bigsnpr

1.12.21

Analysis of Massive SNP Arrays

5packages depend

34.4Kdownloads / year

–test coverage

8/13checks pass

Overview

About

Maintained by Florian PrivéFirst published 2017-12-0518 releasesCRAN page ↗GitHub ↗

Easy-to-use, efficient, flexible and scalable tools for analyzing massive SNP arrays. Privé et al. (2018) doi:10.1093/bioinformatics/bty185.

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("bigsnpr", 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("privefl/bigsnpr")

Development version from privefl/bigsnpr. 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-bigsnpr

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

Health

CRAN checks

5NOTE8OK

Failing flavors

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

Slowest check: 14.7 min · r-devel-linux-x86_64-fedora-clang

Check history

NOTE2026-07-16
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-05-04
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-30
11 OK · 1 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-04-22
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 1 earlier snapshots

NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

Documentation signals are not tracked yet for this package.

Downloads

34.4K

CRAN downloads in the past year

Rank #2,909 · ~94/day · ~2.9K/mo

bigsnpr Releases R versions

Daily download trend is not available in this view yet.

1.6K30 days

5.5K90 days

34.4K1 year

Compare downloads with other packages →

Also on939 r2u6.9K conda_forge

Repository

GitHub ↗ privefl/bigsnpr

223Stars

48Forks

22Open issues

1Open PRs

0Releases

1,158Commits

16Contributors

big-dataparallel-computingrr-packagestatistical-methodspolygenic-scoresbioinformaticspopulation-structure-inference

1,158 commits · Last activity 2026-07-10 · +0.5% stars, 30d

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/privefl/bigsnpr on 2026-07-19.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

Lint, format, editor (1)

RStudio project

Coverage (1)

Codecov

Show all practices

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

39 external dependencies (excludes base and recommended)

Depends (2)

R >= 3.4bigstatsr

Imports (16)

bigassertr bigparallelr bigsparser bigreadr bigutilsr data.table doRNG foreach ggplot2 magrittrMatrixmethodsRcpp runoncestatsvctrs

LinkingTo (6)

bigsparser bigstatsr Rcpp RcppArmadillo rmio roptim

Suggests (19)

bindata covr dbplyr dplyr gaston glue Hmisc microbenchmark pcadapt quadprog RhpcBLASctl rmutil RSpectra RSQLite R.utils spelling testthat tibble xgboost

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

5direct

5indirect

RapidoPGS dartR.base locStra tidypopgen plmmr

Code & Tests

Datasets

People & History

People (4)

Maintainer (1)

Florian Privé

Author, Maintainer

Authors (1)

Florian Privé

Author, Maintainer

Other (3)

Hugues Aschard

Thesis advisor

Michael Blum

Thesis advisor

Bjarni Jóhann Vilhjálmsson

Thesis advisor · added in 1.9.10

Package Timeline

18 releases. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.12.21Latest
2025-08-21 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
1.12.18
2024-11-26 · diff ↗
1.12.15
2024-09-20 · diff ↗
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
1.12.2
2023-03-28 · diff ↗
1.11.6
2022-11-07 · diff ↗
1.11.4
2022-10-21 · diff ↗
1.10.8
2022-07-09 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.9.11
2022-02-16 · diff ↗
1.9.10
2022-02-13 · diff ↗
1.8.1
2021-06-03 · diff ↗
unarchivedReturned to CRAN
2021-06-03

Show 18 earlier events

archivedRemoved from CRAN
2021-05-24
check problems were not corrected in time
R
R 4.1.0 released · 2021-05-18
1.6.1
2021-01-11 · diff ↗
1.5.2
2020-11-01 · diff ↗
1.4.4
2020-07-05 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.3.0
2020-03-09 · diff ↗
1.2.2
2020-02-07 · diff ↗
1.2.1
2020-02-03 · diff ↗
unarchivedReturned to CRAN
2020-02-03
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
0.2.4
2018-02-02 · diff ↗
archivedRemoved from CRAN
2018-02-02
usage restrictions in 'README' were incompatible with a FOSS licence The code was not cross-platform (nor were any 'SystemRequirements' stated), and it again downloaded compiled code from an external source There was a memory-access error detected by ASAN
unarchivedReturned to CRAN
2018-02-02
0.2.2
2017-12-05
archivedRemoved from CRAN
2017-12-05
policy violation It downloaded compiled code from an external source
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-12-05
Total releases: 18 / 9 yrs
License: GPL-3 OSI
Download size: 1.0 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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