R Observatory: Metrics for BWGS version 0.2.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

BWGS

0.2.1Package record

BreedWheat Genomic Selection Pipeline

0packages depend

3.3Kdownloads / year

–test coverage

0/13flavors OK

Overview

About

Maintained by Bangyou ZhengCRAN page ↗GitHub ↗Issues ↗

Package for Breed Wheat Genomic Selection Pipeline. The R package 'BWGS' is developed by Louis Gautier Tran <louis.gautier.tran@gmail.com> and Gilles Charmet <gilles.charmet@inra.fr>. This repository is forked from original repository https://forgemia.inra.fr/umr-gdec/bwgs and modified as a R package.

Install

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

install.packages("BWGS", 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("byzheng/BWGS")

Development version from byzheng/BWGS. 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-bwgs

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-BWGS

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-BWGS

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

13NOTE

Check messages

NOTERd filesr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64

checkRd: (-1) bwgs.cv.Rd:27: Lost braces; missing escapes or markup?
    27 | \item{geno}{Matrix (n x m) of genotypes for the training population: n lines with m markers. Genotypes should be coded {-1, 0, 1}. Missing data are allowed and coded as NA.}
       |                                                                                                                        ^
checkRd: (-1) bwgs.cv.Rd:59: Lost braces; missing escapes or markup?
    59 | \item{r2}{Coefficient of linkage disequilibrium (LD). Setting 0<r2<1 if the genotypic reduction method is in {LD or ANO+LD }.}
       |                                                                                                              ^
checkRd: (-1) bwgs.predict.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{geno_train}{Matrix (n x m) of genotypes for the training population: n lines with m markers. Genotypes should be coded as {-1, 0, 1, NA}. Missing data are allowed and coded as NA.}
       |               
...[truncated]...
redict.Rd:29: Lost braces; missing escapes or markup?
    29 | \item{geno_target}{Matrix (z x m) of genotypes for the target population: z lines with the same m markers as in geno_train. Genotypes should be coded as {-1, 0, 1, NA}. Missing data are allowed and coded as NA. Other arguments are identical to those of bwgs.cv, except pop_reduct_method, nTimes and nFolds, since the prediction is run only once, using the whole training population for model estimation, then applied to the target population.}
       |                                                                                                                                                          ^
checkRd: (-1) bwgs.predict.Rd:49: Lost braces; missing escapes or markup?
    49 | \item{r2}{Coefficient of linkage disequilibrium (LD). Setting 0<r2<1 if the genotypic reduction method is in {LD or ANO+LD }.}
       |                                                                                                              ^

CRAN check page ↗

Slowest check: 1.7 min · r-oldrel-windows-x86_64

Status changes

NOTE13 NOTENow
NOTE14 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.2.1

READMEYes · 62 wordsVignettesNoNEWS· In the repository, left out of the releaseCitation fileNo

Help pages: 4
Examples that run: 0%2 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

3.3K

CRAN downloads in the past year

Rank #13,311 · ~9/day · ~279/mo

Releases R versions

Daily download trend is not available in this view yet.

31530 days

85990 days

3.3K1 year

Compare downloads with other packages →

Also on95 r2u12 autocran68 c2d4u

How downloads are counted

Repository

byzheng/bwgs ↗Account: byzhengFork of vangiangtran/BWGS

1Stars

1Forks

1Open PRs

0Releases

79Commits

5Commit identities

License file reads as GPL-2.0 · 79 commits · Last activity 2023-04-28 · 0% stars, 30d · Default branch at 3.0.0, ahead of CRAN 0.2.1 (checked 2026-10-18)

Responsiveness

not measured

Stars over time

2025-10-04 · 12026-07-07 · 1

How these are measured

PracticesBeta

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

Checks run against github.com/byzheng/bwgs on 2026-10-18.

Continuous integration (3)

GitHub ActionsR CMD check workflowTravis CI (config file)

The R CMD check workflow runs on macOS and Windows

Governance and community (1)

Code of conduct

Docs source (1)

pkgdown

Coverage (1)

Coverage reporting

Show all practicesHide 1 practice

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Installing BWGS adds 15 packages (10 with compiled code, 24 MB of source tarballs). Heaviest: stringi 11 MB, BGLR 4.7 MB, glmnet 2.7 MB.

Depends (1)

R >= 3.5.0

Imports (7)

rrBLUP BGLR glmnet randomForest brnn e1071 stringi

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (3)

Bangyou Zheng

Maintainer since 0.1.0 (2020)

Gilles Charmet

Author

Louis Gautier Tran

Author

Releases (3)

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
R
R 4.2.0 released · 2022-04-22
0.2.1Latest
record
2021-09-23 · current release · diff ↗
0.2.0
record
2021-09-09 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.1.0
record
2020-07-30
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-07-30
Total releases: 3 / 6 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.5.0
Bundled data: 423 KB / 1 file
Download size: 455 KB

Appears in task views

Agricultural Science

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("BWGS")

Format

Zheng, B., Charmet, G., & Tran, L. G. (2021). BWGS: BreedWheat Genomic Selection Pipeline (Version 0.2.1) [Computer software]. https://doi.org/10.32614/CRAN.package.BWGS

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 BWGS version 0.2.1 [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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