R Observatory: Metrics for aroma.apd version 0.7.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

aroma.apd

0.7.1Package record

A Probe-Level Data File Format Used by 'aroma.affymetrix' [deprecated]

1packages depend

6.1Kdownloads / year

18.7%test coverage

13/13flavors OK

Overview

About

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

DEPRECATED. Do not start building new projects based on this package. (The (in-house) APD file format was initially developed to store Affymetrix probe-level data, e.g. normalized CEL intensities. Chip types can be added to APD file and similar to methods in the affxparser package, this package provides methods to read APDs organized by units (probesets). In addition, the probe elements can be arranged optimally such that the elements are guaranteed to be read in order when, for instance, data is read unit by unit. This speeds up the read substantially. This package is supporting the Aroma framework and should not be used elsewhere.)

Changes in 0.7.1

Miscellaneous

Fix DESCRIPTION field URL.

From NEWS.md in the release

Install

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

install.packages("aroma.apd", 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.apd")

Development version from HenrikBengtsson/aroma.apd. 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.apd

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-aroma.apd

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-aroma.apd

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: 1.2 min · r-devel-windows-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 0.7.1

READMEYes · 82 wordsVignettesNoNEWSYes · 100% structured · mentions 0.7.1Citation fileNoWebsiteYes

Help pages: 17 (1 internal)includes a package overview page
Examples that run: 50%5 run in a plain check · 5 hold no code
Exported functions with examples: 67%
Documented parameters: not tracked
Return-value docs: not tracked
Help pages citing references: 6%

How these are measured

Downloads

6.1K

CRAN downloads in the past year

Rank #5,658 · ~17/day · ~507/mo

Releases R versions

Daily download trend is not available in this view yet.

51630 days

1.4K90 days

6.1K1 year

Compare downloads with other packages →

Also on154 r2u12 autocran2.2K conda_forge179 bioconda

How downloads are counted

Repository

henrikbengtsson/aroma.apd ↗Account: HenrikBengtsson

0Stars

0Forks

0Open issues

0Open PRs

0Releases

cranr-package

Last activity 2025-04-06 · Default branch at 0.7.1-9000, ahead of CRAN 0.7.1 (checked 2026-10-11)

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: not measured

How these are measured

PracticesBeta

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

Checks run against github.com/henrikbengtsson/aroma.apd 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 (2)

cran-comments.mdrevdep/

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

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Installing aroma.apd adds 4 packages (0 with compiled code, 792 KB of source tarballs). Heaviest: R.oo 375 KB, R.utils 359 KB, R.huge 34 KB.

Depends (1)

R >= 3.0.0

Imports (4)

R.methodsS3 R.oo R.utils R.huge

LinkingTo (0)

none

Suggests (1)

affxparser

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

1indirect

Imports 1

Depends, Imports or LinkingTo, most downloaded first

aroma.affymetrix

How these are counted

Code & Tests

People & History

People (1)

Henrik Bengtsson

Releases (13)

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
0.7.1Latest
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2025-04-06 · current release · diff ↗
R
R 4.4.0 released · 2024-04-24
0.7.0
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2023-06-23 · diff ↗
R
R 4.3.0 released · 2023-04-21
0.6.1
record
2022-07-18 · diff ↗
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
R
R 3.2.0 released · 2015-04-16
0.6.0
record
2015-02-25 · diff ↗

Show 18 earlier eventsHide 18 earlier events

R
R 3.1.0 released · 2014-04-10
0.5.0
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2014-02-27 · diff ↗
0.4.0
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2013-09-23 · diff ↗
0.3.0
record
2013-08-02 · diff ↗
R
R 3.0.0 released · 2013-04-03
0.2.3
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2012-07-03 · diff ↗
0.2.2
record
2012-04-04 · diff ↗
R
R 2.15.0 released · 2012-03-30
R
R 2.14.0 released · 2011-10-31
0.2.0
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2011-07-24 · diff ↗
R
R 2.13.0 released · 2011-04-13
0.1.8
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2011-02-01 · diff ↗
R
R 2.12.0 released · 2010-10-15
R
R 2.11.0 released · 2010-04-22
R
R 2.10.0 released · 2009-10-26
0.1.7
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2009-10-19 · diff ↗
0.1.6
record
2009-06-14
R
R 2.9.0 released · 2009-04-17

Package metadata

First published: 2009-06-14
Total releases: 13 / 17 yrs
License: LGPL (>= 2.1)
Minimum R: ≥ 3.0.0
Download size: 32 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("aroma.apd")

Format

Bengtsson, H. (2025). aroma.apd: A Probe-Level Data File Format Used by 'aroma.affymetrix' [deprecated] (Version 0.7.1) [Computer software]. https://doi.org/10.32614/CRAN.package.aroma.apd

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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.apd version 0.7.1 [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.

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