R Observatory: Metrics for speakeasyR version 0.1.9

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

speakeasyR

0.1.9Package record

Fast and Robust Multi-Scale Graph Clustering

0packages depend

3.8Kdownloads / year

0.0%test coverage

13/13flavors OK

Overview

About

Maintained by David ConnellCRAN page ↗GitHub ↗Issues ↗

A graph community detection algorithm that aims to be performant on large graphs and robust, returning consistent results across runs. SpeakEasy 2 (SE2), the underlying algorithm, is described in Chris Gaiteri, David R. Connell & Faraz A. Sultan et al. (2023) doi:10.1186/s13059-023-03062-0. The core algorithm is written in 'C', providing speed and keeping the memory requirements low. This implementation can take advantage of multiple computing cores without increasing memory usage. SE2 can detect community structure across scales, making it a good choice for biological data, which often has hierarchical structure. Graphs can be passed to the algorithm as adjacency matrices using base 'R' matrices, the 'Matrix' library, 'igraph' graphs, or any data that can be coerced into a matrix.

Changes in 0.1.9

Fixed

Fix building from source in Windows ARM environment (#2).

From NEWS.md in the release

Install

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

install.packages("speakeasyR", 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("SpeakEasy-2/speakeasyR")

Development version from SpeakEasy-2/speakeasyR. 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-speakeasyr

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-speakeasyR

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-speakeasyR

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: 5.5 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-04-10

Show 2 earlier changesHide 2 earlier changes

WARNING13 OK, 1 WARNING2026-04-09
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.9

READMEYes · 578 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 0.1.9Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 4
Examples that run: 100%4 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

speakeasyR HTML

How these are measured

Downloads

3.8K

CRAN downloads in the past year

Rank #16,231 · ~10/day · ~315/mo

Releases R versions

Daily download trend is not available in this view yet.

34030 days

77990 days

3.8K1 year

Compare downloads with other packages →

Also on385 r2u4 autocran

How downloads are counted

Repository

speakeasy-2/speakeasyr ↗Organization: SpeakEasy-2

3Stars

2Forks

0Open issues

0Open PRs

8Releases

176Commits

3Commit identities

License file reads as GPL-3.0 · 176 commits · Last activity 2026-10-20

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 114
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2024-08-21 · 32026-07-07 · 3

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/speakeasy-2/speakeasyr on 2026-10-25.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Reproducibility and dev environment (1)

Makefile

CRAN release process (1)

cran-comments.md

Git structural (1)

Submodules

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

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

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

Depends (0)

none

Imports (2)

Matrixmethods

LinkingTo (0)

none

Suggests (6)

igraph scRNAseq SummarizedExperiment knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (34)

David Connell

Author, Maintainer since 0.1.0 (2024), Copyright holder

Allan Cornet

Copyright holder, Contributor · added in 0.1.2

Author of arpack.

Gábor Csárdi

Copyright holder, Contributor

Author of igraph C library.

Timothy Davis

Copyright holder, Contributor · added in 0.1.2

Author of CXSPARSE (cs).

Sébastien Fabbro

Copyright holder, Contributor · added in 0.1.2

Contributor to arpack.

Daniel G.

Copyright holder, Contributor · added in 0.1.2

Author of ax_pthread.

Jordi Hermoso

Copyright holder, Contributor · added in 0.1.2

Contributor to arpack.

Szabolcs Horvát

Copyright holder, Contributor

Author of igraph C library.

Ross Ihaka

Copyright holder, Contributor · added in 0.1.2

Author of Mathlib.

Show 16 more contributorsHide 16 contributors

Steven Johnson

Copyright holder, Contributor · added in 0.1.2

Author of ax_pthread.

Sylvestre Ledru

Copyright holder, Contributor · added in 0.1.2

Author of arpack.

Richard Lehoucq

Copyright holder, Contributor · added in 0.1.2

Author of arpack.

Tamás Nepusz

Copyright holder, Contributor

Author of igraph C library.

Minh Nguyen

Copyright holder, Contributor · added in 0.1.2

Author of ax_pthread.

Daniel Noom

Copyright holder, Contributor

Author of igraph C library.

Melissa O'Neill

Copyright holder, Contributor · added in 0.1.2

Author of PCG random number generator.

Elliot Paquette

Copyright holder, Contributor · added in 0.1.2

Contributor to igraph.

Pascal Pons

Copyright holder, Contributor · added in 0.1.2

Contributor to igraph.

Danny Scrensen

Copyright holder, Contributor · added in 0.1.2

Author of arpack and lapack.

Marc Stevens

Copyright holder, Contributor · added in 0.1.2

Author of ax_pthread.

Shinya Tasaki

Copyright holder, Contributor · added in 0.1.4

Provided code used in the gene clustering example.

Vincent Traag

Copyright holder, Contributor

Author of igraph C library.

Phuong Vu

Copyright holder, Contributor · added in 0.1.2

Author of arpack.

Chao Yang

Copyright holder, Contributor · added in 0.1.2

Author of arpack.

Fabio Zanini

Copyright holder, Contributor

Author of igraph C library.

Free Software Foundation, Inc.

Copyright holder · added in 0.1.2

Copyright holder of GPL licenses.

Rice University

Copyright holder · added in 0.1.2

Copyright holder of arpack.

Royal Statistical Society

Copyright holder · added in 0.1.2

Copyright holder of Mathlib.

Scilab Enterprises

Copyright holder · added in 0.1.2

Copyright holder of arpack-ng.

The R Core Team

Copyright holder · added in 0.1.2

Copyright holder of Mathlib.

The R Development Core Team

Copyright holder · added in 0.1.2

Copyright holder of Mathlib.

The Regents of the University of California

Copyright holder · added in 0.1.2

Copyright holder of stdlib's qsort.

The igraph development team

Copyright holder · added in 0.1.2

Copyright holder of igraph C library.

Show 1 more copyright holderHide 1 copyright holder

Chris Gaiteri

Copyright holder

Author of original SpeakEasy 2 algorithm.

Releases (9)

Pick two releases to compare their code metrics.

0.1.9Latest
record
2026-10-20 · current release · diff ↗ ·
listed once in CRAN's queue
Seen in one reading of CRAN's incoming queue, at 2026-10-18 19:08 UTC, so it stayed less than the time between readings.
R
R 4.6.0 released · 2026-04-24
0.1.8
record
2025-09-30 · diff ↗
0.1.7
record
2025-09-05 · diff ↗
0.1.6
record
2025-08-28 · diff ↗
R
R 4.5.0 released · 2025-04-11
0.1.5
record
2025-04-03 · diff ↗
0.1.4
record
2024-09-25 · diff ↗ ·
added 1 export
cluster_genes
unarchivedReturned to CRAN
2024-08-20
0.1.3
record
2024-08-20 · diff ↗
archivedRemoved from CRAN
2024-08-19
issues were not corrected in time
unarchivedReturned to CRAN
2024-07-29
0.1.2
record
2024-07-29 · diff ↗
archivedRemoved from CRAN
2024-06-19
policy violations including misrepresentation of authorship The included sources such as 'glpk' and 'lapack' are not credited System versions are not looked for ASAN errors even in re-submission
0.1.0
record
2024-06-18
R
R 4.4.0 released · 2024-04-24

Across CRAN, the median accepted release of the past year spent 22 hours in the queue, 90% under 11 days.How queue time is measured

Package metadata

First published: 2024-06-18
Total releases: 9 / 2 yrs
License: GPL (>= 3) OSI
Download size: 2.8 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("speakeasyR")

Format

Connell, D., Free Software Foundation, Inc., Rice University, Royal Statistical Society, Scilab Enterprises, The R Core Team, The R Development Core Team, The Regents of the University of California, The igraph development team, Cornet, A., Csárdi, G., Davis, T., Fabbro, S., G., D., Gaiteri, C., Hermoso, J., Horvát, S., Ihaka, R., Johnson, S., Ledru, S., Lehoucq, R., Nepusz, T., Nguyen, M., Noom, D., O'Neill, M., Paquette, E., Pons, P., Scrensen, D., Stevens, M., Tasaki, S., Traag, V., Vu, P., Yang, C., & Zanini, F. (2026). speakeasyR: Fast and Robust Multi-Scale Graph Clustering (Version 0.1.9) [Computer software]. https://doi.org/10.32614/CRAN.package.speakeasyR

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 speakeasyR version 0.1.9 [Data set]. HJJB, LLC. Data release v2026-10-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-26, 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 →