R Observatory: Metrics for bmass version 1.0.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

bmass

1.0.3Package record

Bayesian Multivariate Analysis of Summary Statistics

0packages depend

2.7Kdownloads / year

0.0%test coverage

11/13flavors OK

Overview

About

Maintained by Michael TurchinCRAN page ↗GitHub ↗Issues ↗

Multivariate tool for analyzing genome-wide association study results in the form of univariate summary statistics. The goal of 'bmass' is to comprehensively test all possible multivariate models given the phenotypes and datasets provided. Multivariate models are determined by assigning each phenotype to being either Unassociated (U), Directly associated (D) or Indirectly associated (I) with the genetic variant of interest. Test results for each model are presented in the form of Bayes factors, thereby allowing direct comparisons between models. The underlying framework implemented here is based on the modeling developed in "A Unified Framework for Association Analysis with Multiple Related Phenotypes", M. Stephens (2013) doi:10.1371/journal.pone.0065245.

Changes in 1.0.3

Summary

Patches for 2nd CRAN resubmission

Since previous version (v1.0.2)

Notes

Changed \dontrun{} to \donttest{} in .Rd files

Next steps (if applicable)

See v.1.0.0 'Next steps'

From NEWS.md in the release

Install

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

install.packages("bmass", 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("mturchin20/bmass")

Development version from mturchin20/bmass. 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-bmass

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-bmass

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-bmass

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

2NOTE11OK

Check messages

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Michael Turchin <mturchin20@uchicago.edu>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

Found the following URLs which should use \doi (with the DOI name only):
  File ‘GetModelPriorMatrix.Rd’:
    https://doi.org/10.1371/journal.pone.0065245
  File ‘GlobalLipids2013.GWASsnps.Rd’:
    https://doi.org/10.1038/ng.2797

CRAN check page ↗

Slowest check: 1.1 min · r-devel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTENow
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.3

README· In the repository, left out of the releaseVignettesYes · 2 · dynamicNEWSYes · 100% structured · mentions 1.0.3Citation fileYes · cites a publication

Help pages: 11
Examples that run: 100%4 run in a plain check
Exported functions with examples: 100%
Documented parameters: 95%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (2)

How these are measured

Downloads

2.7K

CRAN downloads in the past year

Rank #16,283 · ~7/day · ~224/mo

Releases R versions

Daily download trend is not available in this view yet.

32130 days

76090 days

2.7K1 year

Compare downloads with other packages →

Also on93 r2u23 autocran

How downloads are counted

Repository

mturchin20/bmass ↗Account: mturchin20

11Stars

1Forks

0Open issues

0Open PRs

8Releases

162Commits

3Commit identities

License file reads as MIT · DESCRIPTION declares GPL (>= 3) · 162 commits · Last activity 2020-09-17 · 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: 30

Stars over time

2024-09-18 · 102026-07-22 · 11

How these are measured

PracticesBeta

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

Checks run against github.com/mturchin20/bmass on 2026-10-18.

Continuous integration (1)

Travis CI (config file)

Docs source (1)

GitHub Pages site last deployed 2020-09-17

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

3 external dependencies (excludes base and recommended)

Installing bmass adds no packages beyond those that come with R.

Depends (1)

R >= 3.3.0

Imports (2)

utilsstats

LinkingTo (0)

none

Suggests (3)

testthat knitr rmarkdown

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)

Michael Turchin

Author, Maintainer since 1.0.3 (2019)

Matthew Stephens

Author

Peter Carbonetto

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
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
1.0.3Latest
record
2019-05-17 · current release
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-05-17
Total releases: 1 / 7 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.3.0
Bundled data: 3.4 KB / 7 files
Download size: 60 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("bmass")

The package provides a citation file, so citation() returns the authors' own entry.

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 bmass version 1.0.3 [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 →