R Observatory: Metrics for erah version 2.2.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

erah

2.2.0Package record

Automated Spectral Deconvolution, Alignment, and Metabolite Identification in GC/MS-Based Untargeted Metabolomics

0packages depend

3.5Kdownloads / year

0.6%test coverage

13/13flavors OK

Overview

About

Maintained by Xavier Domingo-AlmenaraCRAN page ↗GitHub ↗Website ↗Issues ↗

Automated compound deconvolution, alignment across samples, and identification of metabolites by spectral library matching in Gas Chromatography - Mass spectrometry (GC-MS) untargeted metabolomics. Outputs a table with compound names, matching scores and the integrated area of the compound for each sample. Package implementation is described in Domingo-Almenara et al. (2016) doi:10.1021/acs.analchem.6b02927.

Changes in 2.2.0

Faster aligment algorithm implementation.

From inst/NEWS in the release

Install

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

install.packages("erah", 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("xdomingoal/erah-devel")

Development version from xdomingoal/erah-devel. 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-erah

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-erah

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-erah

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: 4.9 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK12 OK2026-04-25
NOTE13 OK, 1 NOTE2026-04-22
ERROR12 OK, 1 NOTE, 1 ERROR2026-04-18

Show 1 earlier changeHide 1 earlier change

NOTE13 OK, 1 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.2.0

READMENoVignettesYes · 1 · staticNEWSYes · 33% structured · mentions 2.2.0Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 34
Examples that run: 17%2 run in a plain check · 10 never run
Exported functions with examples: 41%
Documented parameters: 100%
Return-value docs: 34%
Help pages citing references: 32%

Vignettes (1)

eRah Manual

How these are measured

Downloads

3.5K

CRAN downloads in the past year

Rank #8,041 · ~10/day · ~294/mo

Releases R versions

Daily download trend is not available in this view yet.

41930 days

1.1K90 days

3.5K1 year

Compare downloads with other packages →

Also on372 r2u5 autocran923 bioconda65 c2d4u

How downloads are counted

Repository

xdomingoal/erah-devel ↗Account: xdomingoal

6Stars

6Forks

10Open issues

0Open PRs

0Releases

224Commits

3Commit identities

License file reads as GPL-3.0 · 224 commits · Last activity 2024-02-09 · The default branch showed an older version (2.0.0) than CRAN on 2026-10-21

Responsiveness

How these are sampled

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

Stars over time

2025-05-30 · 62026-07-07 · 6

How these are measured

PracticesBeta

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

Checks run against github.com/xdomingoal/erah-devel 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

Docs source (3)

pkgdown

GitHub Pages site last deployed 2024-02-09 · The repository has a site deploy workflow

pkgdown site last built 2024-02-09, before release 2.2.0 (2025-07-17)

Coverage (1)

Coverage reporting (Codecov)

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

19 external dependencies (excludes base and recommended)

Installing erah adds 35 packages (20 with compiled code, 20 MB of source tarballs). Heaviest: igraph 4.8 MB, JADE 2.3 MB, signal 1.9 MB.

Depends (1)

R >= 4.0

Imports (10)

Rcpp osd HiClimR igraph signal quantregmethodstibble progress furrr

LinkingTo (1)

Rcpp

Suggests (9)

ncdf4 mzR future knitr rmarkdown prettydoc covr gcspikelite testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (8)

Xavier Domingo-Almenara

Jesus Brezmes

Author, Thesis advisor

Alexandre Perera

Author, Thesis advisor

Sara Samino

Author

Maria Vinaixa

Author

Oscar Yanes

Author, Thesis advisor

Jasen P. Finch

Contributor · added in 1.1.1

Adria Olomi

Contributor · added in 2.0.0

Listed in earlier versions (4)

Show 4 peopleHide 4 people

Xavier Correig

no longer listed · 1.0.0 to 1.0.1

Marta Diaz

no longer listed · 1.0.0 to 1.0.1

Lourdes Ibanez

no longer listed · 1.0.0 to 1.0.1

Finch

no longer listed · 2.2.0

Releases (12)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
2.2.0Latest
record
2025-07-18 · current release · diff ↗ ·
removed 1 export
plan
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
unarchivedReturned to CRAN
2023-12-20
2.0.1
record
2023-12-20 · diff ↗
archivedRemoved from CRAN
2023-12-18
issues were not corrected in time Uses Suggested package unconditionally
2.0.0
record
2023-12-02 · diff ↗ ·
added 4 exports
createInstrumentalTable, createPhenoTable, plan, showRTRICurve
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
1.1.2
record
2021-05-11 · diff ↗
1.1.1
record
2020-07-06 · diff ↗
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
1.1.0
record
2018-07-11 · diff ↗ ·
added 1 export
computeRIerror

Show 10 earlier eventsHide 10 earlier events

R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
1.0.5
record
2017-01-14 · diff ↗ ·
added 2 exports
export2CEF, importGMD
1.0.4
record
2016-10-18 · diff ↗ ·
added 1 export
importMSP
1.0.3
record
2016-10-14 · diff ↗
1.0.2
record
2016-09-02 · diff ↗ ·
added 1 export
export2MSP
R
R 3.3.0 released · 2016-05-03
1.0.1
record
2016-04-22 · diff ↗
1.0.0
record
2016-04-15
R
R 3.2.0 released · 2015-04-16

Package metadata

First published: 2016-04-15
Total releases: 12 / 10 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 4.0
Bundled data: 176 KB / 1 file
Download size: 738 KB

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' entry:

citation("erah")

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

It points to 10.1021/acs.analchem.6b02927.

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 erah version 2.2.0 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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