GCalignR

1.0.7

Simple Peak Alignment for Gas-Chromatography Data

0packages depend

3.5Kdownloads / year

66.6%test coverage

13/13checks pass

Overview

About

Maintained by Meinolf OttensmannFirst published 2017-02-068 releasesCRAN page ↗GitHub ↗

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.

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.

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).

Health

CRAN checks

13OK

Slowest check: 4.2 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.08

66.6%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 439 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 93%
References docs: 12%

Downloads

3.5K

CRAN downloads in the past year

Rank #12,095 · ~10/day · ~293/mo

Releases R versions

Daily download trend is not available in this view yet.

26330 days

88290 days

3.5K1 year

Compare downloads with other packages →

Also on109 r2u36 autocran26 c2d4u

Repository

GitHub ↗ mottensmann/gcalignr

7Stars

5Forks

1Open issues

0Open PRs

10Releases

629Commits

3Contributors

License GPL-2.0 · 629 commits · Last activity 2026-05-11 · +16.7% stars, 30d

Stars over time

2024-05-07 · 52026-07-07 · 7

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/mottensmann/gcalignr on 2026-07-19.

Continuous integration (1)

Travis CI

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

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.

Code & Tests

Code Composition

R 3,612 (69%)Rd 1,040 (20%)Vignettes 568 (11%)Other 36 (1%)

Code characteristics

Object systems

S33

Cyclomatic complexity: 2.0 median / 61 max
Test cases: 12 / 0.08 per code line

Test coverage

Line coverage

67%

Expression

68.1%

Tests / Examples

66.6% / 69% ex

Functions

58 15 exported

Complexity

6.6 avg / 61 max

Call network

58 nodes / 41 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

58 functions

Function	Cyclo	Coverage
merge_redundant_rows exp	4	0%
peak_interspace exp	12	0%
read_empower2 exp	2	0%
remove_singletons exp	4	0%
add_linshifts	2	0%
add_linshifts2	2	0%

Datasets

Bundled datasets · 1

Name	Class	Rows × Cols	Also ships in
peak_factors	data.frame	82 × 3	–

People & History

People (4)

Maintainer (1)

Meinolf Ottensmann

Author, Maintainer

Authors (4)

Meinolf Ottensmann

Author, Maintainer

Joseph I. Hoffman

Author

Hazel J. Nichols

Author · added in 1.0.0

Martin Stoffel

Author

Package Timeline

8 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
1.0.7Latest
2024-07-03 · current release · diff ↗
R
R 4.4.0 released · 2024-04-24
1.0.6
2024-01-22 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.0.5
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
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
2018-07-16 · diff ↗
R
R 3.5.0 released · 2018-04-23
1.0.1
2018-01-16 · diff ↗
1.0.0
2017-09-15 · diff ↗

Show 3 earlier events

R
R 3.4.0 released · 2017-04-21
0.1.0
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
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Chemometrics and Computational Physics

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