R Observatory: Metrics for seqinr version 4.2-44

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

seqinr

4.2-44

Biological Sequences Retrieval and Analysis

64packages depend

281Kdownloads / year

–test coverage

8/13checks pass

Overview

About

Maintained by Simon PenelFirst published 2004-11-2251 releasesCRAN page ↗GitHub ↗

Exploratory data analysis and data visualization for biological sequence (DNA and protein) data. Seqinr includes utilities for sequence data management under the ACNUC system described in Gouy, M. et al. (1984) Nucleic Acids Res. 12:121-127 doi:10.1093/nar/12.1Part1.121.

Install

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

install.packages("seqinr", 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("lbbe-software/seqinr")

Development version from lbbe-software/seqinr. 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-seqinr

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

# 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-seqinr

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-seqinr

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

5NOTE8OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc
NOTE r-devel-windows-x86_64

Slowest check: 7.0 min · r-devel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

2

Dependencies · direct

Check history

NOTE2026-07-16
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-08
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 1 FAILURE
ERROR2026-06-07
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSYes · 0% structuredCode of conductNoContributing guideNo

Examples that run: 71%
Documented parameters: not tracked
Return-value docs: not tracked
References docs: 89%

Downloads

281K

CRAN downloads in the past year

Rank #751 · ~770/day · ~23.4K/mo

Releases R versions

Daily download trend is not available in this view yet.

18.6K30 days

69.9K90 days

281K1 year

Compare downloads with other packages →

Also on1.5K r2u156 autocran27.5K conda_forge337 bioconda132 c2d4u

Repository

GitHub ↗ lbbe-software/seqinr

5Stars

2Forks

0Open issues

0Open PRs

2Releases

634Commits

4Contributors

634 commits · Last activity 2026-04-28 · 0% stars, 30d

Stars over time

2025-07-09 · 32026-07-07 · 5

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/lbbe-software/seqinr on 2026-08-09.

Continuous integration (1)

GitHub Actions

Research and citation (1)

codemeta.json

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

Dependencies

Declared dependencies

2 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.10.0

Imports (2)

ade4 segmented

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

64direct

46indirect

and 16 more packages.

Code & Tests

Datasets

People & History

People (8)

Maintainer (1)

Simon Penel

Maintainer · added in 1.1-4

Authors (2)

Delphine Charif

Author

Jean R. Lobry

Author, Copyright holder · added in 1.1-4

Contributors (5)

Olivier Clerc

Contributor · added in 3.1-5

Carolin Frank

Contributor · added in 3.1-5

Anamaria Necşulea

Contributor · added in 3.1-5

Leonor Palmeira

Contributor · added in 1.0-5

Guy Perrière

Contributor · added in 3.1-5

Copyright holders (1)

Jean R. Lobry

Author, Copyright holder · added in 1.1-4

Listed in earlier versions (4)

Jean Lobry

no longer listed · 1.0 to 1.1-2

Anamaria Necsulea

no longer listed · 1.0-5 to 3.1-3

Guy Perriere

no longer listed · 3.0-4 to 3.1-3

Jean R.

no longer listed · 3.1-5 to 4.2-44

Package Timeline

51 releases. Pick two to compare their code metrics. R releases are shown for context.

4.2-44Latest
2026-04-28 · 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
4.2-36
2023-12-08 · diff ↗
R
R 4.3.0 released · 2023-04-21
4.2-30
2023-04-05 · diff ↗
4.2-23
2022-11-28 · diff ↗
4.2-16
2022-05-19 · diff ↗
R
R 4.2.0 released · 2022-04-22
4.2-8
2021-06-09 · diff ↗
R
R 4.1.0 released · 2021-05-18
4.2-5
2020-12-17 · diff ↗
4.2-4
2020-10-10 · diff ↗
R
R 4.0.0 released · 2020-04-24
3.6-1
2019-09-07 · diff ↗

Show 66 earlier events

R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
3.4-5
2017-08-01 · diff ↗
R
R 3.4.0 released · 2017-04-21
3.3-6
2017-04-06 · diff ↗
3.3-3
2016-10-13 · diff ↗
3.3-2
2016-10-07 · diff ↗
3.3-1
2016-09-07 · diff ↗
3.3-0
2016-07-19 · diff ↗
3.2-0
2016-07-07 · diff ↗
3.1-5
2016-06-08 · diff ↗
R
R 3.3.0 released · 2016-05-03
R
R 3.2.0 released · 2015-04-16
3.1-3
2014-12-17 · diff ↗
3.1-2
2014-12-02 · diff ↗
3.0-9
2014-10-31 · diff ↗
R
R 3.1.0 released · 2014-04-10
R
R 3.0.0 released · 2013-04-03
3.0-7
2012-12-13 · diff ↗
R
R 2.15.0 released · 2012-03-30
3.0-6
2012-02-27 · diff ↗
R
R 2.14.0 released · 2011-10-31
3.0-5
2011-10-13 · diff ↗
3.0-4
2011-09-24 · diff ↗
R
R 2.13.0 released · 2011-04-13
3.0-3
2011-04-07 · diff ↗
3.0-1
2010-11-15 · diff ↗
R
R 2.12.0 released · 2010-10-15
3.0-0
2010-08-30 · diff ↗
R
R 2.11.0 released · 2010-04-22
2.0-9
2010-03-20 · diff ↗
2.0-8
2010-02-28 · diff ↗
2.0-7
2009-11-17 · diff ↗
R
R 2.10.0 released · 2009-10-26
2.0-6
2009-10-18 · diff ↗
2.0-5
2009-09-18 · diff ↗
2.0-4
2009-07-01 · diff ↗
2.0-3
2009-04-28 · diff ↗
R
R 2.9.0 released · 2009-04-17
2.0-2
2009-02-06 · diff ↗
2.0-1
2008-12-13 · diff ↗
2.0-0
2008-10-27 · diff ↗
R
R 2.8.0 released · 2008-10-20
1.1-7
2008-07-28 · diff ↗
1.1-6
2008-05-20 · diff ↗
R
R 2.7.0 released · 2008-04-22
1.1-5
2007-12-18 · diff ↗
1.1-4
2007-12-10 · diff ↗
R
R 2.6.0 released · 2007-10-03
1.1-2
2007-09-27 · diff ↗
1.1-1
2007-07-20 · diff ↗
R
R 2.5.0 released · 2007-04-24
1.0-7
2007-04-19 · diff ↗
R
R 2.4.0 released · 2006-10-03
1.0-6
2006-09-06 · diff ↗
1.0-5
2006-07-21 · diff ↗
R
R 2.3.0 released · 2006-04-24
1.0-4
2006-03-30 · diff ↗
R
R 2.2.0 released · 2005-10-06
1.0-3
2005-07-26 · diff ↗
R
R 2.1.0 released · 2005-04-18
1.0-2
2005-03-07 · diff ↗
1.0-1
2005-02-21 · diff ↗
1.0
2004-11-22
R
R 2.0.0 released · 2004-10-04
removedRemoved from CRAN
Versions 1.0-1 to 3.0-9 were removed for copyright violations and misrepresentation of authorship

Package metadata

First published: 2004-11-22
Total releases: 51 / 22 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 2.10.0
Bundled data: 1.4 MB / 30 files
Download size: 3.4 MB for 4.2-36
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("seqinr")

Format

Penel, S., Charif, D., Clerc, O., Frank, C., Lobry, J. R., Necşulea, A., Palmeira, L., & Perrière, G. (2026). seqinr: Biological Sequences Retrieval and Analysis (Version 4.2-44) [Computer software]. https://doi.org/10.32614/CRAN.package.seqinr

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 seqinr version 4.2-44 [Data set]. HJJB, LLC. Data release v2026-08-15. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-15, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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