R Observatory: Metrics for PopGenome version 2.7.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2022-11-22. Its history is shown below.

Reason: issues were not corrected in time

Details below reflect version 2.7.5, its last release before removal.

PopGenome

2.7.5

An Efficient Swiss Army Knife for Population Genomic Analyses

1packages depend

–downloads / year

–test coverage

–checks pass

Overview

About

Maintained by Bastian Pfeifer27 releasesCRAN page ↗

Provides efficient tools for population genomics data analysis, able to process individual loci, large sets of loci, or whole genomes. PopGenome DOI:10.1093/molbev/msu136 not only implements a wide range of population genetics statistics, but also facilitates the easy implementation of new algorithms by other researchers. PopGenome is optimized for speed via the seamless integration of C code.

Install

R (source archive)Ubuntu (r2u)openSUSE (OBS)

url <- "https://cran.r-project.org/src/contrib/Archive/PopGenome/PopGenome_2.7.5.tar.gz"
pkgFile <- "PopGenome_2.7.5.tar.gz"
download.file(url, pkgFile)
install.packages(pkgFile, type = "source", repos = NULL)

This package is no longer on CRAN, so install.packages() cannot fetch it by name. This downloads the last archived source (2.7.5) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

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-popgenome

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

# 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-PopGenome

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

CRAN check results are not tracked yet.

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

2

Dependencies · direct

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 98%
Return-value docs: 75%
References docs: 30%

Downloads

Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on306 r2u165 autocran1.5K conda_forge423 bioconda

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Depends (2)

R >= 2.14.2ff

Imports (1)

methods

LinkingTo (0)

none

Suggests (5)

parallelbigmemory BASIX WhopGenome BlockFeST

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

–indirect (not tracked)

coala

Code & Tests

Datasets

People & History

People (4)

Maintainer (1)

Bastian Pfeifer

Author, Maintainer

Authors (1)

Bastian Pfeifer

Author, Maintainer

Contributors (3)

Ulrich Wittelsbuerger

Contributor

Heng Li

Contributor · added in 2.1.5

Bob Handsaker

Contributor · added in 2.1.5

Package Timeline

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

R
R 4.3.0 released · 2023-04-21
archivedRemoved from CRAN
2022-11-22
issues were not corrected in time
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
2.7.5
2020-01-31 · diff ↗
unarchivedReturned to CRAN
2020-01-31
archivedRemoved from CRAN
2020-01-12
check issues persisted in re-submission LTO and rchk
2.7.2
2020-01-10 · diff ↗
unarchivedReturned to CRAN
2020-01-10
archivedRemoved from CRAN
2020-01-09
check errors were not corrected in time
2.7.1
2019-05-11 · diff ↗
R
R 3.6.0 released · 2019-04-26
2.6.1
2018-05-20 · diff ↗
unarchivedReturned to CRAN
2018-05-20
archivedRemoved from CRAN
2018-05-03
check problems were not corrected despite reminders

Show 33 earlier events

R
R 3.5.0 released · 2018-04-23
2.2.4
2017-07-03 · diff ↗
R
R 3.4.0 released · 2017-04-21
2.2.3
2017-03-24 · diff ↗
2.2.2
2017-03-15 · diff ↗
2.2.0
2017-02-11 · diff ↗
R
R 3.3.0 released · 2016-05-03
2.1.6
2015-05-01 · diff ↗
2.1.5
2015-05-01 · diff ↗
R
R 3.2.0 released · 2015-04-16
R
R 3.1.0 released · 2014-04-10
R
R 3.0.0 released · 2013-04-03
2.1.0
2013-03-17 · diff ↗
2.0.9
2013-03-17 · diff ↗
2.0.8
2013-03-17 · diff ↗
2.0.7
2013-03-17 · diff ↗
2.0.6
2013-03-17 · diff ↗
2.0.5
2013-03-17 · diff ↗
2.0.4
2013-03-17 · diff ↗
2.0.3
2013-03-17 · diff ↗
2.0
2013-03-17 · diff ↗
1.3.0
2013-03-17 · diff ↗
1.2.6
2013-03-17 · diff ↗
1.2.5
2013-03-17 · diff ↗
1.2.3
2013-02-17 · diff ↗
1.2.1
2012-12-27 · diff ↗
R
R 2.15.0 released · 2012-03-30
R
R 2.14.0 released · 2011-10-31
R
R 2.13.0 released · 2011-04-13
1.2.0
2011-03-17 · diff ↗
1.1
2011-03-17 · diff ↗
1.0
2011-03-17
R
R 2.12.0 released · 2010-10-15

Package metadata

Total releases: 27
License: GPL-3 OSI
Minimum R: ≥ 2.14.2
Bundled data: 9.1 KB / 4 files
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("PopGenome")

Format

Pfeifer, B., Wittelsbuerger, U., Li, H., & Handsaker, B. (n.d.). PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses (Version 2.7.5) [Computer software]. Retrieved August 14, 2026, from https://CRAN.R-project.org/package=PopGenome

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 PopGenome version 2.7.5 [Data set]. HJJB, LLC. Data release v2026-08-13. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-13, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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