R Observatory: Metrics for MAGNAMWAR version 2.0.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

MAGNAMWAR

2.0.4Package record

A Pipeline for Meta-Genome Wide Association

0packages depend

3Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by John ChastonCRAN 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. 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-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). 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: ‘John Chaston <john_chaston@byu.edu>’

Found the following (possibly) invalid file URI:
  URI: www.orthomcl.org
    From: inst/doc/using_mag.html

CRAN check page ↗

Slowest check: 2.3 min · r-oldrel-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 2.0.4

READMEYes · 38 wordsVignettesYes · 1 · dynamicNEWSYes · 67% structured · does not mention 2.0.4Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 22
Examples that run: 50%7 run in a plain check · 7 never run
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 93%
Help pages citing references: 14%

Vignettes (1)

Using MAGNAMWAR: a case study with *Drosophila melanogaster*

How these are measured

Downloads

3K

CRAN downloads in the past year

Rank #14,377 · ~8/day · ~247/mo

Releases R versions

Daily download trend is not available in this view yet.

33530 days

81790 days

3K1 year

Compare downloads with other packages →

Also on78 r2u5 autocran

How downloads are counted

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Installing MAGNAMWAR adds 44 packages (26 with compiled code, 46 MB of source tarballs). Heaviest: TH.data 8.2 MB, sp 4.3 MB, lme4 4.1 MB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (3)

John Chaston

Author, Maintainer since 1.0.0 (2017)

Corinne Sexton

Author

Hayden Smith

Contributor

Releases (6)

Pick two releases to compare their code metrics.

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
unarchivedReturned to CRAN
2018-07-12
2.0.4Latest
record
2018-07-12 · current release · diff ↗
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
record
2018-04-19 · diff ↗
2.0.2
record
2018-01-24 · diff ↗
2.0.1
record
2017-12-13 · diff ↗
2.0.0
record
2017-08-28 · diff ↗ ·
removed 13 exports
RASTtogbk, analyze_OrthoMCL, format_MCLfastas, format_afterOrtho, join_repseq, manhat_grp, pdg_v_OG, pdgplot, phydataerror, printOGseqs, qqplotter, surv_append_matrix, write_mcl

added 14 exports
AnalyzeOrthoMCL, CalculatePrincipalCoordinates, FormatAfterOrtho, FormatMCLFastas, JoinRepSeq, ManhatGrp, PDGPlot, PDGvOG, PhyDataError, PrintOGSeqs, QQPlotter, RASTtoGBK, SurvAppendMatrix, WriteMCL

Show 2 earlier eventsHide 2 earlier events

1.0.0
record
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

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 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 MAGNAMWAR version 2.0.4 [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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