R Observatory: Metrics for Vicus version 0.99.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

Vicus

0.99.0Package record

Exploiting Local Structures to Improve Network-Based Analysis of Biological Data

1packages depend

3Kdownloads / year

38.1%test coverage

13/13flavors OK

Overview

About

Maintained by Koki TsuyuzakiCRAN page ↗GitHub ↗

Compared with the similar graph embedding method such as Laplacian Eigenmaps, 'Vicus' can exploit more local structures of graph data. For the details of the methods, see the reference section of 'GitHub' README.md https://github.com/rikenbit/Vicus.

Changes in 0.99.0

Package released

From inst/NEWS in the release

Install

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

install.packages("Vicus", 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("rikenbit/Vicus")

Development version from rikenbit/Vicus. 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-vicus

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-Vicus

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-Vicus

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: 1.8 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.99.0

README· In the repository, left out of the releaseVignettesYes · 1 · dynamicNEWSYes · 0% structured · mentions 0.99.0Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 3includes a package overview page
Examples that run: 100%3 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 33%

Vignettes (1)

Vicus: Exploiting local structures to improve network-based analysis of biological data HTML

How these are measured

Downloads

3K

CRAN downloads in the past year

Rank #13,789 · ~8/day · ~248/mo

Releases R versions

Daily download trend is not available in this view yet.

33330 days

85390 days

3K1 year

Compare downloads with other packages →

Also on81 r2u2 autocran181 conda_forge

How downloads are counted

Repository

rikenbit/vicus ↗Organization: rikenbit

2Stars

0Forks

0Open issues

0Open PRs

1Releases

5Commits

1Commit identities

5 commits · Last activity 2023-03-24 · 0% stars, 30d

Responsiveness

not measured

Stars over time

2023-07-25 · 12026-07-07 · 2

How these are measured

PracticesBeta

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

Checks run against github.com/rikenbit/vicus on 2026-10-21.

Continuous integration (1)

GitHub Actions

Governance and community (3)

Code of conductContributing guideIssue templates

Reproducibility and dev environment (1)

Dockerfile

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Installing Vicus adds 4 packages (4 with compiled code, 3.7 MB of source tarballs). Heaviest: Rcpp 1.8 MB, RcppEigen 1.7 MB, RSpectra 125 KB.

Depends (1)

R >= 3.4.0

Imports (5)

methodsutilsRANNMatrixRSpectra

LinkingTo (0)

none

Suggests (4)

scatterplot3d knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

2indirect

Imports 1

Depends, Imports or LinkingTo, most downloaded first

nnTensor

How these are counted

Code & Tests

People & History

People (1)

Koki Tsuyuzaki

Author, Maintainer since 0.99.0 (2023)

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
0.99.0Latest
record
2023-03-23 · current release
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2023-03-23
Total releases: 1 / 3 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.4.0
Download size: 101 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("Vicus")

Format

Tsuyuzaki, K. (2023). Vicus: Exploiting Local Structures to Improve Network-Based Analysis of Biological Data (Version 0.99.0) [Computer software]. https://doi.org/10.32614/CRAN.package.Vicus

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 Vicus version 0.99.0 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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