R Observatory: Metrics for ukbflow version 0.3.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ukbflow

0.3.4Package record

Streamlined Workflow for UK Biobank Data Extraction, Analysis, and Visualization

0packages depend

2.5Kdownloads / year

74.3%test coverage

13/13flavors OK

Overview

About

Maintained by Yibin ZhouCRAN page ↗GitHub ↗Website ↗Issues ↗

Provides a streamlined workflow for UK Biobank cloud-based analysis on the Research Analysis Platform (RAP). Includes tools for phenotype extraction and decoding, variable derivation, survival and association analysis, genetic risk score computation, and publication-quality visualization. For details on the UK Biobank resource, see Bycroft et al. (2018) doi:10.1038/s41586-018-0579-z.

Changes in 0.3.4

*Released: April 2026*

Bug Fixes

All test-integration-*.R files now call skip_on_cran() at file scope, preventing integration tests from running on CRAN. Resolves CHECK ERROR on r-devel-linux-x86_64-fedora-clang and r-devel-linux-x86_64-fedora-gcc reported by CRAN on 2026-04-08.
RNGkind() is now explicitly set before set.seed() in integration tests that use simulated data, ensuring cross-platform RNG reproducibility.

From NEWS.md in the release

Install

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

install.packages("ukbflow", 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("evanbio/ukbflow")

Development version from evanbio/ukbflow. 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-ukbflow

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-ukbflow

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-ukbflow

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: 5.2 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK9 OK2026-04-09

Show 1 earlier changeHide 1 earlier change

ERROR4 OK, 2 ERROR2026-04-08

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.3.4

READMEYes · 731 wordsVignettesYes · 14 · staticNEWSYes · 100% structured · mentions 0.3.4Citation fileNoWebsiteYes · pkgdown

Help pages: 59 (1 internal)includes a package overview page
Examples that run: 43%25 run in a plain check · 10 only when donttest examples are enabled (R CMD check --as-cran) · 23 never run
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (14)

Association Analysis for UKB Outcomes HTML
Authentication and Project Setup HTML
Decoding UKB Column Names and Values HTML
Deriving Disease Phenotypes from UKB Data HTML
Exploring and Fetching RAP Files HTML
Extracting Phenotype Data HTML
Genetic Risk Score (GRS) Analysis on UKB RAP HTML
Get Started with ukbflow HTML
Installation Guide HTML
Monitoring and Retrieving Extraction Jobs HTML

Show 4 moreHide 4 vignettes

How these are measured

Downloads

2.5K

CRAN downloads in the past year

Rank #13,377 · ~7/day · ~206/mo

Releases R versions

Daily download trend is not available in this view yet.

31430 days

85490 days

2.5K1 year

Compare downloads with other packages →

Also on42 r2u1 autocran

How downloads are counted

Repository

evanbio/ukbflow ↗Account: evanbio

3Stars

0Forks

0Open issues

0Open PRs

7Releases

234Commits

1Commit identities

234 commits · Last activity 2026-06-03 · 0% stars, 30d

Responsiveness

not measured

Stars over time

2026-04-18 · 12026-08-05 · 3

How these are measured

PracticesBeta

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

Checks run against github.com/evanbio/ukbflow on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Governance and community (1)

Contributing guide

Docs source (3)

pkgdown

GitHub Pages site last deployed 2026-08-21 · The repository has a site deploy workflow

pkgdown site last built 2026-08-21

Coverage (1)

Coverage reporting (Codecov)

Show all practicesHide 2 practices

CRAN release process (1)

cran-comments.md

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

20 external dependencies (excludes base and recommended)

Installing ukbflow adds 71 packages (35 with compiled code, 59 MB of source tarballs). Heaviest: stringi 11 MB, data.table 5.7 MB, bslib 5.6 MB.

Depends (1)

R >= 4.1

Imports (14)

broom cli curl data.table dplyr forestploter gt gtsummary jsonlite processx rlangsurvivaltidyselecttools

LinkingTo (0)

none

Suggests (8)

knitr pagedown pROC rmarkdown testthat mockery webshot2 withr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (1)

Yibin Zhou

Author, Maintainer since 0.3.3 (2026)

Releases (2)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.3.4Latest
record
2026-04-08 · current release · diff ↗
0.3.3
record
2026-04-07
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2026-04-07
Total releases: 2 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1
Download size: 1.4 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("ukbflow")

Format

Zhou, Y. (2026). ukbflow: Streamlined Workflow for UK Biobank Data Extraction, Analysis, and Visualization (Version 0.3.4) [Computer software]. https://doi.org/10.32614/CRAN.package.ukbflow

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 ukbflow version 0.3.4 [Data set]. HJJB, LLC. Data release v2026-10-20. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-20, 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 →