R Observatory: Metrics for SNPknock version 0.8.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2025-12-25. Its history is shown below.

Reason: issues were not addressed in time

Details below reflect version 0.8.2, its last release before removal.

SNPknock

0.8.2

Knockoffs for Hidden Markov Models and Genetic Data

0packages depend

–downloads / year

–test coverage

–checks pass

Overview

About

Maintained by Matteo Sesia5 releasesCRAN page ↗

Generate knockoffs for genetic data and hidden Markov models. For more information, see the website below and the accompanying papers: "Gene hunting with hidden Markov model knockoffs", Sesia et al., Biometrika, 2019, (doi:10.1093/biomet/asy033). "Multi-resolution localization of causal variants across the genome", Sesia et al., bioRxiv, 2019, (doi:10.1101/631390).

Install

R (source archive)Ubuntu (r2u)openSUSE (OBS)

url <- "https://cran.r-project.org/src/contrib/Archive/SNPknock/SNPknock_0.8.2.tar.gz"
pkgFile <- "SNPknock_0.8.2.tar.gz"
download.file(url, pkgFile)
install.packages(pkgFile, type = "source", repos = NULL)

This package is no longer on CRAN, so install.packages() cannot fetch it by name. This downloads the last archived source (0.8.2) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

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-snpknock

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

# 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-SNPknock

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

Health

CRAN checks

CRAN check results are not tracked yet.

Code health

Yes

Tests · ratio 0.25

not tracked

Coverage

2

Dependencies · direct

Documentation

READMEYes · 34 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 0% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: not tracked
Return-value docs: not tracked
References docs: 43%

Downloads

Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on367 r2u14 autocran

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.3.0

Imports (2)

Rcpp Rdpack

LinkingTo (3)

Rcpp RcppArmadillo RcppProgress

Suggests (4)

knitr testthatparalleldoParallel

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Maintainer (1)

Matteo Sesia

Author, Maintainer

Authors (1)

Matteo Sesia

Author, Maintainer

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
archivedRemoved from CRAN
2025-12-25
issues were not addressed in time
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
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
0.8.2
2019-05-17 · diff ↗
R
R 3.6.0 released · 2019-04-26
0.7.1
2018-05-30 · diff ↗
0.7.0
2018-05-25 · diff ↗
R
R 3.5.0 released · 2018-04-23
0.5.1
2018-01-09 · diff ↗
0.5
2017-10-10
R
R 3.4.0 released · 2017-04-21

Package metadata

Total releases: 5
License: GPL-3 OSI
Minimum R: ≥ 3.3.0
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("SNPknock")

Format

Sesia, M. (n.d.). SNPknock: Knockoffs for Hidden Markov Models and Genetic Data (Version 0.8.2) [Computer software]. Retrieved August 15, 2026, from https://CRAN.R-project.org/package=SNPknock

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 SNPknock version 0.8.2 [Data set]. HJJB, LLC. Data release v2026-08-15. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-15, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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