R Observatory: Metrics for geneviewer version 0.1.11

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

geneviewer

0.1.11Package record

Gene Cluster Visualizations

0packages depend

3.7Kdownloads / year

39.2%test coverage

13/13flavors OK

Overview

About

Maintained by Niels van der VeldenCRAN page ↗GitHub ↗Issues ↗

Provides tools for plotting gene clusters and transcripts by importing data from GenBank, FASTA, and GFF files. It performs BLASTP and MUMmer alignments [Altschul et al. (1990) doi:10.1016/S0022-2836(05)80360-2; Delcher et al. (1999) doi:10.1093/nar/27.11.2369] and displays results on gene arrow maps. Extensive customization options are available, including legends, labels, annotations, scales, colors, tooltips, and more.

Changes in 0.1.11

Enhancements:

Fix for setting tooltip and legend to FALSE
Fix for links displayed behind graph
Fix for getting proper strand directions in .gbk files
Fix for passing additional CSS styles
Add github actions to build Wasm assets for Shinylive

From NEWS.md in the release

Install

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

install.packages("geneviewer", 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("nvelden/geneviewer")

Development version from nvelden/geneviewer. 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-geneviewer

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-geneviewer

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-geneviewer

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: 2.1 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-07
OK12 OK2026-04-25

Show 1 earlier changeHide 1 earlier change

NOTE13 OK, 1 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.11

READMEYes · 203 wordsVignettes· In the repository, left out of the releaseNEWSYes · 100% structured · mentions 0.1.11Citation fileNo

Help pages: 39 (1 internal)
Examples that run: 74%23 run in a plain check (1 of them under a condition) · 2 only when donttest examples are enabled (R CMD check --as-cran) · 6 never run
Exported functions with examples: 94%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 5%

How these are measured

Downloads

3.7K

CRAN downloads in the past year

Rank #8,157 · ~10/day · ~312/mo

Releases R versions

Daily download trend is not available in this view yet.

38330 days

1.1K90 days

3.7K1 year

Compare downloads with other packages →

Also on99 r2u5 autocran

How downloads are counted

Repository

nvelden/geneviewer ↗Account: nvelden

102Stars

5Forks

3Open issues

0Open PRs

11Releases

409Commits

1Commit identities

geneticsr

409 commits · Last activity 2026-10-24 · 0% stars, 30d · Default branch at 0.2.0, ahead of CRAN 0.1.11 (checked 2026-10-21)

Responsiveness

How these are sampled

PRs merged (all time): 0%
Median days to close, 50 most recently updated closed issues: 4
Median days to close, 50 most recently updated closed PRs: 64

Stars over time

2025-10-16 · 912026-09-23 · 102

How these are measured

PracticesBeta

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

Checks run against github.com/nvelden/geneviewer on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Docs source (2)

pkgdown

GitHub Pages site last deployed 2026-10-21

CRAN release process (1)

cran-comments.md

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

AI coding toolsBeta

This repository shows signs of AI coding tools.

Claude Codefirst seen 2026-10-20
Commits: at least 74 crediting it in the message

Models named in its commits

Claude Opus 5.574 commits · Oct 2026

Counts are commits, not lines of code. Commits by a tool's accounts count once across all of its accounts. Commits crediting it are the largest count among its credit lines, a minimum.How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Installing geneviewer adds 42 packages (24 with compiled code, 35 MB of source tarballs). Heaviest: stringi 11 MB, bslib 5.6 MB, sass 2.9 MB.

Depends (1)

R >= 3.5.0

Imports (6)

htmlwidgets fontawesome magrittr dplyr tidyr rlang

LinkingTo (0)

none

Suggests (7)

knitr rmarkdown shiny biomaRt pwalign Biostrings testthat

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 (1)

Niels van der Velden

Author, Maintainer since 0.1.10 (2025)

Releases (2)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.1.11Latest
record
2025-10-01 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
0.1.10
record
2025-01-10
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2025-01-10
Total releases: 2 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5.0
Bundled data: 62 KB / 6 files
Download size: 1.0 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("geneviewer")

Format

van der Velden, N. (2025). geneviewer: Gene Cluster Visualizations (Version 0.1.11) [Computer software]. https://doi.org/10.32614/CRAN.package.geneviewer

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 geneviewer version 0.1.11 [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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