R Observatory: Metrics for ACNE version 0.9.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ACNE

0.9.2Package record

Affymetrix SNP Probe-Summarization using Non-Negative Matrix Factorization

0packages depend

4.4Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Henrik BengtssonCRAN page ↗GitHub ↗Issues ↗

A summarization method to estimate allele-specific copy number signals for Affymetrix SNP microarrays using non-negative matrix factorization (NMF).

Changes in 0.9.2

Documentation

Add missing package anchors for a few Rd links.

From NEWS.md in the release

Install

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

install.packages("ACNE", 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/ACNE")

Development version from HenrikBengtsson/ACNE. 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-acne

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

CRAN check page ↗

Slowest check: 1.6 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-13
ERROR13 OK, 1 ERROR2026-03-12
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.9.2

READMEYes · 80 wordsVignettesNoNEWSYes · 100% structured · mentions 0.9.2Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 14 (10 internal)includes a package overview page
Examples that run: 100%2 run in a plain check
Exported functions with examples: 0%
Documented parameters: not tracked
Return-value docs: not tracked
Help pages citing references: 21%

How these are measured

Downloads

4.4K

CRAN downloads in the past year

Rank #6,402 · ~12/day · ~367/mo

Releases R versions

Daily download trend is not available in this view yet.

43030 days

1.3K90 days

4.4K1 year

Compare downloads with other packages →

Also on112 r2u

How downloads are counted

Repository

henrikbengtsson/acne ↗Account: HenrikBengtsson

0Stars

0Forks

1Open issues

0Open PRs

0Releases

rpackagecran

Last activity 2025-08-19

Responsiveness

not measured

How these are measured

PracticesBeta

5 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/henrikbengtsson/acne on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Coverage (1)

Coverage reporting

Reproducibility and dev environment (1)

Makefile

CRAN release process (1)

cran-comments.md

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

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Installing ACNE adds 21 packages (4 with compiled code, 8.4 MB of source tarballs). Heaviest: PSCBS 3.4 MB, BiocManager 735 KB, aroma.affymetrix 735 KB. 2 more not on CRAN are not measured.

Depends (2)

R >= 3.0.0aroma.affymetrix

Imports (7)

MASSR.methodsS3 R.oo R.utils (>= 2.1.0)matrixStats R.filesets aroma.core

LinkingTo (0)

none

Suggests (1)

DNAcopy

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (3)

Henrik Bengtsson

Maria Ortiz

Author

Angel Rubio

Author

Releases (8)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.9.2Latest
record
2025-08-19 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
0.9.1
record
2024-02-17 · diff ↗
0.9.0
record
2023-06-25 · 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
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
0.8.1
record
2015-10-27 · diff ↗
R
R 3.2.0 released · 2015-04-16

Show 9 earlier eventsHide 9 earlier events

0.8.0
record
2015-02-23 · diff ↗
R
R 3.1.0 released · 2014-04-10
0.7.0
record
2013-10-19 · diff ↗
R
R 3.0.0 released · 2013-04-03
R
R 2.15.0 released · 2012-03-30
R
R 2.14.0 released · 2011-10-31
0.5.0
record
2011-10-25 · diff ↗ ·
added 1 export
pattern:^[^\\.]
0.4.3
record
2011-09-16
R
R 2.13.0 released · 2011-04-13

Package metadata

First published: 2011-09-16
Total releases: 8 / 15 yrs
License: LGPL (>= 2.1)
Minimum R: ≥ 3.0.0
Download size: 61 KB

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' entry:

citation("ACNE")

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

It points to 10.1093/bioinformatics/btq300.

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 ACNE version 0.9.2 [Data set]. HJJB, LLC. Data release v2026-10-19. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →