R Observatory: Metrics for PINSPlus version 2.0.10

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PINSPlus

2.0.10Package record

Clustering Algorithm for Data Integration and Disease Subtyping

1packages depend

5.5Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Van-Dung PhamCRAN page ↗

Provides a robust approach for omics data integration and disease subtyping. PINSPlus is fast and supports the analysis of large datasets with hundreds of thousands of samples and features. The software automatically determines the optimal number of clusters and then partitions the samples in a way such that the results are robust against noise and data perturbation (Nguyen et al. (2019) <DOI: 10.1093/bioinformatics/bty1049>, Nguyen et al. (2017)<DOI: 10.1101/gr.215129.116>, Nguyen et al. (2021)<DOI: 10.3389/fonc.2021.725133>).

Install

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

install.packages("PINSPlus", 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-pinsplus

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-PINSPlus

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-PINSPlus

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: 3.6 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 2.0.10

READMENoVignettesYes · 1 · dynamicNEWSNoCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 5includes a package overview page
Examples that run: 0%2 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 100%

Vignettes (1)

PINSPlus

How these are measured

Downloads

5.5K

CRAN downloads in the past year

Rank #4,700 · ~15/day · ~455/mo

Releases R versions

Daily download trend is not available in this view yet.

69230 days

1.7K90 days

5.5K1 year

Compare downloads with other packages →

Also on418 r2u12 autocran55 c2d4u

How downloads are counted

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Installing PINSPlus adds 11 packages (7 with compiled code, 7.4 MB of source tarballs). Heaviest: mclust 2.7 MB, Rcpp 1.8 MB, RcppArmadillo 1.0 MB. 1 more not on CRAN is not measured.

Depends (1)

R >= 2.10

Imports (11)

foreach entropy doParallel matrixStats Rcpp RcppParallel FNNclusterirlba mclust impute

LinkingTo (3)

Rcpp RcppArmadillo RcppParallel

Suggests (4)

knitr rmarkdownsurvivalmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Depends, Imports or LinkingTo, most downloaded first

scISR

How these are counted

Code & Tests

Datasets

People & History

People (5)

Van-Dung Pham

Maintainer · added in 2.0.9

Hung Nguyen

Author

Tin Nguyen

Author

Bang Tran

Author · added in 2.0.1

Duc Tran

Author · added in 2.0.1

Maintainer since 2.0.7 (2024), previously Hung Nguyen (1.0.0 to 2.0.6)

Listed in earlier versions (1)

Sangam Shrestha

no longer listed · 1.0.0 to 2.0.0

Releases (14)

Pick two releases to compare their code metrics.

2.0.10Latest
record
2026-09-02 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
2.0.9
record
2025-07-29 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
2.0.7
record
2024-04-05 · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
2.0.6
record
2021-12-14 · diff ↗
R
R 4.1.0 released · 2021-05-18
2.0.5
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2020-08-06 · diff ↗
2.0.4
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2020-05-31 · diff ↗
2.0.3
record
2020-05-28 · diff ↗
R
R 4.0.0 released · 2020-04-24
2.0.2
record
2020-04-13 · diff ↗
2.0.1
record
2020-04-02 · diff ↗

Show 8 earlier eventsHide 8 earlier events

2.0.0
record
2019-06-04 · diff ↗
R
R 3.6.0 released · 2019-04-26
1.0.3
record
2019-01-07 · diff ↗
1.0.2
record
2018-07-17 · diff ↗
1.0.1
record
2018-05-03 · diff ↗
R
R 3.5.0 released · 2018-04-23
1.0.0
record
2018-03-16
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2018-03-16
Total releases: 14 / 8 yrs
License: LGPL · relicensed from GPL in 1.0.1
Minimum R: ≥ 2.10
Bundled data: 594 KB / 3 files
Download size: 744 KB

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' entry:

citation("PINSPlus")

The package provides a citation file, so citation() returns the authors' own entry.

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 PINSPlus version 2.0.10 [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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