R Observatory: Metrics for GCalignR version 1.0.7

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

GCalignR

1.0.7Package record

Simple Peak Alignment for Gas-Chromatography Data

0packages depend

3.8Kdownloads / year

66.6%test coverage

13/13flavors OK

Overview

About

Maintained by Meinolf OttensmannCRAN page ↗GitHub ↗Issues ↗

Aligns peak based on peak retention times and matches homologous peaks across samples. The underlying alignment procedure comprises three sequential steps. (1) Full alignment of samples by linear transformation of retention times to maximise similarity among homologous peaks (2) Partial alignment of peaks within a user-defined retention time window to cluster homologous peaks (3) Merging rows that are likely representing homologous substances (i.e. no sample shows peaks in both rows and the rows have similar retention time means). The algorithm is described in detail in Ottensmann et al., 2018 doi:10.1371/journal.pone.0198311.

Changes in 1.0.7

------------------------------------------------------------------------

replacing defunct vegan::adonis by vegan::adonis2

From NEWS.md in the release

Install

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

install.packages("GCalignR", 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("mottensmann/GCalignR")

Development version from mottensmann/GCalignR. 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-gcalignr

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-GCalignR

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-GCalignR

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: 3.8 min · r-oldrel-macos-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 1.0.7

READMEYes · 439 wordsVignettesYes · 2 · dynamicNEWSYes · 100% structured · mentions 1.0.7Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 25 (2 internal)includes a package overview page
Examples that run: 94%17 run in a plain check · 1 hold no code
Exported functions with examples: 93%
Documented parameters: 100%
Return-value docs: 93%
Help pages citing references: 12%

Vignettes (2)

GCalignR Step by Step HTML
GCalignR: How does the Algorithms work? HTML

How these are measured

Downloads

3.8K

CRAN downloads in the past year

Rank #8,795 · ~11/day · ~319/mo

Releases R versions

Daily download trend is not available in this view yet.

42830 days

1.1K90 days

3.8K1 year

Compare downloads with other packages →

Also on88 r2u7 autocran56 c2d4u

How downloads are counted

Repository

mottensmann/gcalignr ↗Account: mottensmann

7Stars

5Forks

1Open issues

0Open PRs

10Releases

629Commits

3Commit identities

License file reads as GPL-2.0 · 629 commits · Last activity 2026-05-11 · +16.7% stars, 30d · Default branch at 1.0.7.2, ahead of CRAN 1.0.7 (checked 2026-10-22)

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 34
Median days to close, 50 most recently updated closed PRs: 47

Stars over time

2024-05-07 · 52026-10-24 · 7

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/mottensmann/gcalignr on 2026-10-22.

Continuous integration (1)

Travis CI (config file)

Docs source (1)

README.Rmd

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Installing GCalignR adds 39 packages (20 with compiled code, 31 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, Rcpp 1.8 MB.

Depends (1)

R >= 3.2.5

Imports (10)

ggplot2graphicsstatsreadr reshape2 stringrutilspbapplymethodstibble

LinkingTo (0)

none

Suggests (5)

knitr pander rmarkdown testthat vegan

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 (4)

Meinolf Ottensmann

Author, Maintainer since 0.1.0 (2017)

Joseph I. Hoffman

Author

Hazel J. Nichols

Author · added in 1.0.0

Martin Stoffel

Author

Releases (8)

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
1.0.7Latest
record
2024-07-03 · current release · diff ↗
R
R 4.4.0 released · 2024-04-24
1.0.6
record
2024-01-22 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.0.5
record
2023-01-26 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.0.3
record
2020-08-26 · diff ↗
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
1.0.2
record
2018-07-16 · diff ↗ ·
added 1 export
read_empower2
R
R 3.5.0 released · 2018-04-23
1.0.1
record
2018-01-16 · diff ↗
1.0.0
record
2017-09-15 · diff ↗ ·
added 9 exports
choose_optimal_reference, draw_chromatogram, find_peaks, linear_transformation, merge_redundant_rows, read_peak_list, remove_blanks, remove_singletons, simple_chroma

Show 3 earlier eventsHide 3 earlier events

R
R 3.4.0 released · 2017-04-21
0.1.0
record
2017-02-06
R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2017-02-06
Total releases: 8 / 9 yrs
License: GPL (>= 2) | file LICENSE OSI
Minimum R: ≥ 3.2.5
Bundled data: 469 KB / 3 files
Download size: 2.9 MB

Appears in task views

Chemometrics and Computational Physics

Cite

Cite this package

Run in R for the authors' entry:

citation("GCalignR")

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

It points to 10.1371/journal.pone.0198311.

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 GCalignR version 1.0.7 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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