R Observatory: Metrics for onemap version 3.2.6

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

onemap

3.2.6Package record

Construction of Genetic Maps in Experimental Crosses

0packages depend

9.1Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Cristiane TanigutiCRAN page ↗GitHub ↗Issues ↗

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.

Changes in 3.2.6

Adds a few bug fixes
Changes maintainer email address

From NEWS.md in the release

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. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

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

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-02

Show 4 earlier changesHide 4 earlier changes

ERROR11 OK, 1 ERROR2026-04-25
NOTE13 OK, 1 NOTE2026-04-22
ERROR12 OK, 1 NOTE, 1 ERROR2026-04-18
NOTE13 OK, 1 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 3.2.6

README· In the repository, left out of the releaseVignettesYes · 4 · dynamicNEWSYes · 67% structured · mentions 3.2.6Citation fileYes · cites a publication

Help pages: 106 (7 internal)
Examples that run: 38%24 run in a plain check · 39 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 62%
Documented parameters: 100%
Return-value docs: 96%
Help pages citing references: 21%

Vignettes (4)

How these are measured

Downloads

9.1K

CRAN downloads in the past year

Rank #4,597 · ~25/day · ~758/mo

Releases R versions

Daily download trend is not available in this view yet.

64430 days

1.8K90 days

9.1K1 year

Compare downloads with other packages →

Also on410 r2u2 autocran86 c2d4u

How downloads are counted

Repository

cristianetaniguti/onemap ↗Account: CristianetanigutiFork of augusto-garcia/onemap

6Stars

8Forks

2Open issues

0Open PRs

14Releases

1,120Commits

12Commit identities

1,120 commits · Last activity 2026-08-10 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 88%
Median days to close, 50 most recently updated closed issues: 1
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-09-08 · 42026-07-21 · 6

How these are measured

PracticesBeta

7 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/cristianetaniguti/onemap on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Docs source (1)

GitHub Pages site last deployed 2026-08-10

Coverage (1)

Coverage reporting

Reproducibility and dev environment (1)

Dockerfile

Show all practicesHide 1 practice

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

19 external dependencies (excludes base and recommended)

Installing onemap adds 150 packages (80 with compiled code, 128 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (10)

Cristiane Taniguti

Author, Maintainer since 2.1.0 (2017) · 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

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

MDS ordering algorithm

Bastian Schiffthaler

Contributor, Copyright holder · added in 2.8.0

HMM parallelization

Previously maintained by Marcelo Mollinari (2.0-3 to 2.0-4) and Gabriel Rodrigues Alves Margarido (0.1-0 to 2.0-1).

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

Releases (21)

Pick two releases to compare their code metrics.

3.2.6Latest
record
2026-07-11 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
unarchivedReturned to CRAN
2026-01-13
3.2.4
record
2026-01-13 · diff ↗
archivedRemoved from CRAN
2025-12-22
issues were not corrected in time
3.2.2
record
2025-05-16 · diff ↗
unarchivedReturned to CRAN
2025-04-26
3.2.1
record
2025-04-26 · diff ↗
R
R 4.5.0 released · 2025-04-11
archivedRemoved from CRAN
2025-01-25
issues were not corrected in time
3.2.0
record
2025-01-10 · diff ↗ ·
added 8 exports
edit_order_onemap, export_mappoly_genoprob, export_viewpoly, load_onemap_sequences, ord_by_geno, plot_genome_vs_cm, save_onemap_sequences, summary_maps_onemap
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
3.0.0
record
2022-11-26 · diff ↗ ·
removed 2 exports
est_hmm_out, parmap

added 2 exports
keep_only_selected_mks, rf_snp_filter_onemap
R
R 4.2.0 released · 2022-04-22
unarchivedReturned to CRAN
2022-02-11

Show 36 earlier eventsHide 36 earlier events

2.8.2
record
2022-02-11 · diff ↗
archivedRemoved from CRAN
2022-02-10
check problems were not corrected in time
2.8.1
record
2021-12-10 · diff ↗
unarchivedReturned to CRAN
2021-12-01
2.8.0
record
2021-12-01 · diff ↗ ·
added 28 exports
add_redundants, check_data, check_twopts, create_depths_profile, create_probs, empty_onemap_obj, est_hmm_out, est_map_hmm_out, extract_depth, filter_2pts_gaps, filter_missing, filter_prob, group_upgma, map_avoid_unlinked, map_overlapping_batches, parents_haplotypes, parmap, pick_batch_sizes, progeny_haplotypes, progeny_haplotypes_counts, remove_inds, rm_dupli_mks, seeded_map, seq_by_type, sort_by_pos, split_2pts, split_onemap, try_seq_by_seq
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
record
2020-02-17 · diff ↗
2.1.2
record
2019-09-19 · diff ↗ ·
removed 2 exports
pattern:., pattern:map

added 38 exports
Bonferroni_alpha, add_marker, combine_onemap, compare, create_data_bins, draw_map, draw_map2, drop_marker, find_bins, group, group_seq, haldane, kosambi, make_seq, map, marker_type, mds_onemap, onemap_read_vcfR, order_seq, plot_by_segreg_type, rcd, read_mapmaker, read_onemap, record, rf_2pts, rf_graph_table, ripple_seq, select_segreg, seriation, set_map_fun and 8 more
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
2.1.1
record
2017-10-19 · diff ↗
2.1.0
record
2017-10-10 · diff ↗ ·
added 1 export
pattern:map
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
record
2013-09-09 · diff ↗
R
R 3.0.0 released · 2013-04-03
2.0-3
record
2012-12-07 · diff ↗
2.0-1
record
2012-10-29 · diff ↗ ·
added 1 export
pattern:.
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
record
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
record
2009-04-28 · diff ↗
1.0-0
record
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
record
2008-06-10 · diff ↗
0.1-0
record
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

Appears in task views

Agricultural Science

Cite

Cite this package

Run in R for the authors' entry:

citation("onemap")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1111/j.2007.0018-0661.02000.x, 10.1093/gigascience/giad092, 10.1371/journal.pone.0189256.

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 onemap version 3.2.6 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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