R Observatory: Metrics for smer version 0.0.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

smer

0.0.3Package record

Sparse Marginal Epistasis Test

0packages depend

3.5Kdownloads / year

–test coverage

9/13flavors OK

Overview

About

Maintained by Julian StampCRAN page ↗GitHub ↗Website ↗Issues ↗

The Sparse Marginal Epistasis Test is a computationally efficient genetics method which detects statistical epistasis in complex traits; see Stamp et al. (2025, doi:10.1101/2025.01.11.632557) for details.

Changes in 0.0.3

Bug fixes for macOS CRAN checks
Lowered R requirement from 4.4.0 to 4.3.0

From NEWS.md in the release

Install

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

install.packages("smer", 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("lcrawlab/sme")

Development version from lcrawlab/sme. 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-smer

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

4ERROR9OK

Check messages

ERRORwhether package can be installedr-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-release-macos-arm64, r-release-macos-x86_64

r-oldrel-macos-arm64

Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.5/smer.Rcheck/00install.out’ for details.

r-oldrel-macos-x86_64

Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.5/smer.Rcheck/00install.out’ for details.

r-release-macos-arm64

Installation failed.
See ‘/Volumes/Builds/packages/sonoma-arm64/results/4.6/smer.Rcheck/00install.out’ for details.

r-release-macos-x86_64

Installation failed.
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.6/smer.Rcheck/00install.out’ for details.

CRAN check page ↗

Slowest check: 8.7 min · r-devel-windows-x86_64

Status changes

ERROR9 OK, 4 ERRORNow
ERROR8 OK, 1 NOTE, 5 ERROR2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

Documentation signals are not tracked yet for this package.

WebsiteYes · pkgdown

Vignettes (6)

How these are measured

Downloads

3.5K

CRAN downloads in the past year

Rank #10,739 · ~10/day · ~296/mo

smer Releases R versions

Daily download trend is not available in this view yet.

63130 days

96190 days

3.5K1 year

Compare downloads with other packages →

Also on379 r2u

How downloads are counted

Repository

lcrawlab/sme ↗Organization: lcrawlab

4Stars

1Forks

0Open issues

1Open PRs

2Releases

14Commits

2Commit identities

epistasisgeneticscppcranepistasis-analysisepistatisgwasgwas-tools

14 commits · Last activity 2025-08-22 · 0% stars, 30d · The default branch showed an older version (0.0.2) than CRAN on 2026-10-11

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 94
Median days to close, 50 most recently updated closed PRs: 0

How these are measured

PracticesBeta

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

Checks run against github.com/lcrawlab/sme on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2025-08-22 · The repository has a site deploy workflow

pkgdown site last built 2025-08-22, before release 0.0.3 (2026-09-17)

Reproducibility and dev environment (2)

data-raw/Makefile

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

Dependencies

Declared dependencies

18 external dependencies (excludes base and recommended)

Installing smer adds 66 packages (37 with compiled code, 48 MB of source tarballs). Heaviest: BH 14 MB, stringi 11 MB, Rcpp 1.8 MB. 1 more not on CRAN is not measured.

Depends (1)

R >= 4.3.0

Imports (6)

dplyr genio logging mvMAPIT Rcpp tidyr

LinkingTo (6)

BH HighFive Rcpp RcppEigen Rhdf5lib testthat

Suggests (6)

GenomicRanges ggplot2 knitr rmarkdown testthat (>= 3.0.0)xml2

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (3)

Julian Stamp

Maintainer since 0.0.1 (2025), Author

Lorin Crawford

Author

sriramlab

Copyright holder

Author of included mailman algorithm

Listed in earlier versions (1)

Blue Brain Project/EPFL

no longer listed · 0.0.1

Releases (3)

unarchivedReturned to CRAN
2026-09-17
0.0.3Latest
record
2026-09-17 · current release · diff ↗
archivedRemoved from CRAN
2026-09-16
issues were not corrected in time
R
R 4.6.0 released · 2026-04-24
0.0.2
record
2025-08-22 · diff ↗
R
R 4.5.0 released · 2025-04-11
0.0.1
record
2025-01-16
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2025-01-16
Total releases: 3 / 1 yrs
License: MIT + file LICENSE OSI
Download size: 1.3 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("smer")

Format

Stamp, J., sriramlab, & Crawford, L. (2026). smer: Sparse Marginal Epistasis Test (Version 0.0.3) [Computer software]. https://doi.org/10.32614/CRAN.package.smer

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 smer version 0.0.3 [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.

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