R Observatory: Metrics for PACVr version 1.1.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PACVr

1.1.5Package record

Plastome Assembly Coverage Visualization

0packages depend

3.9Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Michael GruenstaeudlCRAN page ↗GitHub ↗Issues ↗

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. 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

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 8.9 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 ERROR2026-06-08
OK13 OK2026-05-10

Show 4 earlier changesHide 4 earlier changes

ERROR12 OK, 1 ERROR2026-05-03
OK12 OK2026-04-26
ERROR10 OK, 3 WARNING, 1 ERROR2026-03-31
WARNING11 OK, 3 WARNING2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.5

READMENoVignettesYes · 1 · staticNEWSNoCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 3 (1 internal)includes a package overview page
Examples that run: 0%1 never run
Exported functions with examples: 50%
Documented parameters: 100%
Return-value docs: 50%
Help pages citing references: 0%

Vignettes (1)

PACVr PDF

How these are measured

Downloads

3.9K

CRAN downloads in the past year

Rank #7,617 · ~11/day · ~328/mo

Releases R versions

Daily download trend is not available in this view yet.

47330 days

1.2K90 days

3.9K1 year

Compare downloads with other packages →

Also on118 r2u

How downloads are counted

Repository

michaelgruenstaeudl/SOFTWARE_PACVr ↗Account: michaelgruenstaeudl

Moved from michaelgruenstaeudl/pacvr.

5Stars

5Forks

0Open issues

0Open PRs

12Releases

584Commits

5Commit identities

genome-analysisgenomicsgenomics-data-visualizationorganellesequencing-coverager

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

Responsiveness

How these are sampled

PRs merged (all time): 81%
Median days to close, 50 most recently updated closed issues: 2
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2025-10-21 · 42026-07-07 · 5

How these are measured

PracticesBeta

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

Checks run against github.com/michaelgruenstaeudl/pacvr 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

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

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Installing PACVr adds 32 packages (19 with compiled code, 25 MB of source tarballs). Heaviest: stringi 11 MB, RCircos 1.8 MB, logger 1.1 MB. 5 more not on CRAN are not measured.

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.

How these are counted

Code & Tests

People & History

People (3)

Michael Gruenstaeudl

Author, Maintainer since 0.8.1 (2019)

Nils Jenke

Contributor

Gregory Smith

Contributor · added in 1.0.5

Releases (12)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.1.5Latest
record
2026-04-18 · current release · diff ↗
1.1.4
record
2026-03-30 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.0.11
record
2024-04-10 · diff ↗
1.0.8
record
2024-02-28 · diff ↗
1.0.7
record
2024-02-05 · diff ↗
1.0.6
record
2024-01-09 · diff ↗
unarchivedReturned to CRAN
2023-12-08
1.0.5
record
2023-12-08 · diff ↗ ·
added 1 export
RCircos.Env
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
record
2020-11-22 · diff ↗ ·
removed 1 export
RCircos.Env

Show 6 earlier eventsHide 6 earlier events

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

Cite

Cite this package

Run in R for the authors' entry:

citation("PACVr")

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

It points to 10.1186/s12859-020-3475-0.

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 v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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