R Observatory: Metrics for BGData version 2.4.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

BGData

2.4.1Package record

A Suite of Packages for Analysis of Big Genomic Data

0packages dependsuggested by 2

4.5Kdownloads / year

63.2%test coverage

13/13flavors OK

Overview

About

Maintained by Alexander GruenebergCRAN page ↗GitHub ↗Issues ↗

An umbrella package providing a phenotype/genotype data structure and scalable and efficient computational methods for large genomic datasets in combination with several other packages: 'BEDMatrix', 'LinkedMatrix', and 'symDMatrix'.

Changes in 2.4.1

Fixed minor native routine registration issue.
Drop defunct CI services.
Update link to paper.

From NEWS.md in the release

Install

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

install.packages("BGData", 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("QuantGen/BGData")

Development version from QuantGen/BGData. 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-bgdata

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-BGData

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-BGData

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: 2.6 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.4.1

READMEYes · 674 wordsVignettesNoNEWSYes · 100% structured · mentions 2.4.1Citation fileYes · cites a publication

Help pages: 21includes a package overview page
Examples that run: 100%12 run in a plain check
Exported functions with examples: 69%
Documented parameters: 89%
Return-value docs: 63%
Help pages citing references: 0%

How these are measured

Downloads

4.5K

CRAN downloads in the past year

Rank #7,922 · ~12/day · ~374/mo

Releases R versions

Daily download trend is not available in this view yet.

46830 days

1.1K90 days

4.5K1 year

Compare downloads with other packages →

Also on374 r2u27 autocran

How downloads are counted

Repository

quantgen/bgdata ↗Organization: QuantGen

34Stars

14Forks

1Open issues

0Open PRs

0Releases

1,011Commits

4Commit identities

rr-pkgcrangeneticsgenomicsgwas

1,011 commits · Last activity 2025-01-20

Responsiveness

How these are sampled

PRs merged (all time): 64%
Median days to close, 50 most recently updated closed issues: 34
Median days to close, 50 most recently updated closed PRs: 5

Stars over time

2024-05-17 · 342026-07-07 · 34

How these are measured

PracticesBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/quantgen/bgdata on 2026-10-18.

Docs source (1)

GitHub Pages site last deployed 2017-02-23

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Installing BGData adds 12 packages (7 with compiled code, 17 MB of source tarballs). Heaviest: BH 14 MB, Rcpp 1.8 MB, ff 321 KB.

Depends (4)

R >= 3.0.2BEDMatrix LinkedMatrix symDMatrix

Imports (7)

methodsparallelcrochet bigmemory synchronicity ff bit

LinkingTo (0)

none

Suggests (4)

data.table lme4 SKAT testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Suggested by 2

Suggests, most downloaded first

LinkedMatrix symDMatrix

How these are counted

Code & Tests

Datasets

People & History

People (4)

Alexander Grueneberg

Author, Maintainer since 1.0.0 (2017)

Gustavo de los Campos

Author

Paulino Perez

Contributor

Ana Vazquez

Contributor

Releases (7)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
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
2.4.1Latest
record
2023-03-22 · current release · diff ↗
R
R 4.2.0 released · 2022-04-22
2.4.0
record
2021-12-08 · diff ↗ ·
added 1 export
FWD
2.3.0
record
2021-10-05 · diff ↗ ·
added 1 export
segments
R
R 4.1.0 released · 2021-05-18
2.2.0
record
2020-08-03 · diff ↗ ·
added 7 exports
geno, geno<-, map, map<-, pheno, pheno<-, preprocess
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
2.1.0
record
2019-01-25 · diff ↗ ·
added 1 export
chunkedMap
2.0.0
record
2018-08-24 · diff ↗ ·
removed 2 exports
crossprod_parallel, tcrossprod_parallel

added 2 exports
findRelated, orderedMerge
R
R 3.5.0 released · 2018-04-23
1.0.0
record
2017-05-11

Show 1 earlier eventHide 1 earlier event

R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-05-11
Total releases: 7 / 9 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.0.2
Download size: 104 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("BGData")

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

It points to 10.1534/g3.119.400018.

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 BGData version 2.4.1 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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