R Observatory: Metrics for hsphase version 3.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

hsphase

3.0.1

Phasing, Pedigree Reconstruction, Sire Imputation and Recombination Events Identification of Half-sib Families Using SNP Data

2packages depend

3.8Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by Mohammad FerdosiFirst published 2013-10-2611 releasesCRAN page ↗

Identification of recombination events, haplotype reconstruction, sire imputation and pedigree reconstruction using half-sib family SNP data.

Install

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

install.packages("hsphase", 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-hsphase

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-hsphase

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-hsphase

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

Health

CRAN checks

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc

Slowest check: 5.9 min · r-devel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

3

Dependencies · direct

Check history

NOTE2026-04-22
10 OK · 4 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
9 OK · 4 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
10 OK · 4 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 94%
References docs: 9%

Downloads

3.8K

CRAN downloads in the past year

Rank #9,319 · ~10/day · ~313/mo

Releases R versions

Daily download trend is not available in this view yet.

22930 days

1K90 days

3.8K1 year

Compare downloads with other packages →

Also on464 r2u16 autocran

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Depends (2)

R >= 3.5.0snowfall

Imports (2)

Rcpp gdata

LinkingTo (2)

RcppArmadillo Rcpp

Suggests (1)

RhpcBLASctl

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

0indirect

HAPTRACE hsrecombi

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

Mohammad Ferdosi

Author, Maintainer

Authors (2)

Mohammad Ferdosi

Author, Maintainer

Cedric Gondro

Author

Package Timeline

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

3.0.1Latest
2026-07-03 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
3.0.0
2026-02-17 · diff ↗
R
R 4.5.0 released · 2025-04-11
2.0.4
2025-04-06 · diff ↗
R
R 4.4.0 released · 2024-04-24
2.0.3
2024-02-16 · 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
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
2.0.2
2018-11-26 · diff ↗
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
2.0.1
2016-12-05 · diff ↗

Show 9 earlier events

R
R 3.3.0 released · 2016-05-03
R
R 3.2.0 released · 2015-04-16
2.0.0
2014-06-27 · diff ↗
R
R 3.1.0 released · 2014-04-10
1.2.6
2014-04-02 · diff ↗
1.2.5
2014-03-28 · diff ↗
1.2.4
2013-10-30 · diff ↗
1.2.3
2013-10-26
R
R 3.0.0 released · 2013-04-03

Package metadata

First published: 2013-10-26
Total releases: 11 / 13 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 161 KB / 3 files
Download size: 910 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("hsphase")

Format

Ferdosi, M., & Gondro, C. (2026). hsphase: Phasing, Pedigree Reconstruction, Sire Imputation and Recombination Events Identification of Half-sib Families Using SNP Data (Version 3.0.1) [Computer software]. https://doi.org/10.32614/CRAN.package.hsphase

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 hsphase version 3.0.1 [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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