R Observatory: Metrics for PeakSegDisk version 2024.10.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PeakSegDisk

2024.10.1Package record

Disk-Based Constrained Change-Point Detection

0packages dependsuggested by 1

8.7Kdownloads / year

74.4%test coverage

13/13flavors OK

Overview

About

Maintained by Toby Dylan HockingCRAN page ↗GitHub ↗Issues ↗

Disk-based implementation of Functional Pruning Optimal Partitioning with up-down constraints doi:10.18637/jss.v101.i10 for single-sample peak calling (independently for each sample and genomic problem), can handle huge data sets (10^7 or more).

Changes in 2024.10.1

src/interface.cpp error -> Rf_error for compilation without remap, thanks CRAN.

From NEWS in the release

Install

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

install.packages("PeakSegDisk", 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("tdhock/PeakSegDisk")

Development version from tdhock/PeakSegDisk. 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-peaksegdisk

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-PeakSegDisk

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-PeakSegDisk

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: 4.5 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 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2024.10.1

READMENoVignettesYes · 3 · dynamicNEWSYes · 100% structured · mentions 2024.10.1Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Cites a JSS article

Help pages: 17
Examples that run: 100%9 run in a plain check
Exported functions with examples: 90%
Documented parameters: 100%
Return-value docs: 90%
Help pages citing references: 0%

Vignettes (3)

How these are measured

Downloads

8.7K

CRAN downloads in the past year

Rank #6,833 · ~24/day · ~722/mo

Releases R versions

Daily download trend is not available in this view yet.

44530 days

1.2K90 days

8.7K1 year

Compare downloads with other packages →

Also on389 r2u8 autocran25 c2d4u

How downloads are counted

Repository

tdhock/peaksegdisk ↗Account: tdhock

4Stars

3Forks

2Open issues

0Open PRs

0Releases

163Commits

1Commit identities

163 commits · Last activity 2024-10-02 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 91%
Median days to close, 50 most recently updated closed issues: 244
Median days to close, 50 most recently updated closed PRs: 7

Stars over time

2023-11-22 · 42026-07-07 · 4

How these are measured

PracticesBeta

2 development-tooling and community-health practices detected across 1 family in the upstream repository

Checks run against github.com/tdhock/peaksegdisk on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

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

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Installing PeakSegDisk adds 1 package (1 with compiled code, 5.7 MB of source tarballs). Heaviest: data.table 5.7 MB.

Depends (1)

R >= 2.10

Imports (1)

data.table

LinkingTo (0)

none

Suggests (6)

testthat ggplot2 future.apply future knitr markdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Suggested by 1

Suggests, most downloaded first

atime

How these are counted

Code & Tests

Datasets

People & History

People (1)

Toby Dylan Hocking

Author, Maintainer since 2018.11.28 (2018)

Listed in earlier versions (1)

Hocking

no longer listed · 2024.10.1

Releases (9)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
2024.10.1Latest
record
2024-10-02 · current release · diff ↗
R
R 4.4.0 released · 2024-04-24
2023.11.27
record
2023-11-28 · diff ↗
2023.9.4
record
2023-09-06 · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
2022.2.1
record
2022-02-02 · diff ↗
R
R 4.1.0 released · 2021-05-18
2020.8.13
record
2020-08-14 · diff ↗
R
R 4.0.0 released · 2020-04-24
2019.9.27
record
2019-11-19 · diff ↗
2019.9.10
record
2019-09-11 · diff ↗ ·
added 1 export
wc2int
2019.7.29
record
2019-07-31 · diff ↗ ·
removed 3 exports
PeakSegFPOP_disk, problem.PeakSegFPOP, problem.sequentialSearch

added 6 exports
writeBedGraph, PeakSegFPOP_file, PeakSegFPOP_dir, PeakSegFPOP_df, PeakSegFPOP_vec, sequentialSearch_dir
R
R 3.6.0 released · 2019-04-26

Show 2 earlier eventsHide 2 earlier events

2018.11.28
record
2018-12-03
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-12-03
Total releases: 9 / 8 yrs
License: GPL-3 OSI
Minimum R: ≥ 2.10
Bundled data: 203 KB / 2 files
Download size: 670 KB

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' entry:

citation("PeakSegDisk")

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

It points to 10.18637/jss.v101.i10.

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 PeakSegDisk version 2024.10.1 [Data set]. HJJB, LLC. Data release v2026-10-20. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-20, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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