ontologySimilarity

2.9

Calculating Ontological Similarities

1packages depend

4.4Kdownloads / year

–test coverage

12/13checks pass

Overview

About

Maintained by Daniel GreeneFirst published 2016-01-139 releasesCRAN page ↗

Calculate similarity between ontological terms and sets of ontological terms based on term information content and assess statistical significance of similarity in the context of a collection of terms sets - Greene et al. 2017 doi:10.1093/bioinformatics/btw763.

Install

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

install.packages("ontologySimilarity", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

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-ontologysimilarity

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-ontologySimilarity

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-ontologySimilarity

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

Health

CRAN checks

1NOTE12OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 9.9 min · r-oldrel-macos-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
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

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 95%
Return-value docs: 100%
References docs: 21%

Downloads

4.4K

CRAN downloads in the past year

Rank #10,934 · ~12/day · ~363/mo

Releases R versions

Daily download trend is not available in this view yet.

26830 days

93390 days

4.4K1 year

Compare downloads with other packages →

Also on430 r2u2 autocran3.8K conda_forge

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (2)

Rcpp ontologyIndex

LinkingTo (1)

Rcpp

Suggests (3)

knitr rmarkdown paintmap

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

SimReg

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

Daniel Greene

Author, Maintainer

Authors (1)

Daniel Greene

Author, Maintainer

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
2.9Latest
2026-02-01 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
2.7
2024-03-29 · diff ↗
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
2.5
2021-02-10 · diff ↗
2.4
2021-02-10 · diff ↗
unarchivedReturned to CRAN
2021-02-10
archivedRemoved from CRAN
2021-01-30
check problems were not corrected in time Unconditional use of cairo-based devices
R
R 4.0.0 released · 2020-04-24
2.3
2019-12-19 · diff ↗
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23

Show 7 earlier events

R
R 3.4.0 released · 2017-04-21
2.2
2016-10-28 · diff ↗
2.1
2016-09-09 · diff ↗
2.0
2016-08-06 · diff ↗
R
R 3.3.0 released · 2016-05-03
1.0
2016-01-13
R
R 3.2.0 released · 2015-04-16

Package metadata

First published: 2016-01-13
Total releases: 9 / 10 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.5.0
Bundled data: 509 KB / 2 files
Download size: 611 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Report a problem with this page →