R Observatory: Metrics for PACVr version 1.1.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PACVr

1.1.5

Plastome Assembly Coverage Visualization

0packages depend

3.3Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Michael GruenstaeudlFirst published 2019-07-2612 releasesCRAN page ↗GitHub ↗

Visualizes the coverage depth of a complete plastid genome as well as the equality of its inverted repeat regions in relation to the circular, quadripartite genome structure and the location of individual genes. For more information, please see Gruenstaeudl and Jenke (2020) doi:10.1186/s12859-020-3475-0.

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("PACVr", 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("michaelgruenstaeudl/PACVr")

Development version from michaelgruenstaeudl/PACVr. 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-pacvr

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

Health

CRAN checks

13OK

Slowest check: 8.7 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.03

not tracked

Coverage

100%

Documentation · exports

14

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-10
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 4 earlier snapshots

ERROR2026-05-03
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-26
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-31
10 OK · 0 NOTE · 3 WARNING · 1 ERROR · 0 FAILURE
WARNING2026-03-10
11 OK · 0 NOTE · 3 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 50%
References docs: 0%

Downloads

3.3K

CRAN downloads in the past year

Rank #8,264 · ~9/day · ~272/mo

Releases R versions

Daily download trend is not available in this view yet.

17830 days

1.1K90 days

3.3K1 year

Compare downloads with other packages →

Also on165 r2u

Repository

GitHub ↗ michaelgruenstaeudl/pacvr

5Stars

5Forks

0Open issues

0Open PRs

12Releases

584Commits

5Contributors

genome-analysisgenomicsgenomics-data-visualizationorganellesequencing-coverager

584 commits · Last activity 2026-04-18 · 0% stars, 30d

Stars over time

2024-04-16 · 32026-07-07 · 5

Repository practices

Upstream repositoryBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/michaelgruenstaeudl/pacvr on 2026-08-09.

Continuous integration (1)

GitHub Actions

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (14)

Biostrings dplyr GenomicAlignments GenomicRanges IRanges logger read.gb RCircos (>= 1.2.0)grDevicesstatsutilstidyr pwalign R6

LinkingTo (0)

none

Suggests (2)

testthat rentrez

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (3)

Maintainer (1)

Michael Gruenstaeudl

Author, Maintainer

Authors (1)

Michael Gruenstaeudl

Author, Maintainer

Contributors (2)

Nils Jenke

Contributor

Gregory Smith

Contributor · added in 1.0.5

Package Timeline

12 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.1.5Latest
2026-04-18 · current release · diff ↗
1.1.4
2026-03-31 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.0.11
2024-04-10 · diff ↗
1.0.8
2024-02-28 · diff ↗
1.0.7
2024-02-05 · diff ↗
1.0.6
2024-01-09 · diff ↗
1.0.5
2023-12-08 · diff ↗
unarchivedReturned to CRAN
2023-12-08
archivedRemoved from CRAN
2023-11-01
requires unavailable package 'genbankr'
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
0.9.4
2020-11-22 · diff ↗

Show 6 earlier events

R
R 4.0.0 released · 2020-04-24
0.9.2
2020-02-21 · diff ↗
0.9.1
2020-02-09 · diff ↗
0.8.2
2019-09-13 · diff ↗
0.8.1
2019-07-26
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-07-26
Total releases: 12 / 7 yrs
License: BSD 3-clause License + file LICENSE
Minimum R: ≥ 3.5.0
Download size: 4.1 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("PACVr")

Format

Gruenstaeudl, M., Jenke, N., & Smith, G. (2026). PACVr: Plastome Assembly Coverage Visualization (Version 1.1.5) [Computer software]. https://doi.org/10.32614/CRAN.package.PACVr

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 PACVr version 1.1.5 [Data set]. HJJB, LLC. Data release v2026-08-15. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-15, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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