R Observatory: Metrics for pmartR version 2.5.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

pmartR

2.5.1Package record

Panomics Marketplace - Quality Control and Statistical Analysis for Panomics Data

0packages depend

4.3Kdownloads / year

–test coverage

8/13flavors OK

Overview

About

Maintained by Lisa BramerCRAN page ↗GitHub ↗Website ↗Issues ↗

Provides functionality for quality control processing and statistical analysis of mass spectrometry (MS) omics data, in particular proteomic (either at the peptide or the protein level), lipidomic, and metabolomic data, as well as RNA-seq based count data and nuclear magnetic resonance (NMR) data. This includes data transformation, specification of groups that are to be compared against each other, filtering of features and/or samples, data normalization, data summarization (correlation, PCA), and statistical comparisons between defined groups. Implements methods described in: Webb-Robertson et al. (2014) doi:10.1074/mcp.M113.030932. Webb-Robertson et al. (2011) doi:10.1002/pmic.201100078. Matzke et al. (2011) doi:10.1093/bioinformatics/btr479. Matzke et al. (2013) doi:10.1002/pmic.201200269. Polpitiya et al. (2008) doi:10.1093/bioinformatics/btn217. Webb-Robertson et al. (2010) doi:10.1021/pr1005247.

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("pmartR", 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("pmartR/pmartR")

Development version from pmartR/pmartR. 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-pmartr

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

Health

CRAN checks

5NOTE8OK

Check messages

NOTER code for possible problemsr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64

Found calls to structure() using deprecated special names:
  pmartR/R/trelliPlots.R (.Names: 5)
'.Names' should be changed to 'names'.

CRAN check page ↗

Slowest check: 7.4 min · r-oldrel-windows-x86_64

Status changes

NOTE8 OK, 5 NOTENow
NOTE11 OK, 2 NOTE2026-07-16
OK12 OK, 1 FAILURE2026-06-08
ERROR12 OK, 1 ERROR2026-06-07
OK12 OK2026-04-25
NOTE11 OK, 3 NOTE2026-04-22

Show 2 earlier changesHide 2 earlier changes

ERROR10 OK, 3 NOTE, 1 ERROR2026-04-18
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.5.1

READMEYes · 710 wordsVignettes· In the repository, left out of the releaseNEWSNoCitation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 207 (14 internal)includes a package overview page
Examples that run: 71%72 run in a plain check (72 of them under a condition) · 22 only when donttest examples are enabled (R CMD check --as-cran) · 7 never run
Exported functions with examples: 78%
Documented parameters: 99%
Return-value docs: 100%
Help pages citing references: 10%

How these are measured

Downloads

4.3K

CRAN downloads in the past year

Rank #6,826 · ~12/day · ~362/mo

Releases R versions

Daily download trend is not available in this view yet.

43430 days

1.3K90 days

4.3K1 year

Compare downloads with other packages →

Also on382 r2u

How downloads are counted

Repository

pmartr/pmartr ↗Organization: pmartR

48Stars

18Forks

10Open issues

2Open PRs

9Releases

1,476Commits

17Commit identities

metabolomics-datapeptidesmass-spectrometrydata-summarizationproteinsmetaboliteslipidsrna-seq-analysis

1,476 commits · Last activity 2025-10-21 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 91%
Median days to close, 50 most recently updated closed issues: 38
Median days to close, 50 most recently updated closed PRs: 6

Stars over time

2025-08-17 · 462026-07-07 · 48

How these are measured

PracticesBeta

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

Checks run against github.com/pmartr/pmartr on 2026-10-22.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Governance and community (1)

Contributing guide

Docs source (3)

pkgdown

GitHub Pages site last deployed 2025-10-22 · The repository has a site deploy workflow

CRAN release process (1)

cran-comments.md

Show all practicesHide 1 practice

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

33 external dependencies (excludes base and recommended)

Installing pmartR adds 46 packages (25 with compiled code, 60 MB of source tarballs). Heaviest: BH 14 MB, stringi 11 MB, ggplot2 6.0 MB. 1 more not on CRAN is not measured.

Depends (1)

R >= 4.1.0

Imports (19)

Rcpp data.table doParallel dplyr ggplot2 e1071 foreachmethodsmvtnorm pcaMethods purrr rrcov stringr tidyr RColorBrewer magrittr parallelly patchwork glmpca

LinkingTo (3)

Rcpp RcppArmadillo BH

Suggests (13)

knitr limma rmarkdown edgeR DESeq2 plotly scales S4Vectorssurvivaltestthat trelliscopejs pmartRdata vdiffr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (7)

Lisa Bramer

Author, Maintainer since 2.4.1 (2023)

Author

Author

Contributor

Contributor

Contributor

Contributor

Releases (8)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
2.5.1Latest
record
2025-10-22 · current release · diff ↗
2.5.0
record
2025-04-23 · diff ↗ ·
removed 1 export
combine_lipidData

added 1 export
combine_omicsData
R
R 4.5.0 released · 2025-04-11
2.4.6
record
2024-10-14 · diff ↗
2.4.5
record
2024-05-21 · diff ↗ ·
added 1 export
normalize_zero_one_scaling
R
R 4.4.0 released · 2024-04-24
unarchivedReturned to CRAN
2024-02-27
archivedRemoved from CRAN
2024-02-27
policy violation Checking creates and leaves behind '~/Downloads'
2.4.4
record
2024-02-27 · diff ↗
2.4.3
record
2024-02-27 · diff ↗ ·
added 4 exports
trelli_rnaseq_boxplot, trelli_rnaseq_heatmap, trelli_rnaseq_histogram, trelli_rnaseq_nonzero_bar
2.4.2
record
2023-12-12 · diff ↗
2.4.1
record
2023-12-06
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-12-06
Total releases: 8 / 3 yrs
License: BSD_2_clause + file LICENSE OSI
Additional repositories: pmartR.github.io
Minimum R: ≥ 4.1.0
Download size: 1.6 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("pmartR")

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

It points to 10.1021/acs.jproteome.2c00610, 10.1021/acs.jproteome.8b00760.

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 pmartR version 2.5.1 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →