R Observatory: Metrics for jackalope version 1.1.6

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

jackalope

1.1.6

A Swift, Versatile Phylogenomic and High-Throughput Sequencing Simulator

0packages depend

9.6Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Lucas A. NellFirst published 2019-06-0412 releasesCRAN page ↗GitHub ↗

Simply and efficiently simulates (i) variants from reference genomes and (ii) reads from both Illumina https://www.illumina.com/ and Pacific Biosciences (PacBio) https://www.pacb.com/ platforms. It can either read reference genomes from FASTA files or simulate new ones. Genomic variants can be simulated using summary statistics, phylogenies, Variant Call Format (VCF) files, and coalescent simulations—the latter of which can include selection, recombination, and demographic fluctuations. 'jackalope' can simulate single, paired-end, or mate-pair Illumina reads, as well as PacBio reads. These simulations include sequencing errors, mapping qualities, multiplexing, and optical/polymerase chain reaction (PCR) duplicates. Simulating Illumina sequencing is based on ART by Huang et al. (2012) doi:10.1093/bioinformatics/btr708. PacBio sequencing simulation is based on SimLoRD by Stöcker et al. (2016) doi:10.1093/bioinformatics/btw286. All outputs can be written to standard file formats.

Install

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

install.packages("jackalope", 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("lucasnell/jackalope")

Development version from lucasnell/jackalope. 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-jackalope

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: 9.3 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.54

not tracked

Coverage

100%

Documentation · exports

3

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
OK2026-07-30
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-07-29
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-12
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 7 earlier snapshots

ERROR2026-06-07
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-02
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-04-10
8 OK · 6 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-09
7 OK · 6 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 556 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 71%
Documented parameters: 99%
Return-value docs: 88%
References docs: 26%

Downloads

9.6K

CRAN downloads in the past year

Rank #4,405 · ~26/day · ~798/mo

Releases R versions

Daily download trend is not available in this view yet.

40330 days

1.8K90 days

9.6K1 year

Compare downloads with other packages →

Also on418 r2u

Repository

GitHub ↗ lucasnell/jackalope

8Stars

3Forks

0Open issues

0Open PRs

10Releases

905Commits

2Contributors

905 commits · Last activity 2025-09-30

Stars over time

2023-04-03 · 82026-07-07 · 8

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/lucasnell/jackalope on 2026-08-23.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Docs source (1)

README.Rmd

Show all practices

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.10

Imports (3)

ape R6 Rcpp

LinkingTo (4)

Rcpp RcppArmadillo RcppProgress Rhtslib

Suggests (6)

coala knitr markdown rmarkdown scrm testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

Lucas A. Nell

Copyright holder, Author, Maintainer

Authors (1)

Lucas A. Nell

Copyright holder, Author, Maintainer

Copyright holders (1)

Lucas A. Nell

Copyright holder, Author, Maintainer

Listed in earlier versions (1)

Lucas A.

no longer listed · 0.1.0 to 1.1.6

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
1.1.6Latest
2025-09-29 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.1.5
2023-11-28 · diff ↗
1.1.4
2023-10-15 · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
1.1.3
2021-07-06 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.1.2
2021-02-10 · diff ↗
1.1.1
2020-06-15 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.1.0
2020-02-28 · diff ↗
1.0.0
2019-11-22 · diff ↗
0.1.3
2019-10-18 · diff ↗

Show 6 earlier events

0.1.2
2019-07-11 · diff ↗
unarchivedReturned to CRAN
2019-07-11
archivedRemoved from CRAN
2019-06-29
memory-access issues remained
0.1.1
2019-06-12 · diff ↗
0.1.0
2019-06-04
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-06-04
Total releases: 12 / 7 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 2.10
Bundled data: 1.0 KB / 1 file
Download size: 1.7 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("jackalope")

Format

Nell, L. A. (2025). jackalope: A Swift, Versatile Phylogenomic and High-Throughput Sequencing Simulator (Version 1.1.6) [Computer software]. https://doi.org/10.32614/CRAN.package.jackalope

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 jackalope version 1.1.6 [Data set]. HJJB, LLC. Data release v2026-08-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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