R Observatory: Metrics for mums2 version 0.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

mums2

0.1.1Package record

Microbial Ecology by Tandem Mass Spectrometry

0packages depend

1.6Kdownloads / year

85.5%test coverage

13/13flavors OK

Overview

About

Maintained by Patrick SchlossCRAN page ↗GitHub ↗Website ↗Issues ↗

Tools that researchers can use to analyze untargeted metabolomics data generated using tandem mass spectroscopy from microbial communities. The overall approach taken to analyze metabolomics data parallels that used to analyze microbial communities using 16S rRNA gene sequencing data. Thus, we have a number of methods a user is able to use to generate data. Firstly, users can import Mass Spectrometry 1(MS1) data and filter it. Users are then able to match Mass Spectrometry 2(MS2) data to the filtered (or unfiltered) MS1 data. With the matched data users are able to cluster it, annotate it, predict de novo chemical formulas and calculate alpha and beta diversity. For chemical formula predictions, this was the method used; "Towards de novo identification of metabolites by analyzing tandem mass spectra" (Sebastian Böcker, Florian Rasche (2008) doi:10.1093/bioinformatics/btn270). The similarity/dissimilarity calculations we used to cluster our data together was: "Spectral entropy outperforms MS/MS dot product similarity for small-molecule compound identification" (Li, Y., Kind, T., Folz, J. et al. (2021) doi:10.1038/s41592-021-01331-z) and "Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking" (Wang, M., Carver, J., Phelan, V. et al. (2021) doi:10.1038/nbt.3597).

Changes in 0.1.1

Fixing clang-UBSAN and noSuggests build errors.
Removing mzR in favor of RaMS.

From NEWS.md in the release

Install

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

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

Development version from mums2/mums2. 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-mums2

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-mums2

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-mums2

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: 19.3 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-26
ERROR5 OK, 2 ERROR2026-06-11

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.1

READMEYes · 168 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 0.1.1Citation fileNoWebsiteYes · pkgdown

The repository also keeps web-only articles.

Help pages: 37 (2 internal)includes a package overview page
Examples that run: 100%34 run in a plain check
Exported functions with examples: 94%
Documented parameters: 100%
Return-value docs: 97%
Help pages citing references: 11%

Vignettes (1)

mums2 HTML

How these are measured

Downloads

1.6K

CRAN downloads in the past year

Rank #10,076 · ~4/day · ~135/mo

Releases R versions

Daily download trend is not available in this view yet.

30330 days

1K90 days

1.6K1 year

Compare downloads with other packages →

Also on76 r2u3 autocran

How downloads are counted

Repository

mums2/mums2 ↗Organization: mums2

1Stars

0Forks

0Open issues

0Open PRs

1Releases

77Commits

3Commit identities

License file reads as GPL-3.0 · 77 commits · Last activity 2026-06-25 · 0% stars, 30d · Default branch at 0.1.1.9000, ahead of CRAN 0.1.1 (checked 2026-10-25)

Responsiveness

How these are sampled

PRs merged (all time): 99%
Median days to close, 50 most recently updated closed issues: 36
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2026-06-03 · 12026-07-07 · 1

How these are measured

PracticesBeta

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

Checks run against github.com/mums2/mums2 on 2026-10-25.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-10-19 · The repository has a site deploy workflow

pkgdown site last built 2026-10-19

CRAN release process (1)

cran-comments.md

Lint, format, editor (2)

lintrRStudio project

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

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Installing mums2 adds 60 packages (30 with compiled code, 55 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (1)

R >= 4.1.0

Imports (9)

clustur Rcpp data.table mpactrutilsstatsparallelxml2 RaMS

LinkingTo (5)

sitmo Rcpp RcppThread testthat RcppProgress

Suggests (5)

knitr rmarkdown testthat tidyverse networkD3

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 (8)

Patrick Schloss

Author, Maintainer since 0.1.0 (2026)

Gregory Johnson

Author

Allison Mason

Author

Yuanyue Li

Contributor, Copyright holder

Marcel Martin

Contributor, Copyright holder

Anton Pervukhin

Contributor, Copyright holder

Florian Rasche

Contributor, Copyright holder

Henner Sudek

Contributor, Copyright holder

Releases (2)

Pick two releases to compare their code metrics.

0.1.1Latest
record
2026-06-25 · current release · diff ↗
0.1.0
record
2026-06-10
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-06-10
Total releases: 2 / 1 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.1.0
Download size: 7.7 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("mums2")

Format

Schloss, P., Johnson, G., Li, Y., Martin, M., Mason, A., Pervukhin, A., Rasche, F., & Sudek, H. (2026). mums2: Microbial Ecology by Tandem Mass Spectrometry (Version 0.1.1) [Computer software]. https://doi.org/10.32614/CRAN.package.mums2

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 mums2 version 0.1.1 [Data set]. HJJB, LLC. Data release v2026-10-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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