R Observatory: Metrics for WebGestaltR version 1.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

WebGestaltR

1.0.1Package record

Gene Set Analysis Toolkit WebGestaltR

0packages depend

9.6Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Zhiao ShiCRAN page ↗GitHub ↗Website ↗

The web version WebGestalt https://www.webgestalt.org supports 12 organisms, 354 gene identifiers and 321,251 function categories. Users can upload the data and functional categories with their own gene identifiers. In addition to the Over-Representation Analysis, WebGestalt also supports Gene Set Enrichment Analysis and Network Topology Analysis. The user-friendly output report allows interactive and efficient exploration of enrichment results. The WebGestaltR package not only supports all above functions but also can be integrated into other pipeline or simultaneously analyze multiple gene lists.

Changes in 1.0.1

Bug fixes

**Fixed installation failure on systems where the Rust toolchain is not on the default PATH.** src/Makevars.in ran rustc --version before extending PATH with ~/.cargo/bin. Each line of a make recipe runs in its own shell, so that extension — applied only to the cargo build line — never reached the version check, which failed with rustc: No such file or directory and aborted the build before cargo ran. Both the Unix and Windows Makevars now share one PATH definition used by every step.

From NEWS.md in the release

Install

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

install.packages("WebGestaltR", 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("bzhanglab/WebGestaltR")

Development version from bzhanglab/WebGestaltR. 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-webgestaltr

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-WebGestaltR

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-WebGestaltR

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: 6.4 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-06
ERROR8 OK, 1 NOTE, 4 ERROR2026-07-31
OK14 OK2026-04-22
ERROR13 OK, 1 ERROR2026-04-18
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.1

READMEYes · 472 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 1.0.1Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 42 (20 internal)includes a package overview page
Examples that run: 0%1 never run
Exported functions with examples: 6%
Documented parameters: 97%
Return-value docs: 94%
Help pages citing references: 0%

Vignettes (1)

installation HTML

How these are measured

Downloads

9.6K

CRAN downloads in the past year

Rank #3,682 · ~26/day · ~796/mo

Releases R versions

Daily download trend is not available in this view yet.

86430 days

2.7K90 days

9.6K1 year

Compare downloads with other packages →

Also on497 r2u1 autocran3.4K conda_forge48 c2d4u

How downloads are counted

Repository

bzhanglab/webgestaltr ↗Organization: bzhanglab

38Stars

15Forks

15Open issues

0Open PRs

1Releases

532Commits

7Commit identities

532 commits · Last activity 2026-08-10 · 0% stars, 30d · Default branch at 1.1.0, ahead of CRAN 1.0.1 (checked 2026-10-22)

Responsiveness

How these are sampled

PRs merged (all time): 86%
Median days to close, 50 most recently updated closed issues: 5
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-07-02 · 372026-07-07 · 38

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/bzhanglab/webgestaltr on 2026-10-22.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Governance and community (1)

Issue templates

Docs source (3)

pkgdown

GitHub Pages site · The repository has a site deploy workflow

CRAN release process (1)

cran-comments.md

Show all practicesHide 1 practice

Lint, format, editor (2)

lintrRStudio project

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

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Installing WebGestaltR adds 49 packages (28 with compiled code, 29 MB of source tarballs). Heaviest: stringi 11 MB, mathjaxr 3.0 MB, Rcpp 1.8 MB.

Depends (1)

R >= 4.0

Imports (16)

methodsdplyr doRNG readrparalleldoParallel foreach jsonlite httr rlang svglite whisker apcluster Rcppclusterpoolr

LinkingTo (1)

Rcpp

Suggests (2)

knitr rmarkdown

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 (6)

Zhiao Shi

Author, Maintainer since 1.0.0 (2026) · added in 0.4.1

John Elizarraras

Author · added in 1.0.0

Yuxing Liao

Author · added in 0.3.0

Jing Wang

Author

Eric Jaehnig

Contributor · added in 0.4.1

Quanhu Sheng

Contributor · added in 0.4.1

Previously maintained by Yuxing Liao (0.3.0 to 0.4.6) and Jing Wang (0.0.5 to 0.1.1).

Releases (16)

Pick two releases to compare their code metrics.

1.0.1Latest
record
2026-08-05 · current release · diff ↗
1.0.0
record
2026-07-30 · diff ↗ ·
added 2 exports
WebGestaltRMultiOmics, multiswGsea
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
0.4.6
record
2023-06-01 · diff ↗
R
R 4.3.0 released · 2023-04-21
0.4.5
record
2023-02-16 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
0.4.4
record
2020-07-24 · diff ↗
R
R 4.0.0 released · 2020-04-24
0.4.3
record
2020-01-16 · diff ↗
0.4.2
record
2019-09-17 · diff ↗
0.4.1
record
2019-07-03 · diff ↗
0.4.0
record
2019-04-27 · diff ↗

Show 13 earlier eventsHide 13 earlier events

R
R 3.6.0 released · 2019-04-26
0.3.1
record
2019-03-15 · diff ↗ ·
added 1 export
loadGeneSet
0.3.0
record
2019-01-18 · diff ↗ ·
removed 1 export
readGMT

added 12 exports
WebGestaltRBatch, affinityPropagation, goSlimSummary, idMapping, idToSymbol, listArchiveUrl, listIdType, prepareGseaInput, prepareInputMatrixGsea, readGmt, swGsea, weightedSetCover
R
R 3.5.0 released · 2018-04-23
0.1.1
record
2017-05-11 · diff ↗
0.1.0
record
2017-05-02 · diff ↗
0.0.9
record
2017-04-26 · diff ↗
R
R 3.4.0 released · 2017-04-21
unarchivedReturned to CRAN
2017-03-08
0.0.8
record
2017-03-08 · diff ↗
archivedRemoved from CRAN
2017-03-05
policy violation
0.0.5
record
2017-02-26
R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2017-02-26
Total releases: 16 / 9 yrs
License: LGPL
Minimum R: ≥ 4.0
Download size: 4.2 MB

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' entry:

citation("WebGestaltR")

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

It points to 10.1093/nar/gkae456.

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 WebGestaltR version 1.0.1 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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