imports (12)

methodsvctrs tibble ape crayon dplyr pillar stringi stringr stringdist readr rlang

LinkingTo (0)

none

Suggests (4)

knitr rmarkdown testthat covr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

refdb

Suggests, most downloaded first

tidysq

How these are counted

Code & Tests

Datasets

People & History

People (1)

Francois Keck

Releases (5)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.1.5Latest
record
2025-09-29 · current release · diff ↗
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
0.1.4
record
2022-09-06 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.1.3
record
2021-09-03 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.1.2
record
2020-11-26 · diff ↗
0.1.1
record
2020-07-27
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-07-27
Total releases: 5 / 6 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.1.0
Bundled data: 3.7 KB / 1 file
Download size: 691 KB

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' entry:

citation("bioseq")

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

It points to 10.1111/2041-210x.13490.

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 bioseq version 0.1.5 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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