R Observatory: Metrics for MEGENA version 1.3.7

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2026-04-15. Its history is shown below.

Reason: issues were not corrected despite reminders

Details below reflect version 1.3.7, its last release before removal.

MEGENA

1.3.7

Multiscale Clustering of Geometrical Network

0packages depend

3.3Kdownloads / year

–test coverage

–checks pass

Overview

About

Maintained by Won-Min Song5 releasesCRAN page ↗GitHub ↗

Co-Expression Network Analysis by adopting network embedding technique. Song W.-M., Zhang B. (2015) Multiscale Embedded Gene Co-expression Network Analysis. PLoS Comput Biol 11(11): e1004574. <doi: 10.1371/journal.pcbi.1004574>.

Install

R (source archive)pak (dev)Ubuntu (r2u)openSUSE (OBS)

url <- "https://cran.r-project.org/src/contrib/Archive/MEGENA/MEGENA_1.3.7.tar.gz"
pkgFile <- "MEGENA_1.3.7.tar.gz"
download.file(url, pkgFile)
install.packages(pkgFile, type = "source", repos = NULL)

This package is no longer on CRAN, so install.packages() cannot fetch it by name. This downloads the last archived source (1.3.7) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("songw01/MEGENA")

Development version from songw01/MEGENA. 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-megena

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

# 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-MEGENA

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

Health

CRAN checks

CRAN check results are not tracked yet.

Code health

None

Tests · ratio 0.00

not tracked

Coverage

11

Dependencies · direct

Check history

NOTE2026-03-10
8 OK · 6 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 90 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 25%
Documented parameters: not tracked
Return-value docs: not tracked
References docs: 16%

Downloads

3.3K

CRAN downloads in the past year

Rank #24,922 · ~9/day · ~279/mo

Releases R versions

Daily download trend is not available in this view yet.

030 days

090 days

3.3K1 year

Compare downloads with other packages →

Also on444 r2u17 autocran

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Depends (4)

R >= 3.4.0doParallel foreach igraph

Imports (8)

RcppMatrixggplot2 reshape fpcclusterggrepel (>= 0.5)ggraph

LinkingTo (2)

Rcpp BH

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code & Tests

People & History

People (2)

Other (2)

Won-Min Song

Contributor

Bin Zhang

Contributor

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
archivedRemoved from CRAN
2026-04-15
issues were not corrected despite reminders
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
1.3.7
2018-09-10 · diff ↗
unarchivedReturned to CRAN
2018-09-10
archivedRemoved from CRAN
2018-06-02
check problems were not corrected despite reminders
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
1.3.6
2017-01-10 · diff ↗
1.3.5-2
2016-10-25 · diff ↗

Show 3 earlier events

1.3.4-6
2016-10-06 · diff ↗
1.3.4-1
2016-07-11
R
R 3.3.0 released · 2016-05-03

Package metadata

Total releases: 5
License: GPL (>= 3) OSI
Minimum R: ≥ 3.4.0
Bundled data: 1.8 MB / 2 files
Download size: 1.9 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("MEGENA")

Format

Song, W., & Zhang, B. (n.d.). MEGENA: Multiscale Clustering of Geometrical Network (Version 1.3.7) [Computer software]. Retrieved August 15, 2026, from https://CRAN.R-project.org/package=MEGENA

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 MEGENA version 1.3.7 [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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