R Observatory: Metrics for mSigTools version 1.0.7

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

mSigTools

1.0.7Package record

Mutational Signature Analysis Tools

0packages depend

2.4Kdownloads / year

95.0%test coverage

8/13flavors OK

Overview

About

Maintained by Steven RozenCRAN page ↗GitHub ↗Issues ↗

Utility functions for mutational signature analysis as described in Alexandrov, L. B. (2020) doi:10.1038/s41586-020-1943-3. This package provides two groups of functions. One is for dealing with mutational signature "exposures" (i.e. the counts of mutations in a sample that are due to each mutational signature). The other group of functions is for matching or comparing sets of mutational signatures. 'mSigTools' stands for mutational Signature analysis Tools.

Changes in 1.0.7

Renamed exported function best_reconstruction_QP to find_best_reconstruction_QP.

From NEWS.md in the release

Install

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

install.packages("mSigTools", 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("Rozen-Lab/mSigTools")

Development version from Rozen-Lab/mSigTools. 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-msigtools

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-mSigTools

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-mSigTools

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

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:
  mSigTools/tests/testthat/test_TP_FP_FN_avg_sim.R (.Dim: 2, .Dimnames: 2)
  mSigTools/tests/testthat/test_internal_matches.R (.Dim: 2, .Dimnames: 2)
  mSigTools/tests/testthat/test_match_two_sig_sets.R (.Dim: 4, .Dimnames: 4)
  mSigTools/tests/testthat/test_sig_dist_matrix.R (.Dim: 2, .Dimnames: 2)
'.Dim' should be changed to 'dim'.
'.Dimnames' should be changed to 'dimnames'.

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Steven Rozen <steverozen@pm.me>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

CRAN check page ↗

Slowest check: 1.4 min · r-oldrel-windows-x86_64

Status changes

NOTE8 OK, 5 NOTENow
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.7

READMEYes · 56 wordsVignettesNoNEWSYes · 100% structured · mentions 1.0.7Citation fileYes · software entry onlyWebsitenot declared in DESCRIPTION

Help pages: 11 (1 internal)
Examples that run: 100%10 run in a plain check
Exported functions with examples: 100%
Documented parameters: 90%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

2.4K

CRAN downloads in the past year

Rank #19,205 · ~7/day · ~204/mo

Releases R versions

Daily download trend is not available in this view yet.

22530 days

68990 days

2.4K1 year

Compare downloads with other packages →

Also on79 r2u3 autocran

How downloads are counted

Repository

rozen-lab/msigtools ↗Organization: Rozen-Lab

2Stars

2Forks

0Open issues

0Open PRs

3Releases

59Commits

2Commit identities

License file reads as GPL-3.0 · 59 commits · Last activity 2024-04-13 · Default branch at 1.0.8, ahead of CRAN 1.0.7 (checked 2026-10-21)

Responsiveness

not measured

How these are measured

PracticesBeta

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

Checks run against github.com/rozen-lab/msigtools on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on macOS and Windows

Docs source (1)

README.Rmd

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Installing mSigTools adds 7 packages (6 with compiled code, 3.8 MB of source tarballs). Heaviest: Rcpp 1.8 MB, RcppParallel 744 KB, clue 727 KB.

Depends (0)

none

Imports (4)

clue philentropy quadprog sets

LinkingTo (0)

none

Suggests (4)

cosmicsig ICAMS spelling testthat

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 (2)

Steven Rozen

Author, Maintainer since 1.0.5 (2022)

Nanhai Jiang

Author

Releases (2)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
1.0.7Latest
record
2023-01-13 · current release · diff ↗ ·
added 2 exports
find_best_reconstruction_QP, optimize_exposure_QP
1.0.5
record
2022-08-30
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-08-30
Total releases: 2 / 4 yrs
License: GPL-3 OSI
Download size: 35 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("mSigTools")

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

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 mSigTools version 1.0.7 [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.

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