AhoCorasickTrie

0.1.3

Fast Searching for Multiple Keywords in Multiple Texts

1packages depend

4.9Kdownloads / year

70.1%test coverage

13/13checks pass

Overview

About

Maintained by Matt ChambersFirst published 2016-07-293 releasesCRAN page ↗GitHub ↗

Aho-Corasick is an optimal algorithm for finding many keywords in a text. It can locate all matches in a text in O(N+M) time; i.e., the time needed scales linearly with the number of keywords (N) and the size of the text (M). Compare this to the naive approach which takes O(N*M) time to loop through each pattern and scan for it in the text. This implementation builds the trie (the generic name of the data structure) and runs the search in a single function call. If you want to search multiple texts with the same trie, the function will take a list or vector of texts and return a list of matches to each text. By default, all 128 ASCII characters are allowed in both the keywords and the text. A more efficient trie is possible if the alphabet size can be reduced. For example, DNA sequences use at most 19 distinct characters and usually only 4; protein sequences use at most 26 distinct characters and usually only 20. UTF-8 (Unicode) matching is not currently supported.

Install

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

install.packages("AhoCorasickTrie", 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("chambm/AhoCorasickTrie")

Development version from chambm/AhoCorasickTrie. 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-ahocorasicktrie

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-AhoCorasickTrie

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-AhoCorasickTrie

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

Health

CRAN checks

13OK

Slowest check: 1.7 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 1.70

70.1%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-04-22
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
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

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

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

Downloads

4.9K

CRAN downloads in the past year

Rank #10,036 · ~13/day · ~408/mo

Releases R versions

Daily download trend is not available in this view yet.

35530 days

1.1K90 days

4.9K1 year

Compare downloads with other packages →

Also on451 r2u12 autocran3.9K conda_forge231 bioconda8 c2d4u

Repository

GitHub ↗ chambm/ahocorasicktrie

11Stars

3Forks

2Open issues

0Open PRs

0Releases

9Commits

1Contributors

License Apache-2.0 · 9 commits · Last activity 2025-02-05 · 0% stars, 30d

Stars over time

2025-07-04 · 112026-07-07 · 11

Repository practices

Upstream repositoryBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/chambm/ahocorasicktrie on 2026-07-19.

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (1)

Rcpp

LinkingTo (1)

Rcpp

Suggests (2)

microbenchmark testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

prozor

Code & Tests

People & History

People (3)

Maintainer (1)

Matt Chambers

Author, Maintainer

Authors (2)

Matt Chambers

Author, Maintainer

Tomas Petricek

Author, Copyright holder

Tomas Petricek

Author, Copyright holder

Vanderbilt University

Package Timeline

3 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
0.1.3Latest
2025-02-05 · current release · diff ↗
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
0.1.2
2020-09-29 · 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
R
R 3.4.0 released · 2017-04-21
0.1.0
2016-07-29
R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2016-07-29
Total releases: 3 / 10 yrs
License: Apache License 2.0 OSI
Download size: 13 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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