R Observatory: Metrics for CancerEvolutionVisualization version 2.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

CancerEvolutionVisualization

2.0.1Package record

Publication Quality Phylogenetic Tree Plots

0packages depend

2.7Kdownloads / year

67.4%test coverage

13/13flavors OK

Overview

About

Maintained by Paul BoutrosCRAN page ↗GitHub ↗Issues ↗

Generates tree plots with precise branch lengths, gene annotations, and cellular prevalence. The package handles complex tree structures (angles, lengths, etc.) and can be further refined as needed by the user.

Changes in 2.0.1

ADDED

GitHub links for code and bug reports

BUG

Fixed S3 naming conflict in heatmap functions, using safe "create." prefix

From NEWS in the release

Install

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

install.packages("CancerEvolutionVisualization", 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("uclahs-cds/package-CancerEvolutionVisualization")

Development version from uclahs-cds/package-CancerEvolutionVisualization. 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-cancerevolutionvisualization

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-CancerEvolutionVisualization

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-CancerEvolutionVisualization

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: 2.0 min · r-oldrel-macos-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.0.1

README· In the repository, left out of the releaseVignettesYes · 1 · dynamicNEWSYes · 33% structured · mentions 2.0.1Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 2
Examples that run: 100%1 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

User Guide HTML

How these are measured

Downloads

2.7K

CRAN downloads in the past year

Rank #12,831 · ~7/day · ~227/mo

Releases R versions

Daily download trend is not available in this view yet.

25830 days

88890 days

2.7K1 year

Compare downloads with other packages →

Also on85 r2u28 autocran

How downloads are counted

Repository

uclahs-cds/public-R-CancerEvolutionVisualization ↗Organization: uclahs-cds

Moved from uclahs-cds/package-cancerevolutionvisualization.

2Stars

0Forks

13Open issues

1Open PRs

1Releases

1,046Commits

9Commit identities

License file reads as GPL-2.0 · 1,046 commits · Last activity 2026-08-17 · 0% stars, 30d · Default branch at 3.0.0, ahead of CRAN 2.0.1 (checked 2026-10-21) · Discussions: 3 posts

Responsiveness

How these are sampled

PRs merged (all time): 95%
Median days to close, 50 most recently updated closed issues: 271
Median days to close, 50 most recently updated closed PRs: 14

Stars over time

2022-10-15 · 12026-07-07 · 2

How these are measured

PracticesBeta

3 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/uclahs-cds/package-cancerevolutionvisualization on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux

Governance and community (1)

PR template (inherited from uclahs-cds)

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

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Installing CancerEvolutionVisualization adds 23 packages (17 with compiled code, 25 MB of source tarballs). Heaviest: stringi 11 MB, BoutrosLab.plotting.general 2.9 MB, Rcpp 1.8 MB.

Depends (5)

R >= 3.5.0graphicsgridgridExtra gtable

Imports (5)

plyrgrDevicesutilsstringr BoutrosLab.plotting.general

LinkingTo (0)

none

Suggests (2)

testthat knitr

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 (4)

Paul Boutros

Maintainer since 1.0.1 (2022)

Adriana Salcedo

Author

Dan Knight

Author

Helena Winata

Contributor

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
2.0.1Latest
record
2023-11-21 · current release · diff ↗
R
R 4.3.0 released · 2023-04-21
1.0.1
record
2022-10-04
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-10-04
Total releases: 2 / 4 yrs
License: GPL-2 OSI
Minimum R: ≥ 3.5.0
Bundled data: 0.1 KB / 1 file
Download size: 161 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("CancerEvolutionVisualization")

Format

Paul Boutros, Adriana Salcedo, Dan Knight, & Helena Winata. (2023). CancerEvolutionVisualization: Publication Quality Phylogenetic Tree Plots (Version 2.0.1) [Computer software]. https://doi.org/10.32614/CRAN.package.CancerEvolutionVisualization

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 CancerEvolutionVisualization version 2.0.1 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, 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 →