R Observatory: Metrics for PAC version 1.1.6

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PAC

1.1.6Package record

Partition-Assisted Clustering and Multiple Alignments of Networks

0packages depend

3.8Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Ye Henry LiCRAN page ↗

Implements partition-assisted clustering and multiple alignments of networks. It 1) utilizes partition-assisted clustering to find robust and accurate clusters and 2) discovers coherent relationships of clusters across multiple samples. It is particularly useful for analyzing single-cell data set. Please see Li et al. (2017) doi:10.1371/journal.pcbi.1005875 for detail method description.

Install

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

install.packages("PAC", 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-pac

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-PAC

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-PAC

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: 3.5 min · r-devel-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 OK2026-04-22

Show 2 earlier changesHide 2 earlier changes

ERROR13 OK, 1 ERROR2026-04-18
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.6

READMENoVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 23
Examples that run: 100%2 run in a plain check
Exported functions with examples: 13%
Documented parameters: 100%
Return-value docs: 63%
Help pages citing references: 0%

Vignettes (1)

Using the PAC package HTML

How these are measured

Downloads

3.8K

CRAN downloads in the past year

Rank #7,484 · ~10/day · ~314/mo

Releases R versions

Daily download trend is not available in this view yet.

58630 days

1.2K90 days

3.8K1 year

Compare downloads with other packages →

Also on352 r2u2 autocran

How downloads are counted

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Installing PAC adds 31 packages (18 with compiled code, 23 MB of source tarballs). Heaviest: ggplot2 6.0 MB, igraph 4.8 MB, Rcpp 1.8 MB.

Depends (0)

none

Imports (8)

Rcpp igraph parmigene infotheo dplyr Rtsne ggplot2 ggrepel

LinkingTo (1)

Rcpp

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

People & History

People (2)

Ye Henry Li

Author, Maintainer · added in 1.0.6

Dangna Li

Author

Maintainer since 1.0.0 (2016)

Listed in earlier versions (2)

Henry Li

no longer listed · 1.0.0 to 1.0.5

Li

no longer listed · 1.1.6

Releases (16)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.1.6Latest
record
2025-12-16 · current release · diff ↗
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
1.1.4
record
2021-02-18 · diff ↗
1.1.3
record
2020-12-14 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.1.2
record
2020-03-20 · diff ↗
R
R 3.6.0 released · 2019-04-26
1.1.1
record
2019-01-03 · diff ↗
1.1.0
record
2018-10-09 · diff ↗
R
R 3.5.0 released · 2018-04-23
unarchivedReturned to CRAN
2018-03-06

Show 14 earlier eventsHide 14 earlier events

1.0.10
record
2018-03-06 · diff ↗
archivedRemoved from CRAN
2018-03-02
usage of archived package 'NMF' was unconditional
1.0.9
record
2017-08-16 · diff ↗ ·
added 5 exports
MINetworkPlot_topEdges, constellationPlot, getExtraneousCladeSubpopulations, renamePrunedSubpopulations, runElbowPointAnalysis
1.0.8
record
2017-04-30 · diff ↗
R
R 3.4.0 released · 2017-04-21
1.0.7
record
2017-03-10 · diff ↗
1.0.6
record
2017-01-23 · diff ↗ ·
removed 6 exports
clusterNames, clusterPropHeatmap, filteredResults_JSON, makeList, packedCircleInput, signalLevelHeatmap

added 7 exports
MAN, annotateClades, annotationMatrix_withSubpopProp, getRepresentativeNetworks, heatmapInput, refineSubpopulationLabels, samplePass
R
R 3.3.0 released · 2016-05-03
1.0.5
record
2016-04-10 · diff ↗
1.0.3
record
2016-03-29 · diff ↗ ·
added 1 export
BSPLeaveCenter
1.0.2
record
2016-03-29 · diff ↗
1.0.1
record
2016-03-27 · diff ↗
1.0.0
record
2016-03-25
R
R 3.2.0 released · 2015-04-16

Package metadata

First published: 2016-03-25
Total releases: 16 / 10 yrs
License: GPL-3 OSI
Download size: 1.4 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("PAC")

Format

Li, Y. H., & Li, D. (2025). PAC: Partition-Assisted Clustering and Multiple Alignments of Networks (Version 1.1.6) [Computer software]. https://doi.org/10.32614/CRAN.package.PAC

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 PAC version 1.1.6 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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