R Observatory: Metrics for flashier version 1.0.7

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

flashier

1.0.7Package record

Empirical Bayes Matrix Factorization

1packages dependsuggested by 1

6.2Kdownloads / year

0.0%test coverage

13/13flavors OK

Overview

About

Maintained by Jason WillwerscheidCRAN page ↗GitHub ↗Issues ↗

Methods for matrix factorization based on Wang and Stephens (2021) https://jmlr.org/papers/v22/20-589.html.

Install

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

install.packages("flashier", 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("willwerscheid/flashier")

Development version from willwerscheid/flashier. 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-flashier

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-flashier

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-flashier

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: 7.6 min · r-release-macos-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.7

READMEYes · 143 wordsVignettesYes · 2 · dynamicNEWSNoCitation fileNo

Help pages: 38
Examples that run: 100%10 run in a plain check
Exported functions with examples: 26%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 11%

Vignettes (2)

How these are measured

Downloads

6.2K

CRAN downloads in the past year

Rank #9,375 · ~17/day · ~521/mo

Releases R versions

Daily download trend is not available in this view yet.

41530 days

1K90 days

6.2K1 year

Compare downloads with other packages →

Also on97 r2u10 autocran

How downloads are counted

Repository

willwerscheid/flashier ↗Account: willwerscheid

18Stars

13Forks

36Open issues

1Open PRs

1Releases

631Commits

6Commit identities

631 commits · Last activity 2026-07-01 · +5.9% stars, 30d · Default branch at 1.0.60, ahead of CRAN 1.0.7 (checked 2026-10-18)

Responsiveness

How these are sampled

PRs merged (all time): 82%
Median days to close, 50 most recently updated closed issues: 42
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-05-08 · 122026-10-17 · 18

How these are measured

PracticesBeta

4 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/willwerscheid/flashier on 2026-10-18.

Docs source (2)

pkgdown

GitHub Pages site last deployed 2026-07-01

Reproducibility and dev environment (1)

data-raw/

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Installing flashier adds 42 packages (22 with compiled code, 38 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, invgamma 2.5 MB.

Depends (3)

R >= 3.4ebnm magrittr

Imports (9)

Matrixparalleldplyr stringr tibble tidyr softImpute irlba ggplot2

LinkingTo (0)

none

Suggests (7)

ashr cowplot testthat knitr rmarkdown RcppML rsvd

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

mr.mashr

Suggests, most downloaded first

mashr

How these are counted

Code & Tests

Datasets

People & History

People (6)

Jason Willwerscheid

Author, Maintainer since 1.0.7 (2023)

Author

Author

Author

Contributor

Contributor

Releases (1)

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
1.0.7Latest
record
2023-10-17 · current release
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-10-17
Total releases: 1 / 3 yrs
License: BSD_3_clause + file LICENSE OSI
Minimum R: ≥ 3.4
Bundled data: 350 KB / 2 files
Download size: 863 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("flashier")

Format

Willwerscheid, J., Carbonetto, P., Stephens, M., Wang, G., Wang, W., & Weine, E. (2023). flashier: Empirical Bayes Matrix Factorization (Version 1.0.7) [Computer software]. https://doi.org/10.32614/CRAN.package.flashier

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 flashier version 1.0.7 [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.

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