R Observatory: Metrics for aroma.affymetrix version 3.2.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

aroma.affymetrix

3.2.3Package record

Analysis of Large Affymetrix Microarray Data Sets

1packages depend

7.8Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Henrik BengtssonCRAN page ↗GitHub ↗Website ↗Issues ↗

A cross-platform R framework that facilitates processing of any number of Affymetrix microarray samples regardless of computer system. The only parameter that limits the number of chips that can be processed is the amount of available disk space. The Aroma Framework has successfully been used in studies to process tens of thousands of arrays. This package has actively been used since 2006.

Install

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

install.packages("aroma.affymetrix", 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/aroma.affymetrix")

Development version from HenrikBengtsson/aroma.affymetrix. 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-aroma.affymetrix

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: 7.6 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-12
ERROR12 OK, 1 ERROR2026-06-07
OK12 OK2026-04-25

Show 1 earlier changeHide 1 earlier change

NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 3.2.3

README· In the repository, left out of the releaseVignettesNoNEWSYes · 33% structuredCitation fileYes · cites a publicationWebsiteYes

Help pages: 329 (218 internal)includes a package overview page
Examples that run: 14%1 run in a plain check · 6 never run
Exported functions with examples: 0%
Documented parameters: not tracked
Return-value docs: not tracked
Help pages citing references: 5%

How these are measured

Downloads

7.8K

CRAN downloads in the past year

Rank #4,214 · ~21/day · ~652/mo

Releases R versions

Daily download trend is not available in this view yet.

85130 days

2.1K90 days

7.8K1 year

Compare downloads with other packages →

Also on237 r2u1.8K bioconda

How downloads are counted

Repository

henrikbengtsson/aroma.affymetrix ↗Account: HenrikBengtsson

12Stars

3Forks

8Open issues

0Open PRs

0Releases

911Commits

4Commit identities

rpackageaffymetrixcopy-numberexpressiondnarnaanalysis

911 commits · Last activity 2025-12-14 · 0% stars, 30d · Default branch at 3.2.3-9001, ahead of CRAN 3.2.3 (checked 2026-10-11)

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 3
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-10-07 · 122026-07-07 · 12

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/aroma.affymetrix 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

Governance and community (1)

Code of conduct

Coverage (1)

Coverage reporting

Reproducibility and dev environment (1)

Makefile

Show all practicesHide 2 practices

CRAN release process (2)

cran-comments.mdrevdep/

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

27 external dependencies (excludes base and recommended)

Installing aroma.affymetrix adds 20 packages (4 with compiled code, 7.7 MB of source tarballs). Heaviest: PSCBS 3.4 MB, BiocManager 735 KB, R.rsp 665 KB. 2 more not on CRAN are not measured.

Depends (3)

R >= 3.2.0R.utils aroma.core

Imports (12)

methodsR.methodsS3 R.oo R.cache (>= 0.14.0)R.devices R.filesets aroma.apdMASSsplinesmatrixStats listenv future

LinkingTo (0)

none

Suggests (16)

DBI RColorBrewer Biobase BiocGenerics affxparser affy (>= 1.46.0)affyPLM aroma.light gcrma (>= 2.40.0)limma oligo oligoClasses (>= 1.30.0)pdInfoBuilder preprocessCore AffymetrixDataTestFiles dChipIO

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Depends 1

Depends, Imports or LinkingTo, most downloaded first

ACNE

How these are counted

Code & Tests

People & History

People (7)

Henrik Bengtsson

James Bullard

Contributor · added in 2.14.2

Kasper Hansen

Contributor · added in 2.14.2

Pierre Neuvial

Contributor · added in 1.7.0

Elizabeth Purdom

Contributor

Mark Robinson

Contributor

Ken Simpson

Contributor

Releases (46)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
3.2.3Latest
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2025-08-19 · current release · diff ↗
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R 4.5.0 released · 2025-04-11
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R 4.4.0 released · 2024-04-24
3.2.2
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2024-02-18 · diff ↗
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R 4.3.0 released · 2023-04-21
3.2.1
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2022-07-18 · diff ↗
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R 4.2.0 released · 2022-04-22
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R 4.1.0 released · 2021-05-18
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R 4.0.0 released · 2020-04-24
3.2.0
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2019-06-23 · diff ↗
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R 3.6.0 released · 2019-04-26
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R 3.5.0 released · 2018-04-23
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R 3.4.0 released · 2017-04-21
3.1.0
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2017-03-24 · diff ↗

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R 3.3.0 released · 2016-05-03
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R 3.2.0 released · 2015-04-16
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R 3.1.0 released · 2014-04-10
3.0.3
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2013-10-17 · diff ↗ ·
removed 1 export
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R 3.0.0 released · 2013-04-03
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R 2.15.0 released · 2012-03-30
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R 2.14.0 released · 2011-10-31
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R 2.13.0 released · 2011-04-13
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R 2.12.0 released · 2010-10-15
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R 2.11.0 released · 2010-04-22
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2009-11-01 · diff ↗
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R 2.10.0 released · 2009-10-26
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2.3.0
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2011-11-02 · diff ↗ ·
added 2 exports
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2.2.0
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2.1.8
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1.1.1
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2009-06-29
R
R 2.9.0 released · 2009-04-17

Package metadata

First published: 2009-06-29
Total releases: 46 / 17 yrs
License: LGPL (>= 2.1)
Minimum R: ≥ 3.2.0
Download size: 735 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("aroma.affymetrix")

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

It points to 10.1093/bioinformatics/btn016, 10.1093/bioinformatics/btp371.

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 aroma.affymetrix version 3.2.3 [Data set]. HJJB, LLC. Data release v2026-10-17. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-17, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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