R Observatory: Metrics for MAGNAMWAR version 2.0.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

MAGNAMWAR

2.0.4

A Pipeline for Meta-Genome Wide Association

0packages depend

2.7Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by John ChastonFirst published 2017-04-266 releasesCRAN page ↗

Correlates variation within the meta-genome to target species phenotype variations in meta-genome with association studies. Follows the pipeline described in Chaston, J.M. et al. (2014) doi:10.1128/mBio.01631-14.

Install

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

install.packages("MAGNAMWAR", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

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-magnamwar

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

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-MAGNAMWAR

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-MAGNAMWAR

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 2.3 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

13

Dependencies · direct

Check history

NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 38 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 57%
Documented parameters: 100%
Return-value docs: 93%
References docs: 14%

Downloads

2.7K

CRAN downloads in the past year

Rank #14,206 · ~7/day · ~225/mo

Releases R versions

Daily download trend is not available in this view yet.

16830 days

72690 days

2.7K1 year

Compare downloads with other packages →

Also on126 r2u15 autocran

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.0

Imports (13)

ape coxme doParallel dplyr foreach iterators lme4 multcompparallelplyr qqmansurvivalseqinr

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (3)

Maintainer (1)

John Chaston

Author, Maintainer

Authors (2)

John Chaston

Author, Maintainer

Corinne Sexton

Author

Contributors (1)

Hayden Smith

Contributor

Package Timeline

6 releases. Pick two to compare their code metrics. R releases are shown for context.

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
R
R 3.6.0 released · 2019-04-26
2.0.4Latest
2018-07-12 · current release · diff ↗
unarchivedReturned to CRAN
2018-07-12
archivedRemoved from CRAN
2018-05-09
check problems were not corrected despite reminders
R
R 3.5.0 released · 2018-04-23
2.0.3
2018-04-19 · diff ↗
2.0.2
2018-01-24 · diff ↗
2.0.1
2017-12-13 · diff ↗
2.0.0
2017-08-28 · diff ↗

Show 2 earlier events

1.0.0
2017-04-26
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-04-26
Total releases: 6 / 9 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.0
Bundled data: 24 KB / 8 files
Download size: 1.6 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("MAGNAMWAR")

Format

Chaston, J., Sexton, C., & Smith, H. (2018). MAGNAMWAR: A Pipeline for Meta-Genome Wide Association (Version 2.0.4) [Computer software]. https://doi.org/10.32614/CRAN.package.MAGNAMWAR

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 MAGNAMWAR version 2.0.4 [Data set]. HJJB, LLC. Data release v2026-08-15. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-15, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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