R Observatory: Metrics for uwot version 0.2.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

uwot

0.2.5

The Uniform Manifold Approximation and Projection (UMAP) Method for Dimensionality Reduction

27packages dependsuggested by 33

752.4Kdownloads / year

84.7%test coverage

13/13flavors OK

Overview

About

Maintained by James MelvilleCRAN page ↗GitHub ↗Website ↗Issues ↗

An implementation of the Uniform Manifold Approximation and Projection dimensionality reduction by McInnes et al. (2018) doi:10.48550/arXiv.1802.03426. It also provides means to transform new data and to carry out supervised dimensionality reduction. An implementation of the related LargeVis method of Tang et al. (2016) doi:10.48550/arXiv.1602.00370 is also provided. This is a complete re-implementation in R (and C++, via the 'Rcpp' package): no Python installation is required. See the uwot website (https://github.com/jlmelville/uwot) for more documentation and examples.

Changes in 0.2.5

Bug fixes and minor improvements

New parameter: n_build_threads. Controls the number of threads used to build the nearest

neighbor index when using nn_method = "hnsw" or nn_method = "nndescent". With a given seed,

setting n_build_threads = 1 will give deterministic nearest neighbor results when using either of

those methods (at the cost of some speed). If you are using the default Annoy-based method, this

parameter does nothing: it has always used one thread to build the index. Thank you

hsuknowledge for pointing out the issue around determinism.

(<https://github.com/jlmelville/uwot/issues/139>).

When passing a list of two matrices to nn_method to represent a pre-computed k-nearest neighbor

graph, you may specify the indices and distances as index and distance respectively. This

improves compatibility with the BiocNeighbors package. Thank you

hsuknowledge for pointing out the mismatch in naming convention

Show all changes in 0.2.5Hide the rest of the changes in 0.2.5

(<https://github.com/jlmelville/uwot/issues/140>).

Parallel-loop helpers now propagate worker exceptions from threaded code, although hopefully that

never happens.

default_num_threads now returns an integer.
The C++ sources now explicitly target the C++17 standard.

From NEWS.md in the release

Install

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

install.packages("uwot", 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("jlmelville/uwot")

Development version from jlmelville/uwot. 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-uwot

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-uwot

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-uwot

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: 8.4 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-09-05
NOTE11 OK, 2 NOTE2026-07-16
OK12 OK2026-04-25
NOTE12 OK, 2 NOTE2026-04-22
ERROR11 OK, 2 NOTE, 1 ERROR2026-04-18

Show 3 earlier changesHide 3 earlier changes

NOTE12 OK, 2 NOTE2026-04-10
ERROR11 OK, 2 NOTE, 1 ERROR2026-04-09
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.2.5

README· In the repository, left out of the releaseVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 0.2.5Citation fileNoWebsiteYes · pkgdown

The repository also keeps web-only articles.

Help pages: 12
Examples that run: 100%12 run in a plain check
Exported functions with examples: 100%
Documented parameters: 99%
Return-value docs: 92%
Help pages citing references: 50%

Vignettes (1)

uwot

How these are measured

Downloads

752.4K

CRAN downloads in the past year

Rank #444 · ~2.1K/day · ~62.7K/mo

Releases R versions

Daily download trend is not available in this view yet.

65.9K30 days

185.3K90 days

752.4K1 year

Compare downloads with other packages →

Also on28.1K r2u10 autocran212K conda_forge737 c2d4u

How downloads are counted

Repository

jlmelville/uwot ↗Account: jlmelville

370Stars

30Forks

15Open issues

0Open PRs

26Releases

1,075Commits

12Commit identities

rumapdimensionality-reduction

License file reads as GPL-3.0 · 1,075 commits · Last activity 2026-10-04 · +0.3% stars, 30d · Default branch at 0.2.5.9000, ahead of CRAN 0.2.5 (checked 2026-10-11)

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 232
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-10-15 · 3462026-10-15 · 370

How these are measured

PracticesBeta

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

Checks run against github.com/jlmelville/uwot on 2026-10-11.

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 (3)

pkgdown

GitHub Pages site last deployed 2026-10-04 · The repository has a site deploy workflow

pkgdown site last built 2026-10-04

Coverage (1)

Coverage reporting (Codecov)

CRAN release process (2)

cran-comments.mdrevdep/

Show all practicesHide 1 practice

Lint, format, editor (1)

Lint workflow

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Installing uwot adds 10 packages (8 with compiled code, 19 MB of source tarballs). Heaviest: BH 14 MB, Rcpp 1.8 MB, RcppEigen 1.7 MB.

Depends (1)

Matrix

Imports (6)

FNN irlbamethodsRcpp RcppAnnoy RSpectra

LinkingTo (4)

dqrng Rcpp RcppAnnoy RcppProgress

Suggests (7)

bigstatsr covr knitr RcppHNSW rmarkdown rnndescent testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

27direct

50indirect

Imports 27

Suggested by 33

Show the 48 most downloaded packagesHide the 48 most downloaded packages

Depends, Imports or LinkingTo, most downloaded first

Suggests, most downloaded first

factoextra graphlayouts tidydr rbiom pagoda2 bundle conos solitude specmine ProjectionBasedClustering MiscMetabar myTAI ggmlR healthyR.ai langevitour huggingfaceR gedi2 dyndimred textplot inferCSN doc2vec

and 12 more packages that suggest it on CRAN ↗

How these are counted

Code & Tests

People & History

People (7)

James Melville

Mohamed Nadhir Djekidel

Contributor · added in 0.1.5

Dirk Eddelbuettel

Contributor · added in 0.1.15

Hugo Gruson

Contributor · added in 0.2.4

Yuhan Hao

Contributor · added in 0.1.9

Aaron Lun

Contributor · added in 0.1.5

Wouter van der Bijl

Contributor · added in 0.2.3

Releases (17)

Pick two releases to compare their code metrics.

0.2.5Latest
record
2026-08-29 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
0.2.4
record
2025-11-10 · diff ↗
R
R 4.5.0 released · 2025-04-11
0.2.3
record
2025-02-24 · diff ↗
R
R 4.4.0 released · 2024-04-24
0.2.2
record
2024-04-21 · diff ↗
0.2.1
record
2024-04-15 · diff ↗ ·
added 1 export
umap2
0.1.16
record
2023-06-29 · diff ↗
0.1.15
record
2023-06-26 · diff ↗ ·
added 3 exports
optimize_graph_layout, simplicial_set_intersect, simplicial_set_union
R
R 4.3.0 released · 2023-04-21
0.1.14
record
2022-08-22 · diff ↗ ·
added 1 export
similarity_graph
0.1.13
record
2022-08-16 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.1.11
record
2021-12-02 · diff ↗
R
R 4.1.0 released · 2021-05-18

Show 10 earlier eventsHide 10 earlier events

0.1.10
record
2020-12-15 · diff ↗
0.1.9
record
2020-11-15 · diff ↗
R
R 4.0.0 released · 2020-04-24
0.1.8
record
2020-03-16 · diff ↗ ·
added 1 export
unload_uwot
0.1.5
record
2019-12-04 · diff ↗
0.1.4
record
2019-09-23 · diff ↗
R
R 3.6.0 released · 2019-04-26
0.1.3
record
2019-04-08 · diff ↗
0.1.2
record
2019-04-06
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2019-04-06
Total releases: 17 / 7 yrs
License: GPL (>= 3) OSI
Download size: 604 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("uwot")

Format

Melville, J., Djekidel, M. N., Eddelbuettel, D., Gruson, H., Hao, Y., Lun, A., & van der Bijl, W. (2026). uwot: The Uniform Manifold Approximation and Projection (UMAP) Method for Dimensionality Reduction (Version 0.2.5) [Computer software]. https://doi.org/10.32614/CRAN.package.uwot

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 uwot version 0.2.5 [Data set]. HJJB, LLC. Data release v2026-10-17. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-17, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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