R Observatory: Metrics for BoolNet version 2.1.9

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

BoolNet

2.1.9Package record

Construction, Simulation and Analysis of Boolean Networks

0packages dependsuggested by 3

9.4Kdownloads / year

–test coverage

0/13flavors OK

Overview

About

Maintained by Hans A. KestlerCRAN page ↗

Functions to reconstruct, generate, and simulate synchronous, asynchronous, probabilistic, and temporal Boolean networks. Provides also functions to analyze and visualize attractors in Boolean networks doi:10.1093/bioinformatics/btq124.

Install

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

install.packages("BoolNet", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

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-boolnet

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-BoolNet

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-BoolNet

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) getPathToAttractor.Rd:23: Lost braces; missing escapes or markup?
    23 |   Specifies whether the actual attractor states are included in the resulting table or not. If \code{includeAttractorStates = "all"} (which is the default behaviour), the sequence ends when the attractor was traversed once. If \code{includeAttractorStates = "first"}, only the first state of attractor is added to the sequence. This corresponds to the behaviour prior to \pkg{BoolNet} version 1.5. If {includeAttractorStates = "none"}, the sequence ends with the last non-attractor state. In this case, the sequence can be empty if the start state is an attractor state.
       |                                                                                                                                                                                                                                                                                                                                            
...[truncated]...

checkRd: (-1) simulateSymbolicModel.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulateSymbolicModel.Rd:66-70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulateSymbolicModel.Rd:72-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) testNetworkProperties.Rd:131: Lost braces; missing escapes or markup?
   131 | If {perturb="functions"} or \code{perturb="transitions"} and \code{accumulate=FALSE}, the function returns a vector of percentages of original attractors found in each of the perturbed copies of the original network. If \code{accumulate=TRUE}, the function returns the overall percentage of original attractors found in all perturbed copies.
       |    ^
checkRd: (-1) testNetworkProperties.Rd:140: Lost braces
   140 | code{params} can hold parameters \code{numSamples, flipBits} corresponding to the parameters of \code{\link{perturbTrajectories}} that define how many initial states are drawn and how many bits are flipped.
       |     ^

Additional issues

musl

CRAN check page ↗

Slowest check: 3.5 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 2.1.9

READMENoVignettesYes · 1 · dynamicNEWSYes · does not mention 2.1.9Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 47
Examples that run: 17%7 run in a plain check · 34 never run
Exported functions with examples: 100%
Documented parameters: 97%
Return-value docs: 95%
Help pages citing references: 26%

How these are measured

Downloads

9.4K

CRAN downloads in the past year

Rank #4,046 · ~26/day · ~779/mo

Releases R versions

Daily download trend is not available in this view yet.

90930 days

2.2K90 days

9.4K1 year

Compare downloads with other packages →

Also on565 r2u43 autocran4.2K conda_forge27 c2d4u

How downloads are counted

Dependencies

Declared dependencies

2 external dependencies (excludes base and recommended)

Installing BoolNet adds 10 packages (7 with compiled code, 8.9 MB of source tarballs). Heaviest: igraph 4.8 MB, vctrs 1.0 MB, XML 937 KB.

Depends (0)

none

Imports (2)

igraph XML

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Suggested by 3

Suggests, most downloaded first

Binarize BiTrinA pastboon

How these are counted

Code & Tests

Datasets

People & History

People (6)

Hans A. Kestler

Author, Maintainer since 1.3 (2009)

Martin Hopfensitz

Author · added in 1.4

Christoph Müssel

Author · added in 1.43

Dao Zhou

Author

Armin Biere

Contributor · added in 2.1.0

contributed PicoSAT code

Troy D. Hanson

Contributor

contributed uthash macros

Listed in earlier versions (4)

Show 4 peopleHide 4 people

Hans Kestler

no longer listed · 1.3 to 2.0.2

Christoph Muessel

no longer listed · 1.3 to 1.42

Hans A.

no longer listed · 2.1.0 to 2.1.9

Troy D.

no longer listed · 2.1.0 to 2.1.9

Releases (25)

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
2.1.9Latest
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2023-10-02 · current release · diff ↗
R
R 4.3.0 released · 2023-04-21
2.1.8
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2023-02-27 · diff ↗
2.1.7
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2022-09-04 · diff ↗
R
R 4.2.0 released · 2022-04-22
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
2.1.5
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2019-04-16 · diff ↗
2.1.4
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2018-06-07 · diff ↗
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
2.1.3
record
2016-11-21 · diff ↗

Show 29 earlier eventsHide 29 earlier events

R
R 3.3.0 released · 2016-05-03
R
R 3.2.0 released · 2015-04-16
2.1.1
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2015-02-25 · diff ↗
2.1.0
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2015-02-23 · diff ↗
2.0.2
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2014-12-11 · diff ↗
2.0.1
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2014-08-26 · diff ↗
2.0
record
2014-07-17 · diff ↗ ·
added 7 exports
generateCanalyzing, generateNestedCanalyzing, perturbTrajectories, simulateSymbolicModel, testTransitionRobustness, truthTableToSymbolic, symbolicToTruthTable
R
R 3.1.0 released · 2014-04-10
1.63
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2014-03-31 · diff ↗
1.62
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2013-12-03 · diff ↗
R
R 3.0.0 released · 2013-04-03
1.61
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2013-03-20 · diff ↗
1.60
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2012-12-12 · diff ↗ ·
removed 6 exports
print.AttractorInfo, print.BooleanNetwork, print.BooleanNetworkCollection, print.BooleanStateInfo, print.TransitionTable, print.MarkovSimulation

added 3 exports
loadSBML, saveNetwork, toSBML
1.51
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2012-06-11 · diff ↗
1.50
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2012-04-10 · diff ↗ ·
added 5 exports
plotSequence, sequenceToLaTeX, getAttractorSequence, generateState, generateTimeSeries
R
R 2.15.0 released · 2012-03-30
1.46
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2012-01-17 · diff ↗
1.45
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2011-11-22 · diff ↗
R
R 2.14.0 released · 2011-10-31
R
R 2.13.0 released · 2011-04-13
1.44
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2011-04-11 · diff ↗
1.43
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2011-01-24 · diff ↗
R
R 2.12.0 released · 2010-10-15
1.42
record
2010-06-16 · diff ↗ ·
added 1 export
getPathToAttractor
1.41
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2010-05-22 · diff ↗
R
R 2.11.0 released · 2010-04-22
1.4
record
2010-02-28 · diff ↗ ·
added 8 exports
loadBioTapestry, plotPBNTransitions, getTransitionProbabilities, markovSimulation, testNetworkProperties, testAttractorRobustness, testIndegree, print.MarkovSimulation
1.3
record
2009-11-16
R
R 2.10.0 released · 2009-10-26

Package metadata

First published: 2009-11-16
Total releases: 25 / 17 yrs
License: Artistic-2.0 OSI
Bundled data: 1.8 KB / 4 files
Download size: 1.5 MB

Appears in task views

Network Analysis

Cite

Cite this package

Run in R for the authors' entry:

citation("BoolNet")

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

It points to 10.1093/bioinformatics/btq124.

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 BoolNet version 2.1.9 [Data set]. HJJB, LLC. Data release v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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