R Observatory: Metrics for QBMS version 2.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

QBMS

2.0.0Package record

Query the Breeding Management System(s)

1packages depend

4.6Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Khaled Al-ShamaaCRAN page ↗GitHub ↗Website ↗Issues ↗

This R package assists breeders in linking data systems with their analytic pipelines, a crucial step in digitizing breeding processes. It supports querying and retrieving phenotypic and genotypic data from systems like 'EBS' https://ebs.excellenceinbreeding.org/, 'BMS' https://bmspro.io, 'BreedBase' https://breedbase.org, 'GIGWA' https://github.com/SouthGreenPlatform/Gigwa2 (using 'BrAPI' https://brapi.org calls), , and 'Germinate' https://germinateplatform.github.io/get-germinate/. Extra helper functions support environmental data sources, including 'TerraClimate' https://www.climatologylab.org/terraclimate.html and 'FAO' 'HWSDv2' https://gaez.fao.org/pages/hwsd soil database.

Changes in 2.0.0

Add Germinate support using BrAPI v2 calls.
Add new generic genotyping functions including list_variantsets(), set_variantset(), get_variantset(), get_variants(), and get_marker_map().
Add new get_trial_pedigree() function supports db compliance with BrAPI v2.
Add new generic login() function wraps around all engine specific login_* functions.
Fix a BreedBase login bug caused by incorrect httr2 form encoding when sending credentials.
Move special-case processing from qbms.R (before/after API calls) into the new internal engine.R module script.

From NEWS.md in the release

Install

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

install.packages("QBMS", 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("icarda/QBMS")

Development version from icarda/QBMS. 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-qbms

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-QBMS

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-QBMS

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: 1.9 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-15
ERROR12 OK, 1 ERROR2026-08-14
OK13 OK2026-08-05

Show 2 earlier changesHide 2 earlier changes

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

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.0.0

READMEYes · 799 wordsVignettesYes · 7 · staticNEWSYes · 100% structured · mentions 2.0.0Citation fileYes · software entry onlyWebsiteYes · pkgdown

Help pages: 67
Examples that run: 100%40 run in a plain check (39 of them under a condition)
Exported functions with examples: 77%
Documented parameters: 100%
Return-value docs: 96%
Help pages citing references: 3%

Vignettes (7)

How these are measured

Downloads

4.6K

CRAN downloads in the past year

Rank #8,716 · ~12/day · ~380/mo

Releases R versions

Daily download trend is not available in this view yet.

38830 days

1.1K90 days

4.6K1 year

Compare downloads with other packages →

Also on129 r2u9 autocran25 c2d4u

How downloads are counted

Repository

icarda/qbms ↗Organization: icarda

11Stars

5Forks

5Open issues

0Open PRs

4Releases

472Commits

4Commit identities

License file reads as GPL-3.0 · 472 commits · Last activity 2026-10-10 · 0% stars, 30d · Default branch at 3.0.0, ahead of CRAN 2.0.0 (checked 2026-10-11)

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 34
Median days to close, 50 most recently updated closed PRs: 22

Stars over time

2025-05-11 · 92026-08-28 · 11

How these are measured

PracticesBeta

6 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/icarda/qbms on 2026-10-11.

Governance and community (1)

Code of conduct

Docs source (2)

pkgdown

GitHub Pages site last deployed 2026-10-10

Research and citation (1)

CITATION.cff

Lint, format, editor (2)

lintrRStudio project

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

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Installing QBMS adds 33 packages (20 with compiled code, 17 MB of source tarballs). Heaviest: RSQLite 4.2 MB, Rcpp 1.8 MB, terra 1.5 MB.

Depends (1)

R >= 3.1.0

Imports (11)

httr2 jsonlitetcltkutilsRNetCDFstatsterra RSQLite DBI future future.apply

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown remotes

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Depends, Imports or LinkingTo, most downloaded first

qrlabelr

How these are counted

Code & Tests

People & History

People (5)

Khaled Al-Shamaa

Author, Maintainer since 0.6 (2021)

Johan Aparicio

Contributor · added in 0.9.0

Mariano Omar Crimi

Contributor

Zakaria Kehel

Contributor

ICARDA

Copyright holder

Releases (8)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
2.0.0Latest
record
2025-07-31 · current release · diff ↗ ·
added 8 exports
get_marker_map, get_trial_pedigree, get_variants, get_variantset, list_variantsets, login, login_germinate, set_variantset
R
R 4.5.0 released · 2025-04-11
1.5.0
record
2024-09-18 · diff ↗ ·
added 3 exports
gigwa_get_allelematrix, gigwa_get_markers, gigwa_get_sequences
R
R 4.4.0 released · 2024-04-24
1.0.0
record
2024-03-07 · diff ↗ ·
added 7 exports
get_hwsd2, ini_hwsd2, ini_terraclimate, login_breedbase, login_oauth2, scan_brapi_endpoints, set_token
R
R 4.3.0 released · 2023-04-21
0.9.1
record
2023-03-28 · diff ↗
0.9.0
record
2023-03-28 · diff ↗ ·
added 6 exports
calc_biovars, get_germplasm_attributes, get_qbms_connection, get_terraclimate, gigwa_get_metadata, set_qbms_connection
0.8.0
record
2022-05-19 · diff ↗ ·
added 9 exports
gigwa_get_samples, gigwa_get_variants, gigwa_list_dbs, gigwa_list_projects, gigwa_list_runs, gigwa_set_db, gigwa_set_project, gigwa_set_run, login_gigwa
R
R 4.2.0 released · 2022-04-22
0.7.0
record
2022-03-02 · diff ↗ ·
added 1 export
get_pedigree_table
0.6
record
2021-10-19
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-10-19
Total releases: 8 / 5 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.1.0
Download size: 101 KB

Appears in task views

Agricultural Science

Cite

Cite this package

Run in R for the authors' entry:

citation("QBMS")

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

It points to 10.32614/cran.package.qbms.

The repository also keeps a CITATION.cff.

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 QBMS version 2.0.0 [Data set]. HJJB, LLC. Data release v2026-10-19. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →