R Observatory: Metrics for PSCBS version 0.68.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PSCBS

0.68.0Package record

Analysis of Parent-Specific DNA Copy Numbers

2packages dependsuggested by 1

11.1Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Henrik BengtssonCRAN page ↗GitHub ↗Issues ↗

Segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.

Changes in 0.68.0

Documentation

Fix minor help-page issues.

Bug Fixes

segmentByCBS() had an internal bug which triggered an error on could not find function "nbrOfSegments", which began with **future** 1.40.0.

From NEWS.md in the release

Install

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

install.packages("PSCBS", 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("HenrikBengtsson/PSCBS")

Development version from HenrikBengtsson/PSCBS. 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-pscbs

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

Health

CRAN checks

13OK

Additional issues

donttest

CRAN check page ↗

Slowest check: 10.4 min · r-release-macos-x86_64

Status changes

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 0.68.0

READMEYes · 250 wordsVignettesYes · 2 · dynamicNEWSYes · 100% structured · mentions 0.68.0Citation fileYes · cites a publication

Help pages: 83 (72 internal)includes a package overview page
Examples that run: 75%6 run in a plain check · 2 never run
Exported functions with examples: 50%
Documented parameters: not tracked
Return-value docs: not tracked
Help pages citing references: 12%

How these are measured

Downloads

11.1K

CRAN downloads in the past year

Rank #3,763 · ~30/day · ~928/mo

Releases R versions

Daily download trend is not available in this view yet.

1K30 days

2.6K90 days

11.1K1 year

Compare downloads with other packages →

Also on197 r2u30.5K bioconda70 c2d4u

How downloads are counted

Repository

henrikbengtsson/pscbs ↗Account: HenrikBengtsson

10Stars

4Forks

10Open issues

1Open PRs

0Releases

826Commits

4Commit identities

rpackage

826 commits · Last activity 2025-04-18 · 0% stars, 30d · Default branch at 0.68.0-9000, ahead of CRAN 0.68.0 (checked 2026-10-21)

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 23
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-08-19 · 82026-08-11 · 10

How these are measured

PracticesBeta

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

Checks run against github.com/henrikbengtsson/pscbs on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Governance and community (2)

Code of conductContributing guide

Docs source (1)

GitHub Pages site last deployed 2021-03-10

Coverage (1)

Coverage reporting

Show all practicesHide 2 practices

Reproducibility and dev environment (1)

Makefile

CRAN release process (1)

revdep/

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

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Installing PSCBS adds 10 packages (3 with compiled code, 2.1 MB of source tarballs). Heaviest: future 477 KB, R.oo 375 KB, R.utils 359 KB. 2 more not on CRAN are not measured.

Depends (1)

R >= 3.2.0

Imports (13)

R.methodsS3 R.oo R.utils R.cache matrixStats aroma.light (>= 2.4.0)DNAcopy futureparallelgraphicsgrDevicesstatsutils

LinkingTo (0)

none

Suggests (3)

R.rsp R.devices ggplot2

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

3indirect

Imports 2

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

aroma.core aroma.cn

Suggests, most downloaded first

jointseg

How these are counted

Code & Tests

People & History

People (7)

Henrik Bengtsson

Author, Maintainer, Copyright holder · added in 3.0.1

Pierre Neuvial

Author · added in 3.0.1

Adam B. Olshen

Author · added in 3.0.1

Richard A. Olshen

Author · added in 3.0.1

Venkatraman E. Seshan

Author · added in 3.0.1

Paul T. Spellman

Author · added in 3.0.1

Frank E Harrell Jr

Contributor · added in 0.66.0

Weighted quantile estimator adopted from Hmisc::wtd.quantile()

Maintainer since 0.11.0 (2011)

Listed in earlier versions (7)

Show 7 peopleHide 7 people

H. Bengtsson