MALDIrppa

1.1.0-3

MALDI Mass Spectrometry Data Robust Pre-Processing and Analysis

1packages depend

3.9Kdownloads / year

32.1%test coverage

13/13checks pass

Overview

About

Maintained by Javier Palarea-AlbaladejoFirst published 2017-07-2912 releasesCRAN page ↗GitHub ↗

Provides methods for quality control and robust pre-processing and analysis of MALDI mass spectrometry data (Palarea-Albaladejo et al. (2018) doi:10.1093/bioinformatics/btx628).

Install

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

install.packages("MALDIrppa", 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("Japal/MALDIrppa")

Development version from Japal/MALDIrppa. 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-maldirppa

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-MALDIrppa

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-MALDIrppa

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 3.3 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.08

32.1%

Coverage · measured lines

Dependencies · direct

Check history

OK2026-05-12
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
WARNING2026-05-11
12 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 231 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: not tracked
Return-value docs: not tracked
References docs: 0%

Downloads

3.9K

CRAN downloads in the past year

Rank #11,248 · ~11/day · ~321/mo

Releases R versions

Daily download trend is not available in this view yet.

29930 days

95090 days

3.9K1 year

Compare downloads with other packages →

Also on119 r2u35 autocran2.2K conda_forge344 bioconda84 c2d4u

Repository

GitHub ↗ japal/maldirppa

3Stars

2Forks

0Open issues

0Open PRs

0Releases

98Commits

3Contributors

mass-spectrometrypre-processingr-package

98 commits · Last activity 2025-07-27

Stars over time

2025-06-08 · 32026-07-07 · 3

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/japal/maldirppa on 2026-07-19.

Continuous integration (1)

GitHub Actions

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Depends (6)

R >= 3.2.5MALDIquant signal robustbaselatticewaveslim

Imports (0)

none

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

MSclassifR

Code & Tests

Code Composition

Rd 1,103 (35%)R 1,000 (31%)Other 617 (19%)Vignettes 473 (15%)

Code characteristics

Object systems

S32

Cyclomatic complexity: 4.0 median / 28 max
Test cases: 8 / 0.08 per code line

Test coverage

Line coverage

32%

Expression

34.5%

Tests / Examples

32.1% / 40% ex

Functions

27 0 exported

Complexity

6.6 avg / 28 max

Call network

27 nodes / 11 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

27 functions

Function	Cyclo	Coverage
.exportFasta	13	0%
.exportNexus	28	0%
.plot.patterns	4	0%
addMetadata	2	0%
alignPeaks	2	0%
deletePeaks	3	0%

Datasets

Bundled datasets · 1

Name	Class	Rows × Cols	Also ships in
type	data.frame	400 × 4	–

People & History

People (2)

Maintainer (1)

Javier Palarea-Albaladejo

Maintainer, Author

Authors (1)

Javier Palarea-Albaladejo

Maintainer, Author

Contributors (1)

Paolo Ribeca

Contributor · added in 1.0.5

Listed in earlier versions (3)

Insightful Corp.

no longer listed · 1.0.5 to 1.0.5-1

William Constantine

no longer listed · 1.0.5 to 1.0.5-1

Keith L. Davidson

no longer listed · 1.0.5 to 1.0.5-1

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.1.0-3Latest
2025-07-27 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.1.0-2
2024-01-25 · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
1.1.0-1
2022-03-29 · diff ↗
1.1.0
2022-02-14 · diff ↗
1.0.5-1
2021-10-15 · diff ↗
unarchivedReturned to CRAN
2021-10-15
archivedRemoved from CRAN
2021-10-06
maintainer is unable to correct it
R
R 4.1.0 released · 2021-05-18
1.0.5
2020-09-13 · diff ↗
unarchivedReturned to CRAN
2020-09-13
archivedRemoved from CRAN
2020-08-02
check problems were not corrected in time

Show 12 earlier events

1.0.4
2020-07-19 · diff ↗
1.0.3
2020-07-19 · diff ↗
unarchivedReturned to CRAN
2020-07-19
archivedRemoved from CRAN
2020-06-09
suggested archived package 'wmtsa' but did not use it conditionally
1.0.2
2020-05-28 · diff ↗
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
1.0.1-2
2018-11-09 · diff ↗
R
R 3.5.0 released · 2018-04-23
1.0.1
2017-09-19 · diff ↗
1.0.0
2017-07-29
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-07-29
Total releases: 12 / 9 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.2.5
Bundled data: 967 KB / 2 files
Download size: 3.8 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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