R Observatory: Metrics for sequoia version 3.2.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

sequoia

3.2.0

Pedigree Inference from SNPs

0packages depend

8.5Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Jisca HuismanFirst published 2017-02-1325 releasesCRAN page ↗

Multi-generational pedigree inference from incomplete data on hundreds of SNPs, including parentage assignment and sibship clustering. See Huisman (2017) (DOI:10.1111/1755-0998.12665) for more information.

Install

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

install.packages("sequoia", 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-sequoia

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-sequoia

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-sequoia

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

Health

CRAN checks

13OK

Slowest check: 10.1 min · r-devel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

5

Dependencies · direct

Check history

OK2026-08-04
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
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 2 earlier snapshots

ERROR2026-03-30
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 siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 77%
Documented parameters: 95%
Return-value docs: 83%
References docs: 6%

Downloads

8.5K

CRAN downloads in the past year

Rank #4,760 · ~23/day · ~708/mo

Releases R versions

Daily download trend is not available in this view yet.

34030 days

1.6K90 days

8.5K1 year

Compare downloads with other packages →

Also on438 r2u17 autocran

Repository

GitHub ↗ jiscah/jiscah.github.io

1Stars

0Forks

0Open issues

0Open PRs

0Releases

57Commits

1Contributors

57 commits · Last activity 2026-01-04

Stars over time

2023-11-03 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/jiscah/jiscah.github.io on 2026-08-16.

Reproducibility and dev environment (1)

data-raw/

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (5)

plyrstatsutilsgraphicscli

LinkingTo (0)

none

Suggests (10)

openxlsx knitr rmarkdown bookdown kinship2 R.rsp hexbin data.table vcfR adegenet

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

Jisca Huisman

Author, Maintainer

Authors (1)

Jisca Huisman

Author, Maintainer

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
3.2.0Latest
2026-01-09 · current release · diff ↗
3.1.3
2025-11-18 · diff ↗
3.0.3
2025-08-19 · diff ↗
R
R 4.5.0 released · 2025-04-11
2.11.2
2024-05-28 · diff ↗
2.11.1
2024-05-27 · diff ↗
R
R 4.4.0 released · 2024-04-24
2.9.0
2024-03-01 · diff ↗
2.8.3
2023-12-19 · diff ↗
2.7.2
2023-09-06 · diff ↗
2.5.6
2023-04-22 · diff ↗
R
R 4.3.0 released · 2023-04-21
2.5.3
2023-03-21 · diff ↗
2.4.1
2023-01-08 · diff ↗
unarchivedReturned to CRAN
2023-01-08

Show 24 earlier events

R
R 4.2.0 released · 2022-04-22
archivedRemoved from CRAN
2021-12-06
check problems were not corrected in time
2.3.5
2021-05-22 · diff ↗
R
R 4.1.0 released · 2021-05-18
2.3.4
2021-05-15 · diff ↗
2.3.3
2021-05-03 · diff ↗
2.3.2
2021-04-29 · diff ↗
2.0.7
2020-05-18 · diff ↗
unarchivedReturned to CRAN
2020-05-18
archivedRemoved from CRAN
2020-04-24
check problems were not corrected in time
R
R 4.0.0 released · 2020-04-24
1.3.3
2019-06-20 · diff ↗
1.3.1
2019-06-14 · diff ↗
R
R 3.6.0 released · 2019-04-26
1.1.1
2018-08-13 · diff ↗
R
R 3.5.0 released · 2018-04-23
1.0.2
2018-04-01 · diff ↗
1.0.0
2018-03-29 · diff ↗
0.9.3
2017-07-25 · diff ↗
0.9.2
2017-07-18 · diff ↗
R
R 3.4.0 released · 2017-04-21
0.8.1
2017-03-10 · diff ↗
0.7.2
2017-02-13
R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2017-02-13
Total releases: 25 / 9 yrs
License: GPL-2 OSI
Minimum R: ≥ 3.5.0
Bundled data: 265 KB / 13 files
Download size: 2.7 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("sequoia")

Format

Huisman, J. (2026). sequoia: Pedigree Inference from SNPs (Version 3.2.0) [Computer software]. https://doi.org/10.32614/CRAN.package.sequoia

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 sequoia version 3.2.0 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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