R Observatory: Metrics for bioLeak version 0.3.8

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

bioLeak

0.3.8Package record

Leakage-Safe Modeling and Auditing for Genomic and Clinical Data

0packages dependsuggested by 1

4.1Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Selcuk KorkmazCRAN page ↗GitHub ↗Issues ↗

Prevents and detects information leakage in biomedical machine learning. Provides leakage-resistant split policies (subject-grouped, batch-blocked, study leave-out, time-ordered), guarded preprocessing (train-only imputation, normalization, filtering, feature selection), cross-validated fitting with common learners, permutation-gap auditing, batch and fold association tests, and duplicate detection.

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("bioLeak", 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("selcukorkmaz/bioLeak")

Development version from selcukorkmaz/bioLeak. 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-bioleak

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

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 9.1 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-10

Show 2 earlier changesHide 2 earlier changes

ERROR12 OK, 1 ERROR2026-05-03
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.3.8

READMEYes · 1,108 wordsVignettesYes · 1 · evaluation depends on the environmentNEWSYes · 100% structured · does not mention 0.3.8Citation fileNo

Help pages: 58 (6 internal)
Examples that run: 92%23 run in a plain check (6 of them under a condition) · 2 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 50%
Documented parameters: 98%
Return-value docs: 100%
Help pages citing references: 2%

Vignettes (1)

bioLeak: Leakage-Aware Biomedical Modeling

How these are measured

Downloads

4.1K

CRAN downloads in the past year

Rank #7,586 · ~11/day · ~343/mo

Releases R versions

Daily download trend is not available in this view yet.

52130 days

1.2K90 days

4.1K1 year

Compare downloads with other packages →

Also on140 r2u

How downloads are counted

Repository

selcukorkmaz/bioleak ↗Account: selcukorkmaz

5Stars

0Forks

0Open issues

0Open PRs

1Releases

157Commits

1Commit identities

157 commits · Last activity 2026-09-26 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-10-20 · 12026-07-07 · 5

How these are measured

PracticesBeta

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

Checks run against github.com/selcukorkmaz/bioleak on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Docs source (1)

pkgdown

Coverage (1)

Coverage reporting

Lint, format, editor (1)

RStudio project

Show all practicesHide 1 practice

Git structural (1)

.gitattributes

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

AI coding toolsBeta

This repository shows signs of AI coding tools.

Codexfirst seen 2025-10-20
Pull request it wrote: opened by a project member
Claude Codefirst seen 2026-01-16
Seen in the repository: .claude
Named in .Rbuildignore: .claude
Named in .gitignore: .claude
Commits: at least 1 crediting it in the message

Models named in its commits

Claude Opus 51 commit · Sep 2026

Counts are commits, not lines of code. Commits by a tool's accounts count once across all of its accounts. Commits crediting it are the largest count among its credit lines, a minimum.How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

33 external dependencies (excludes base and recommended)

Installing bioLeak adds 35 packages (17 with compiled code, 30 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, isoband 1.5 MB. 1 more not on CRAN is not measured.

Depends (1)

R >= 4.3

Imports (9)

digest genericsmethodsstatsutilsSummarizedExperimentgraphicshardhat parsnip

LinkingTo (0)

none

Suggests (29)

BiocParallel splitGraph cli dials FNN future future.apply ggplot2 glmnet mice missForest pkgload ranger randomForest recipes RANN rsample tune VIM withr workflows xgboost yardstick pROC PRROCsurvivalknitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Suggested by 1

Suggests, most downloaded first

splitGraph

How these are counted

Code & Tests

People & History

People (1)

Selcuk Korkmaz

Author, Maintainer since 0.1.0 (2026)

Releases (7)

Pick two releases to compare their code metrics.

0.3.8Latest
record
2026-05-21 · current release · diff ↗ ·
added 1 export
plot_dlsi_repeats
0.3.7
record
2026-04-29 · diff ↗ ·
removed 2 exports
.guard_ensure_levels, .guard_fit

added 16 exports
as_leaksplits, audit_batch_assoc, audit_duplicates, audit_info, audit_perm_gap, audit_target_assoc, dlsi_R_eff, dlsi_ci, dlsi_metric, dlsi_p_value, dlsi_repeats, dlsi_robust, dlsi_tier, fit_metrics, guard_ensure_levels, guard_fit
R
R 4.6.0 released · 2026-04-24
0.3.6
record
2026-04-11 · diff ↗
0.3.5
record
2026-03-26 · diff ↗ ·
added 1 export
delta_lsi
0.3.0
record
2026-03-05 · diff ↗ ·
added 4 exports
benchmark_leakage_suite, check_split_overlap, cv_ci, guard_to_recipe
0.2.0
record
2026-02-11 · diff ↗
0.1.0
record
2026-02-06
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2026-02-06
Total releases: 7 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.3
Download size: 848 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("bioLeak")

Format

Korkmaz, S. (2026). bioLeak: Leakage-Safe Modeling and Auditing for Genomic and Clinical Data (Version 0.3.8) [Computer software]. https://doi.org/10.32614/CRAN.package.bioLeak

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 bioLeak version 0.3.8 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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