R Observatory: Metrics for cosmicsig version 1.3.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

cosmicsig

1.3.1Package record

Mutational Signatures from COSMIC (Catalogue of Somatic Mutations in Cancer)

0packages dependsuggested by 1

4.7Kdownloads / year

66.7%test coverage

13/13flavors OK

Overview

About

Maintained by Steven RozenCRAN page ↗GitHub ↗Issues ↗

A data package with 2 main package variables: 'signature' and 'etiology'. The 'signature' variable contains the latest mutational signature profiles released on COSMIC https://cancer.sanger.ac.uk/signatures/ for 3 mutation types: * Single base substitutions in the context of preceding and following bases, * Doublet base substitutions, and * Small insertions and deletions. 'cosmicsig' stands for COSMIC signatures. Please run ?'cosmicsig' for more information.

Changes in 1.3.1

Use the \doi{} Rd macro for the Alexandrov et al. 2020 reference on the package help page, replacing the previous \href{https://doi.org/...}{doi:...} form, as requested by CRAN.

From NEWS.md in the release

Install

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

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

Development version from Rozen-Lab/cosmicsig. 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-cosmicsig

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-cosmicsig

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-cosmicsig

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: 1.1 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK12 OK2026-04-26
NOTE8 OK, 6 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.3.1

READMEYes · 68 wordsVignettesNoNEWSYes · 100% structured · mentions 1.3.1Citation fileYes · software entry only

Help pages: 13includes a package overview page
Examples that run: 100%12 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

4.7K

CRAN downloads in the past year

Rank #5,513 · ~13/day · ~393/mo

Releases R versions

Daily download trend is not available in this view yet.

47230 days

1.5K90 days

4.7K1 year

Compare downloads with other packages →

Also on156 r2u9 autocran

How downloads are counted

Repository

rozen-lab/cosmicsig ↗Organization: Rozen-Lab

1Stars

0Forks

0Open issues

0Open PRs

2Releases

95Commits

2Commit identities

95 commits · Last activity 2026-04-21

Responsiveness

not measured

Stars over time

2022-02-23 · 12026-07-07 · 1

How these are measured

PracticesBeta

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

Checks run against github.com/rozen-lab/cosmicsig 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

Docs source (2)

README.Rmd

GitHub Pages site last deployed 2026-04-22

Reproducibility and dev environment (1)

data-raw/

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)

AI coding toolsBeta

This repository shows signs of AI coding tools.

Claude Codefirst seen 2026-04-19
Seen in the repository: CLAUDE.md
Named in .Rbuildignore: .claude, CLAUDE.md
Commits: at least 7 crediting it in the message

Models named in its commits

Claude Opus 4.77 commits · Apr 2026

Counts are commits, not lines of code. Commits by a tool's accounts count once across all of its accounts. Commits crediting it are the largest count among its credit lines, a minimum.How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

2 external dependencies (excludes base and recommended)

Installing cosmicsig adds no packages beyond those that come with R.

Depends (1)

R >= 3.5

Imports (0)

none

LinkingTo (0)

none

Suggests (2)

testthat usethis

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Suggested by 1

Suggests, most downloaded first

mSigTools

How these are counted

Code & Tests

Datasets

People & History

People (2)

Steven Rozen

Author, Maintainer since 1.0.7 (2021)

Nanhai Jiang

Author

Releases (3)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.3.1Latest
record
2026-04-21 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.1.1
record
2023-08-30 · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
1.0.7
record
2021-12-20
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-12-20
Total releases: 3 / 5 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5
Bundled data: 2.6 MB / 8 files
Download size: 2.9 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("cosmicsig")

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 cosmicsig version 1.3.1 [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.

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