mpactr

0.3.3

Correction of Preprocessed MS Data

1packages depend

3.6Kdownloads / year

98.0%test coverage

13/13checks pass

Overview

About

Maintained by Patrick SchlossFirst published 2024-09-107 releasesCRAN page ↗GitHub ↗

An 'R' implementation of the 'python' program Metabolomics Peak Analysis Computational Tool ('MPACT') (Robert M. Samples, Sara P. Puckett, and Marcy J. Balunas (2023) doi:10.1021/acs.analchem.2c04632). Filters in the package serve to address common errors in tandem mass spectrometry preprocessing, including: (1) isotopic patterns that are incorrectly split during preprocessing, (2) features present in solvent blanks due to carryover between samples, (3) features whose abundance is greater than user-defined abundance threshold in a specific group of samples, for example media blanks, (4) ions that are inconsistent between technical replicates, and (5) in-source fragment ions created during ionization before fragmentation in the tandem mass spectrometry workflow.

Install

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

install.packages("mpactr", 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("mums2/mpactr")

Development version from mums2/mpactr. 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-mpactr

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-mpactr

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-mpactr

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

Health

CRAN checks

13OK

Slowest check: 5.9 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 28.14

98.0%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 1 earlier snapshots

NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 239 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

3.6K

CRAN downloads in the past year

Rank #8,144 · ~10/day · ~300/mo

Releases R versions

Daily download trend is not available in this view yet.

32230 days

1.3K90 days

3.6K1 year

Compare downloads with other packages →

Also on583 r2u39 autocran

Repository

GitHub ↗ mums2/mpactr

2Stars

0Forks

2Open issues

0Open PRs

6Releases

151Commits

3Contributors

License GPL-3.0 · 151 commits · Last activity 2026-07-27

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/mums2/mpactr on 2026-07-30.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Docs source (1)

README.Rmd

Show all practices

Lint, format, editor (2)

lintrRStudio project

Governance and community (1)

Issue templates

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

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (8)

cli data.table ggplot2 R6 Rcppstatstreemapify viridis

LinkingTo (1)

Rcpp

Suggests (9)

knitr rmarkdown testthat tidyverse plotly Hmisc corrplot ggdendro ggtext

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

mums2

Code & Tests

People & History

People (3)

Maintainer (1)

Patrick Schloss

Author, Maintainer, Copyright holder

Authors (3)

Patrick Schloss

Author, Maintainer, Copyright holder

Gregory Johnson

Author

Allison Mason

Author

Patrick Schloss

Author, Maintainer, Copyright holder

Package Timeline

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

0.3.3Latest
2026-05-21 · current release · diff ↗
0.3.2
2026-05-15 · diff ↗
R
R 4.6.0 released · 2026-04-24
0.3.1
2025-09-28 · diff ↗
unarchivedReturned to CRAN
2025-09-28
archivedRemoved from CRAN
2025-09-22
errors were not corrected in time
0.3.0
2025-09-08 · diff ↗
R
R 4.5.0 released · 2025-04-11
0.2.1
2025-03-29 · diff ↗
0.2.0
2025-03-13 · diff ↗
0.1.0
2024-09-10
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-09-10
Total releases: 7 / 2 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.5.0
Bundled data: 156 KB / 1 file
Download size: 4.6 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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