R Observatory: Metrics for Oncotree version 0.3.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

Oncotree

0.3.5Package record

Estimating Oncogenetic Trees

0packages depend

3.3Kdownloads / year

–test coverage

0/13flavors OK

Overview

About

Maintained by Aniko SzaboCRAN page ↗GitHub ↗Issues ↗

Construct and evaluate directed tree structures that model the process of occurrence of genetic alterations during carcinogenesis as described in Szabo, A. and Boucher, K (2002) doi:10.1016/S0025-5564(02)00086-X.

Install

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

install.packages("Oncotree", 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("anikoszabo/Oncotree")

Development version from anikoszabo/Oncotree. 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-oncotree

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-Oncotree

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-Oncotree

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

13NOTE

Check messages

NOTERd filesr-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, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64

checkRd: (-1) oncotree.fit.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) oncotree.fit.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) oncotree.fit.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) oncotree.fit.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) oncotree.fit.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly

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

Maintainer: ‘Aniko Szabo <aszabo@mcw.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Aniko",
                      family = "Szabo",
                      role = c("aut", "cre"),
                      email = "aszabo@mcw.edu"),
               person(given = "Lisa",
                      family = "Pappas",
                      role = "aut"))
as necessary.

CRAN check page ↗

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

Status changes

NOTE13 NOTENow
NOTE14 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.3.5

READMENoVignettesYes · 2 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 9 (1 internal)includes a package overview page
Examples that run: 100%8 run in a plain check
Exported functions with examples: 100%
Documented parameters: 75%
Return-value docs: 83%
Help pages citing references: 22%

Vignettes (2)

How these are measured

Downloads

3.3K

CRAN downloads in the past year

Rank #15,653 · ~9/day · ~277/mo

Releases R versions

Daily download trend is not available in this view yet.

29730 days

79290 days

3.3K1 year

Compare downloads with other packages →

Also on99 r2u7 autocran

How downloads are counted

Repository

anikoszabo/oncotree ↗Account: anikoszabo

0Stars

0Forks

0Open issues

0Open PRs

1Releases

8Commits

1Commit identities

8 commits · Last activity 2023-09-28

Responsiveness

not measured

Releases over time

2023-09-28 · 12026-07-07 · 1

How these are measured

PracticesBeta

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

Checks run against github.com/anikoszabo/oncotree on 2026-10-21.

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

0 external dependencies (excludes base and recommended)

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

Depends (2)

R >= 2.3.1boot

Imports (0)

none

LinkingTo (0)

none

Suggests (1)

lattice

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 (from the free-text Author field) (2)

Aniko Szabo

Lisa Pappas

Maintainer since 0.3 (2009)

Releases (6)

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
0.3.5Latest
record
2023-09-28 · current release · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
0.3.4
record
2022-04-11 · diff ↗
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
R
R 3.2.0 released · 2015-04-16
R
R 3.1.0 released · 2014-04-10
0.3.3
record
2013-12-13 · diff ↗

Show 12 earlier eventsHide 12 earlier events

R
R 3.0.0 released · 2013-04-03
0.3.2
record
2012-11-13 · diff ↗ ·
removed 1 export
pattern:.

added 13 exports
ancestors, bootstrap.oncotree, distribution.oncotree, error.rates<-, generate.data, least.common.ancestor, marginal.distr, oncotree.fit, plot.boottree, plot.oncotree, print.boottree, print.oncotree, pstree.oncotree
0.3.1
record
2012-10-29 · diff ↗ ·
added 1 export
pattern:.
R
R 2.15.0 released · 2012-03-30
R
R 2.14.0 released · 2011-10-31
R
R 2.13.0 released · 2011-04-13
R
R 2.12.0 released · 2010-10-15
R
R 2.11.0 released · 2010-04-22
R
R 2.10.0 released · 2009-10-26
R
R 2.9.0 released · 2009-04-17
0.3
record
2009-03-12
R
R 2.8.0 released · 2008-10-20

Package metadata

First published: 2009-03-12
Total releases: 6 / 17 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 2.3.1
Bundled data: 0.5 KB / 1 file
Download size: 418 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("Oncotree")

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 Oncotree version 0.3.5 [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.

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