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ExtremaRank v0.5.0 — practical native R workflows

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@heise3 heise3 released this 06 Oct 16:33
v0.5.0
30325ae

ExtremaRank v0.5.0 improves native R sample/donor-deletion audits for practical omics workflows. It runs directly in R with native C++ exact arithmetic and optional Bioconductor models; no Python bridge is used.

  • Explicit planned/evaluated/failed/not-run coverage and correct zero-refit/partial statuses.
  • Candidate membership/sign changes, actual unit witnesses, observed rank ranges and selection fractions.
  • Declared model contrasts, whole-site/batch deletion and custom repeated-observation models.
  • Disk/summary score modes, self-contained checksum exports, resumable model fits and reproducible PSOCK workers.
  • Delayed/HDF5 row-block pseudobulk, numeric storage guards, preflight counts, summaries, plots and an executable R vignette.
  • Cached exact value orders and a stronger conditional Welch variance floor; optional influence traversal preserves exact decisions.

Validation: local R CMD check has zero errors, warnings or notes; 439,536 independent Fraction checks have zero failures. Twelve native real-data analyses and five fitted-model analyses preserve the frozen v0.4 results. Serial and parallel stochastic tests match. Full coverage and failures are retained in results/v05.

Native certificates apply to frozen inputs and declared deletion budgets. Fitted-model results describe observed executed refits and do not certify unseen deletions. Memory estimates are not peak RAM guarantees. Data/source attribution remains in DATA_LICENSE.md.

R installation (restart R before upgrading an already loaded native package):

source("https://raw.githubusercontent.com/heise3/ExtremaRank/v0.5.0/r/install_extremarank.R")
install_extremarank()
library(extremarank)

R 4.6 binaries target Windows x86_64 and CRAN macOS R.framework arm64/x86_64. Other supported R versions and Homebrew R use the small source archive and a C++17 compiler. SHA256SUMS records every release asset. The full source archive additionally includes reproducible benchmarks, prior outputs and attributed example data.

Chinese v0.5 guide · Validation records · Welch bound derivation

All 12 CI jobs passed at commit 30325ae3544c2b594589dcc51660fa3b9ae68f13: native R / eight jobs, Python / four jobs. Core R package checks on Linux, Windows and both Mac architectures have Status: OK. The model job requires every optional dependency and explicitly ran HDF5-backed aggregation and serial/PSOCK equality tests.

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