R Observatory: Metrics for kmer version 1.1.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

kmer

1.1.3

Fast K-Mer Counting and Clustering for Biological Sequence Analysis

3packages depend

11.2Kdownloads / year

60.7%test coverage

13/13checks pass

Overview

About

Maintained by Shaun WilkinsonFirst published 2018-03-067 releasesCRAN page ↗GitHub ↗

Contains tools for rapidly computing distance matrices and clustering large sequence datasets using fast alignment-free k-mer counting and recursive k-means partitioning. See Vinga and Almeida (2003) doi:10.1093/bioinformatics/btg005 for a review of k-mer counting methods and applications for biological sequence analysis.

Install

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

install.packages("kmer", 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("shaunpwilkinson/kmer")

Development version from shaunpwilkinson/kmer. 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-kmer

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-kmer

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-kmer

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

Health

CRAN checks

13OK

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

Code health

Yes

Tests · ratio 0.09

60.7%

Coverage · measured lines

3

Dependencies · direct

Check history

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
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-22
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 2 earlier snapshots

ERROR2026-04-18
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 197 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 60%
Documented parameters: not tracked
Return-value docs: not tracked
References docs: 83%

Downloads

11.2K

CRAN downloads in the past year

Rank #4,851 · ~31/day · ~930/mo

Releases R versions

Daily download trend is not available in this view yet.

40330 days

1.6K90 days

11.2K1 year

Compare downloads with other packages →

Also on434 r2u17 autocran3.3K conda_forge72 c2d4u

Repository

GitHub ↗ shaunpwilkinson/kmer

29Stars

6Forks

3Open issues

0Open PRs

2Releases

56Commits

2Contributors

56 commits · Last activity 2026-01-23

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/shaunpwilkinson/kmer on 2026-08-23.

Continuous integration (1)

Travis CI

CRAN release process (1)

cran-comments.md

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

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (3)

openssl phylogram Rcpp

LinkingTo (1)

Rcpp

Suggests (5)

ape dendextend knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

3direct

2indirect

aphid copyseparator insect

Code & Tests

People & History

People (1)

Maintainer (1)

Shaun Wilkinson

Author, Maintainer

Authors (1)

Shaun Wilkinson

Author, Maintainer

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.1.3Latest
2026-01-23 · 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
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
1.1.2
2019-05-20 · diff ↗
R
R 3.6.0 released · 2019-04-26
1.1.1
2019-03-15 · diff ↗
1.1.0
2018-07-04 · diff ↗
R
R 3.5.0 released · 2018-04-23
1.0.2
2018-04-07 · diff ↗
1.0.1
2018-03-16 · diff ↗
1.0.0
2018-03-06

Show 1 earlier events

R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2018-03-06
Total releases: 7 / 8 yrs
License: GPL-3 OSI
Download size: 314 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("kmer")

Format

Wilkinson, S. (2026). kmer: Fast K-Mer Counting and Clustering for Biological Sequence Analysis (Version 1.1.3) [Computer software]. https://doi.org/10.32614/CRAN.package.kmer

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 kmer version 1.1.3 [Data set]. HJJB, LLC. Data release v2026-08-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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