R Observatory: Metrics for BinaryDosage version 2.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

BinaryDosage

2.0.0Package record

Creates, Merges, and Reads Binary Dosage Files

1packages depend

2.6Kdownloads / year

94.0%test coverage

13/13flavors OK

Overview

About

Maintained by John MorrisonCRAN page ↗Declared funders: NCI, NHLBI and 1 more

Tools to create binary dosage files from either VCF or GEN files, merge binary dosage files, and read binary dosage files. Binary dosage files tend to have quicker read times than VCF and GEN formats. There is a small increase in size compared to compressed VCF and GEN files.

Changes in 2.0.0

Removed CXX_STD = CXX11 from src/Makevars; the package now builds with the default C++17 standard.
Added Format 5 binary dosage files, a new format using per-SNP gzip compression and a companion RDS metadata file (.bdinfo).
vcftobd5() — convert a bgzipped VCF file to Format 5.
getbd5info() — load and validate a Format 5 file pair.
getbd5snp() — read a single SNP from a Format 5 file by index or ID.
Added vcftobd() as the new recommended function for converting VCF files to binary dosage format (requires the vcfppR package). The previous vcftobd() has been renamed to vcftobdlegacy() and emits a deprecation message.
Added updatebd() to convert any legacy binary dosage file (formats 1–4) to Format 5.

Show all changes in 2.0.0Hide the rest of the changes in 2.0.0

Added subsetbd() to create a new Format 5 file containing a subset of SNPs and/or subjects from any binary dosage file (formats 1–5). Filtering options: minimum MAF, SNP location vector, SNP location range, and subject ID vector.
Added mergebd() to merge two or more Format 5 files into a single Format 5 file. Automatically performs a subject merge (unique subjects, common SNPs) or a SNP merge (unique SNPs, common subjects) depending on the input files.
Extended getsnp() and bdapply() to support Format 5 files.

From NEWS.md in the release

Install

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

install.packages("BinaryDosage", 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-binarydosage

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-BinaryDosage

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-BinaryDosage

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: 4.6 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK7 OK2026-05-02
NOTE5 OK, 1 NOTE2026-04-30

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.0.0

READMEYes · 2,115 wordsVignettesYes · 11 · dynamicNEWSYes · 100% structured · mentions 2.0.0Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 26 (4 internal)
Examples that run: 100%16 run in a plain check
Exported functions with examples: 73%
Documented parameters: 99%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (11)

Show 1 moreHide 1 vignette

Using VCF Files

How these are measured

Downloads

2.6K

CRAN downloads in the past year

Rank #8,336 · ~7/day · ~218/mo

Releases R versions

Daily download trend is not available in this view yet.

38230 days

1.1K90 days

2.6K1 year

Compare downloads with other packages →

Also on400 r2u28 autocran

How downloads are counted

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Installing BinaryDosage adds 32 packages (12 with compiled code, 26 MB of source tarballs). Heaviest: ggplot2 6.0 MB, data.table 5.7 MB, Rcpp 1.8 MB.

Depends (0)

none

Imports (3)

Rcpp digest prodlim

LinkingTo (1)

Rcpp

Suggests (4)

knitr rmarkdown testthat vcfppR

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Depends, Imports or LinkingTo, most downloaded first

GxEScanR

How these are counted

Code & Tests

Datasets

People & History

People (4)

John Morrison

Author, Maintainer since 1.0.0 (2020)

NCI

Funder · added in 2.0.0

CA196559; CA201407

NHLBI

Funder · added in 2.0.0

HL115606

NIEHS

Funder

ES007048

Releases (2)

Pick two releases to compare their code metrics.

unarchivedReturned to CRAN
2026-04-29
2.0.0Latest
record
2026-04-29 · current release · diff ↗ ·
added 9 exports
closebd5con, getbd5snp, getbd5snp_buf, getbd5snp_con, mergebd, openbd5con, subsetbd, updatebd, vcftobdlegacy
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
1.0.0
record
2020-01-13
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2020-01-13
Total releases: 2 / 6 yrs
License: GPL-3 OSI
Download size: 228 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("BinaryDosage")

Format

Morrison, J., NCI, NCI, NHLBI, & NIEHS. (2026). BinaryDosage: Creates, Merges, and Reads Binary Dosage Files (Version 2.0.0) [Computer software]. https://doi.org/10.32614/CRAN.package.BinaryDosage

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 BinaryDosage version 2.0.0 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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