R Observatory: Metrics for rMVP version 1.4.6

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

rMVP

1.4.6Package record

Memory-Efficient, Visualize-Enhanced, Parallel-Accelerated GWAS Tool

0packages depend

7.7Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Xiaolei LiuCRAN page ↗GitHub ↗Issues ↗

A memory-efficient, visualize-enhanced, parallel-accelerated Genome-Wide Association Study (GWAS) tool. It can (1) effectively process large data, (2) rapidly evaluate population structure, (3) efficiently estimate variance components several algorithms, (4) implement parallel-accelerated association tests of markers three methods, (5) globally efficient design on GWAS process computing, (6) enhance visualization of related information. 'rMVP' contains three models GLM (Alkes Price (2006) DOI:10.1038/ng1847), MLM (Jianming Yu (2006) DOI:10.1038/ng1702) and FarmCPU (Xiaolei Liu (2016) doi:10.1371/journal.pgen.1005767); variance components estimation methods EMMAX (Hyunmin Kang (2008) DOI:10.1534/genetics.107.080101;), FaSTLMM (method: Christoph Lippert (2011) DOI:10.1038/nmeth.1681, R implementation from 'GAPIT2': You Tang and Xiaolei Liu (2016) DOI:10.1371/journal.pone.0107684 and 'SUPER': Qishan Wang and Feng Tian (2014) DOI:10.1371/journal.pone.0107684), and HE regression (Xiang Zhou (2017) DOI:10.1214/17-AOAS1052).

Install

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

install.packages("rMVP", 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("xiaolei-lab/rMVP")

Development version from xiaolei-lab/rMVP. 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-rmvp

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-rMVP

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-rMVP

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: 5.2 min · r-devel-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
OK12 OK2026-04-25

Show 5 earlier changesHide 5 earlier changes

NOTE12 OK, 2 NOTE2026-04-22
ERROR11 OK, 2 NOTE, 1 ERROR2026-04-18
NOTE12 OK, 2 NOTE2026-04-10
ERROR11 OK, 2 NOTE, 1 ERROR2026-04-09
NOTE4 OK, 2 NOTE2026-03-15

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.4.6

README· In the repository, left out of the releaseVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 29 (1 internal)
Examples that run: 27%7 run in a plain check · 19 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 94%
Documented parameters: 99%
Return-value docs: 94%
Help pages citing references: 0%

How these are measured

Downloads

7.7K

CRAN downloads in the past year

Rank #3,691 · ~21/day · ~640/mo

Releases R versions

Daily download trend is not available in this view yet.

88530 days

2.6K90 days

7.7K1 year

Compare downloads with other packages →

Also on400 r2u11 autocran8.4K conda_forge130 c2d4u

How downloads are counted

Repository

xiaolei-lab/rmvp ↗Organization: xiaolei-lab

341Stars

81Forks

46Open issues

2Open PRs

4Releases

953Commits

8Commit identities

License file reads as Apache-2.0 · 953 commits · Last activity 2026-05-27 · +0.9% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 75%
Median days to close, 50 most recently updated closed issues: 74
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2025-10-09 · 3122026-09-28 · 341

How these are measured

PracticesBeta

3 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/xiaolei-lab/rmvp 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

Reproducibility and dev environment (1)

Dockerfile

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

AI coding toolsBeta

This repository shows signs of AI coding tools.

Claude Codefirst seen on or before 2026-02-28
Commits: at least 5 crediting it in the message

Models named in its commits

Claude Sonnet 4.65 commits · Feb to Mar 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

11 external dependencies (excludes base and recommended)

Installing rMVP adds 9 packages (6 with compiled code, 19 MB of source tarballs). Heaviest: BH 14 MB, Rcpp 1.8 MB, RcppEigen 1.7 MB.

Depends (1)

R >= 3.3

Imports (8)

utilsstatsmethodsgraphicsgrDevicesMASSbigmemory RhpcBLASctl

LinkingTo (6)

Rcpp RcppArmadillo RcppEigen RcppProgress BH bigmemory

Suggests (3)

knitr testthat 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 (15)

Xiaolei Liu

Maintainer since 0.99.15 (2019), Author, Copyright holder

Author

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Releases (17)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
unarchivedReturned to CRAN
2026-03-14
1.4.6Latest
record
2026-03-14 · current release · diff ↗
archivedRemoved from CRAN
2026-02-13
issues were not corrected in time
1.4.5
record
2025-07-23 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.4.0
record
2025-01-22 · diff ↗
1.3.5
record
2025-01-10 · diff ↗
1.3.0
record
2024-12-17 · diff ↗
1.1.1
record
2024-08-31 · diff ↗ ·
removed 1 export
MVP.calk
R
R 4.4.0 released · 2024-04-24
1.0.8
record
2023-11-27 · diff ↗
1.0.7
record
2023-09-01 · diff ↗ ·
added 1 export
MVP.calk
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

Show 14 earlier eventsHide 14 earlier events

1.0.6
record
2021-04-18 · diff ↗
1.0.5
record
2021-03-02 · diff ↗
1.0.4
record
2020-09-01 · diff ↗
1.0.3
record
2020-07-17 · diff ↗ ·
added 22 exports
MVP, MVP.BRENT.Vg.Ve, MVP.Data, MVP.Data.Kin, MVP.Data.PC, MVP.EMMA.Vg.Ve, MVP.FarmCPU, MVP.GLM, MVP.HE.Vg.Ve, MVP.Hist, MVP.K.VanRaden, MVP.MLM, MVP.PCA, MVP.PCAplot, MVP.Report, MVP.Report.Density, MVP.Report.QQplot, as.big.matrix, attach.big.matrix, deepcopy, is.big.matrix, new
unarchivedReturned to CRAN
2020-05-07
1.0.0
record
2020-05-07 · diff ↗
R
R 4.0.0 released · 2020-04-24
archivedRemoved from CRAN
2020-04-03
installation problems were not corrected in time required OpenMP Simple fix needed to issues reported by LTO
unarchivedReturned to CRAN
2020-03-19
0.99.18
record
2020-03-19 · diff ↗
0.99.17
record
2019-10-18 · diff ↗
0.99.16
record
2019-09-24 · diff ↗
0.99.15
record
2019-08-30
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-08-30
Total releases: 17 / 7 yrs
License: Apache License 2.0 OSI
Minimum R: ≥ 3.3
Bundled data: 777 KB / 1 file
Download size: 871 KB

Appears in task views

Agricultural Science

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("rMVP")

Format

Liu, X., Kang, H., Li, X., Tang, Z., Tian, F., Wang, Q., Xu, J., Yin, D., Yin, L., Yuan, X., Zhang, H., Zhang, Z., Zhao, S., Zhou, X., & Zhu, M. (2026). rMVP: Memory-Efficient, Visualize-Enhanced, Parallel-Accelerated GWAS Tool (Version 1.4.6) [Computer software]. https://doi.org/10.32614/CRAN.package.rMVP

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 rMVP version 1.4.6 [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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