onemap

3.2.6

Construction of Genetic Maps in Experimental Crosses

0packages depend

10.7Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Cristiane TanigutiFirst published 2008-06-0821 releasesCRAN page ↗GitHub ↗

Analysis of molecular marker data from model and non-model systems. For the later, it allows statistical analysis by simultaneously estimating linkage and linkage phases (genetic map construction) according to Wu and colleagues (2002) doi:10.1006/tpbi.2002.1577. All analysis are based on multi-point approaches using hidden Markov models.

Install

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

install.packages("onemap", 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("cristianetaniguti/onemap")

Development version from cristianetaniguti/onemap. 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-onemap

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-onemap

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-onemap

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

Health

CRAN checks

13OK

Slowest check: 7.8 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

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
OK2026-05-02
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-25
11 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-04-22
13 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 2 earlier snapshots

ERROR2026-04-18
12 OK · 1 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
13 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 38%
Documented parameters: 100%
Return-value docs: 96%
References docs: 21%

Downloads

10.7K

CRAN downloads in the past year

Rank #4,141 · ~29/day · ~893/mo

Releases R versions

Daily download trend is not available in this view yet.

62930 days

2.3K90 days

10.7K1 year

Compare downloads with other packages →

Also on425 r2u11 autocran36 c2d4u

Repository

GitHub ↗ cristianetaniguti/onemap

6Stars

8Forks

2Open issues

0Open PRs

14Releases

1,117Commits

12Contributors

1,117 commits · Last activity 2026-07-09 · +20% stars, 30d

Stars over time

2022-04-04 · 32026-07-07 · 5

Repository practices

Upstream repositoryBeta

4 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/cristianetaniguti/onemap on 2026-07-19.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

Dockerfile

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

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

Dependencies

Declared dependencies

19 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.6.0

Imports (19)

ggplot2 plotly reshape2 RcppgraphicsmethodsstatsutilsgrDevicessmacof princurveparalleldplyr tidyr htmlwidgets ggpubr RColorBrewer dendextend vcfR

LinkingTo (1)

Rcpp

Suggests (5)

knitr rmarkdown testthat stringr gatepoints

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 13,499 (60%)Rd 5,270 (23%)C++ 2,696 (12%)Vignettes 757 (3%)C 394 (2%)

Code characteristics

Object systems

S319

Cyclomatic complexity: 5.5 median / 99 max

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

189 74 exported

Complexity

11.1 avg / 99 max

Call network

189 nodes / 232 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

Per-function coverage is not measured for this package yet.

People & History

People (10)

Maintainer (1)

Cristiane Taniguti

Author, Maintainer · added in 2.1.0

Authors (4)

Cristiane Taniguti

Author, Maintainer · added in 2.1.0

Augusto Garcia

Author, Contributor · added in 2.0-3

Gabriel Margarido

Author · added in 2.0-3

Marcelo Mollinari

Author · added in 1.0-0

Contributors (7)

Augusto Garcia

Author, Contributor · added in 2.0-3

Rodrigo Amadeu

Contributor · added in 2.1.0

Karl Broman

Contributor · added in 2.0-3

Getulio Ferreira

Contributor · added in 2.1.2

Jeekin Lau

Contributor · added in 3.2.0

Katharine Preedy

Contributor, Copyright holder · added in 2.8.0

Bastian Schiffthaler

Contributor, Copyright holder · added in 2.8.0

Katharine Preedy

Contributor, Copyright holder · added in 2.8.0

Bastian Schiffthaler

Contributor, Copyright holder · added in 2.8.0

Listed in earlier versions (2)

with contributions from Antonio Augusto Franco Garcia.

no longer listed · 0.1-0 to 2.0-1

Gabriel Rodrigues Alves Margarido

no longer listed · 0.1-0 to 2.0-1

Package Timeline

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

3.2.6Latest
2026-07-11 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
3.2.4
2026-01-13 · diff ↗
unarchivedReturned to CRAN
2026-01-13
archivedRemoved from CRAN
2025-12-22
issues were not corrected in time
3.2.2
2025-05-16 · diff ↗
3.2.1
2025-04-26 · diff ↗
unarchivedReturned to CRAN
2025-04-26
R
R 4.5.0 released · 2025-04-11
archivedRemoved from CRAN
2025-01-25
issues were not corrected in time
3.2.0
2025-01-10 · diff ↗
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
3.0.0
2022-11-26 · diff ↗
R
R 4.2.0 released · 2022-04-22
2.8.2
2022-02-11 · diff ↗

Show 36 earlier events

unarchivedReturned to CRAN
2022-02-11
archivedRemoved from CRAN
2022-02-10
check problems were not corrected in time
2.8.1
2021-12-10 · diff ↗
2.8.0
2021-12-01 · diff ↗
unarchivedReturned to CRAN
2021-12-01
archivedRemoved from CRAN
2021-11-01
email to the maintainer was returned
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
2.1.3
2020-02-17 · diff ↗
2.1.2
2019-09-19 · diff ↗
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
2.1.1
2017-10-19 · diff ↗
2.1.0
2017-10-10 · diff ↗
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
R
R 3.2.0 released · 2015-04-16
R
R 3.1.0 released · 2014-04-10
2.0-4
2013-09-09 · diff ↗
R
R 3.0.0 released · 2013-04-03
2.0-3
2012-12-07 · diff ↗
2.0-1
2012-10-29 · diff ↗
R
R 2.15.0 released · 2012-03-30
R
R 2.14.0 released · 2011-10-31
R
R 2.13.0 released · 2011-04-13
2.0-0
2011-02-22 · diff ↗
R
R 2.12.0 released · 2010-10-15
R
R 2.11.0 released · 2010-04-22
R
R 2.10.0 released · 2009-10-26
1.0-1
2009-04-28 · diff ↗
1.0-0
2009-04-17 · diff ↗
R
R 2.9.0 released · 2009-04-17
R
R 2.8.0 released · 2008-10-20
0.1-1
2008-06-10 · diff ↗
0.1-0
2008-06-08
R
R 2.7.0 released · 2008-04-22

Package metadata

First published: 2008-06-08
Total releases: 21 / 18 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.6.0
Bundled data: 238 KB / 12 files
Download size: 528 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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