R Observatory: Metrics for viewpoly version 1.0.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

viewpoly

1.0.3Package record

A Shiny App to Visualize Genetic Maps and QTL Analysis in Polyploid Species

0packages depend

3Kdownloads / year

37.0%test coverage

13/13flavors OK

Overview

About

Maintained by Cristiane TanigutiCRAN page ↗GitHub ↗Issues ↗

Provides a graphical user interface to integrate, visualize and explore results from linkage and quantitative trait loci analysis, together with genomic information for autopolyploid species. The app is meant for interactive use and allows users to optionally upload different sources of information, including gene annotation and alignment files, enabling the exploitation and search for candidate genes in a genome browser. In its current version, 'VIEWpoly' supports inputs from 'MAPpoly', 'polymapR', 'diaQTL', 'QTLpoly', 'polyqtlR', 'GWASpoly', and 'HIDECAN' packages.

Changes in 1.0.3

Avoid Rmarkdown links to redirect app page to home
Add helper function to prevent includeMarkdown to write temporary files into user library directory
Increase color accessibility on buttons
Add GitHub actions to build shinyapps.io when main is updated

From NEWS.md in the release

Install

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

install.packages("viewpoly", 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("Breeding-Insight/viewpoly")

Development version from Breeding-Insight/viewpoly. 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-viewpoly

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-viewpoly

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-viewpoly

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: 2.8 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-09-10
ERROR9 OK, 3 NOTE, 1 ERROR2026-07-12
NOTE13 NOTE2026-06-09
ERROR12 NOTE, 1 ERROR2026-06-08
NOTE3 OK, 11 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.3

READMEYes · 866 wordsVignettesNoNEWSYes · 100% structured · mentions 1.0.3Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 42 (40 internal)
Examples that run: no examples
Exported functions with examples: 0%
Documented parameters: 100%
Return-value docs: 0%
Help pages citing references: 10%

How these are measured

Downloads

3K

CRAN downloads in the past year

Rank #8,069 · ~8/day · ~253/mo

Releases R versions

Daily download trend is not available in this view yet.

39830 days

1.1K90 days

3K1 year

Compare downloads with other packages →

Also on132 r2u6 autocran

How downloads are counted

Repository

breeding-insight/viewpoly ↗Organization: Breeding-InsightFork of mmollina/viewpoly

0Stars

0Forks

0Open PRs

1Releases

351Commits

6Commit identities

License file reads as GPL-3.0 · 351 commits · Last activity 2026-09-02

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: 0

Commits over time

2026-07-12 · 3422026-09-15 · 351

How these are measured

PracticesBeta

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

Checks run against github.com/breeding-insight/viewpoly on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Coverage (1)

Coverage reporting

Reproducibility and dev environment (1)

Dockerfile

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Show all practicesHide 1 practice

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

26 external dependencies (excludes base and recommended)

Installing viewpoly adds 138 packages (63 with compiled code, 122 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (1)

R >= 4.1.0

Imports (23)

shiny shinyjs shinyWidgets config golem JBrowseR dplyr tidyr DT ggplot2 ggpubr plotly vroom abind reshape2statsutilshttr curl hidecan purrr bs4Dash markdown

LinkingTo (0)

none

Suggests (5)

testthat rlang pkgload vdiffr shinytest

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (11)

Cristiane Taniguti

Author, Maintainer since 0.1.0 (2021)

Olivia Angelin-Bonnet

Author · added in 0.4.1

Jeekin Lau

Author

Marcelo Mollinari

Author

Gabriel de Siqueira Gesteira

Author · added in 0.3.1

David Byrne

Contributor

Oscar Riera-Lizarazu

Contributor · added in 0.1.1

Susan Thomson

Contributor · added in 0.4.1

Zhao-Bang Zeng

Contributor

Guilherme da Silva Pereira

Contributor · added in 0.3.1

University of Florida Breeding Insight

Copyright holder · added in 1.0.2

Listed in earlier versions (3)

Show 3 peopleHide 3 people

Gabriel Gesteira

no longer listed · 0.1.0 to 0.2.0

Guilherme Pereira

no longer listed · 0.1.0 to 0.2.0

Oscar Riera-Lizarau

no longer listed · 0.1.0

Releases (8)

Pick two releases to compare their code metrics.

1.0.3Latest
record
2026-09-02 · current release · diff ↗
1.0.2
record
2026-07-10 · diff ↗
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
0.4.1
record
2024-03-28 · diff ↗
R
R 4.3.0 released · 2023-04-21
0.3.2
record
2022-11-01 · diff ↗
0.3.1
record
2022-10-11 · diff ↗
0.2.0
record
2022-06-07 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.1.1
record
2022-01-03 · diff ↗
0.1.0
record
2021-12-16
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-12-16
Total releases: 8 / 5 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.1.0
Download size: 7.9 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("viewpoly")

Format

Taniguti, C., Angelin-Bonnet, O., Breeding Insight, U. o. F., Byrne, D., Lau, J., Mollinari, M., Riera-Lizarazu, O., Thomson, S., Zeng, Z., da Silva Pereira, G., & de Siqueira Gesteira, G. (2026). viewpoly: A Shiny App to Visualize Genetic Maps and QTL Analysis in Polyploid Species (Version 1.0.3) [Computer software]. https://doi.org/10.32614/CRAN.package.viewpoly

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 viewpoly version 1.0.3 [Data set]. HJJB, LLC. Data release v2026-10-20. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-20, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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