R Observatory: Metrics for SmCCNet version 2.0.7

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SmCCNet

2.0.7Package record

Sparse Multiple Canonical Correlation Network Analysis Tool ('SmCCNet')

0packages depend

2.3Kdownloads / year

0.9%test coverage

13/13flavors OK

Overview

About

Maintained by Abhinav PundirCRAN page ↗GitHub ↗Website ↗

A canonical correlation based framework ('SmCCNet') designed for the construction of phenotype-specific multi-omics networks. This framework adeptly integrates single or multiple omics data types along with a quantitative or binary phenotype of interest. It offers a streamlined setup process that can be tailored manually or configured automatically, ensuring a flexible and user-friendly experience. Methods are described in Shi et al. (2019) "Unsupervised discovery of phenotype-specific multi-omics networks" doi:10.1093/bioinformatics/btz226.

Install

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

install.packages("SmCCNet", 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("KechrisLab/SmCCNet")

Development version from KechrisLab/SmCCNet. 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-smccnet

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

# 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-SmCCNet

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

Additional issues

donttest

CRAN check page ↗

Slowest check: 3.6 min · r-oldrel-macos-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK6 OK2026-04-29

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.0.7

READMENoVignettesYes · 3 · dynamicNEWSYes · 100% structuredCitation fileNoWebsiteYes · pkgdown

Help pages: 20 (2 internal)
Examples that run: 77%10 run in a plain check (1 of them under a condition) · 3 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 81%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 5%

Vignettes (3)

How these are measured

Downloads

2.3K

CRAN downloads in the past year

Rank #9,304 · ~6/day · ~193/mo

Releases R versions

Daily download trend is not available in this view yet.

39130 days

1K90 days

2.3K1 year

Compare downloads with other packages →

Also on98 r2u3 autocran

How downloads are counted

Repository

kechrislab/smccnet ↗Organization: KechrisLab

32Stars

5Forks

1Open issues

0Open PRs

1Releases

84Commits

4Commit identities

84 commits · Last activity 2026-05-08 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 0%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-09-25 · 302026-07-07 · 32

How these are measured

PracticesBeta

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

Checks run against github.com/kechrislab/smccnet on 2026-10-11.

Continuous integration (1)

GitHub Actions

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-05-08 · The repository has a site deploy workflow

pkgdown site last built 2026-05-08

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

21 external dependencies (excludes base and recommended)

Installing SmCCNet adds 40 packages (18 with compiled code, 39 MB of source tarballs). Heaviest: ggplot2 6.0 MB, data.table 5.7 MB, igraph 4.8 MB.

Depends (1)

R >= 3.5

Imports (12)

EnvStats future pROC splsMatrixpbapply igraph magrittr rlist furrr purrr pracma

LinkingTo (0)

none

Suggests (11)

knitr rmarkdown bookdown testthat dplyr reshape2 shadowtext tidyverseparallelmltools caret

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 (9)

Abhinav Pundir

Maintainer since 2.0.6 (2026) · added in 2.0.6

Katerina Kechris

Author

Iain Konigsberg

Author · added in 2.0.0

Weixuan Liu

Author · added in 2.0.0

Katherine Pratte

Author · added in 2.0.0

Laura Saba

Author

W. Jenny Shi

Author

Thao Vu

Author · added in 2.0.0

Yonghua Zhuang

Author · added in 2.0.0

Previously maintained by Weixuan Liu (2.0.0 to 2.0.3) and W. Jenny Shi (0.99.0).

Listed in earlier versions (1)

Shi

no longer listed · 2.0.6 to 2.0.7

Releases (7)

Pick two releases to compare their code metrics.

2.0.7Latest
record
2026-05-01 · current release · diff ↗
unarchivedReturned to CRAN
2026-04-28
2.0.6
record
2026-04-28 · diff ↗
R
R 4.6.0 released · 2026-04-24
archivedRemoved from CRAN
2025-06-12
issues were not corrected despite reminders
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
2.0.3
record
2024-04-16 · diff ↗
2.0.2
record
2024-01-13 · diff ↗
2.0.1
record
2023-10-03 · diff ↗
2.0.0
record
2023-10-02 · diff ↗ ·
removed 3 exports
getMultiOmicsModules, getRobustPseudoWeights, plotMultiOmicsNetwork

added 15 exports
%>%, aggregateCVSingle, classifierEval, dataPreprocess, fastAutoSmCCNet, getCanCorMulti, getCanWeightsMulti, getOmicsModules, getRobustWeightsMulti, getRobustWeightsMultiBinary, getRobustWeightsSingle, getRobustWeightsSingleBinary, networkPruning, scalingFactorInput, summarizeNetSHy
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

Show 2 earlier eventsHide 2 earlier events

0.99.0
record
2019-03-04
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2019-03-04
Total releases: 7 / 7 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5
Bundled data: 1.4 MB / 2 files
Download size: 6.5 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("SmCCNet")

Format

Pundir, A., Kechris, K., Konigsberg, I., Liu, W., Pratte, K., Saba, L., Shi, W. J., Vu, T., & Zhuang, Y. (2026). SmCCNet: Sparse Multiple Canonical Correlation Network Analysis Tool ('SmCCNet') (Version 2.0.7) [Computer software]. https://doi.org/10.32614/CRAN.package.SmCCNet

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 SmCCNet version 2.0.7 [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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