SmCCNet

2.0.7

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

0packages depend

1.3Kdownloads / year

85.9%test coverage

13/13checks pass

Overview

About

Maintained by Abhinav PundirFirst published 2026-04-297 releasesCRAN page ↗GitHub ↗

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.

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).

Health

CRAN checks

13OK

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

Code health

Yes

Tests · ratio 0.01

85.9%

Coverage · measured lines

94%

Documentation · exports

Dependencies · direct

Check history

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-29
6 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 77%
Documented parameters: 100%
Return-value docs: 100%
References docs: 5%

Downloads

1.3K

CRAN downloads in the past year

Rank #8,529 · ~4/day · ~108/mo

Releases R versions

Daily download trend is not available in this view yet.

32230 days

1.3K90 days

1.3K1 year

Compare downloads with other packages →

Also on139 r2u38 autocran

Repository

GitHub ↗ kechrislab/smccnet

32Stars

5Forks

1Open issues

0Open PRs

1Releases

84Commits

4Contributors

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

Stars over time

2025-02-16 · 282026-07-07 · 32

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/kechrislab/smccnet on 2026-07-19.

Continuous integration (1)

GitHub Actions

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

21 external dependencies (excludes base and recommended)

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.

Code & Tests

Code Composition

R 2,607 (46%)Vignettes 2,090 (37%)Rd 852 (15%)Other 162 (3%)

Code characteristics

Cyclomatic complexity: 4.0 median / 62 max
Test cases: 1 / 0.01 per code line

Test coverage

Line coverage

Expression

1.0%

Tests / Examples

0.9% / 25% ex

Functions

23 15 exported

Complexity

9 avg / 62 max

Call network

23 nodes / 25 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

23 functions

Function	Cyclo	Coverage
aggregateCVSingle exp	3	0%
classifierEval exp	7	0%
fastAutoSmCCNet exp	54	0%
getAbar exp	4	0%
getCanCorMulti exp	1	0%
getCanWeightsMulti exp	7	0%

People & History

People (9)

Maintainer (1)

Abhinav Pundir

Maintainer · added in 2.0.6

Authors (8)

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

Listed in earlier versions (1)

Shi

no longer listed · 2.0.6 to 2.0.7

Package Timeline

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

2.0.7Latest
2026-05-02 · current release · diff ↗
2.0.6
2026-04-29 · diff ↗
unarchivedReturned to CRAN
2026-04-28
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
2024-04-16 · diff ↗
2.0.2
2024-01-13 · diff ↗
2.0.1
2023-10-03 · diff ↗
2.0.0
2023-10-02 · diff ↗
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 events

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

Package metadata

First published: 2026-04-29
Total releases: 7 / 1 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5
Bundled data: 1.4 MB / 2 files
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

Report a problem with this page →