R Observatory: Metrics for ips version 0.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ips

0.1.1

Interfaces to Phylogenetic Software in R

0packages depend

11.9Kdownloads / year

–test coverage

8/13checks pass

Overview

About

Maintained by Martin R. SmithFirst published 2014-11-105 releasesCRAN page ↗GitHub ↗

Functions that wrap popular phylogenetic software for sequence alignment, masking of sequence alignments, and estimation of phylogenies and ancestral character states.

Install

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

install.packages("ips", 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("heibl/ips")

Development version from heibl/ips. 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-ips

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

# 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-ips

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-ips

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

Health

CRAN checks

5NOTE8OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc
NOTE r-devel-windows-x86_64

Slowest check: 3.0 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

8

Dependencies · direct

Check history

NOTE2026-07-16
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-07-11
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-19
11 OK · 0 NOTE · 0 WARNING · 2 ERROR · 0 FAILURE
OK2026-06-13
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-04
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 3 earlier snapshots

OK2026-05-14
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-05-11
11 OK · 0 NOTE · 0 WARNING · 2 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 318 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 96%
Documented parameters: 100%
Return-value docs: 79%
References docs: 42%

Downloads

11.9K

CRAN downloads in the past year

Rank #4,094 · ~33/day · ~989/mo

Releases R versions

Daily download trend is not available in this view yet.

50930 days

2K90 days

11.9K1 year

Compare downloads with other packages →

Also on122 r2u26 autocran1.6K conda_forge55 c2d4u

Repository

GitHub ↗ heibl/ips

12Stars

4Forks

5Open issues

2Open PRs

0Releases

97Commits

5Contributors

97 commits · Last activity 2026-06-25

PRs over time

2026-07-09 · 12026-07-30 · 2

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/heibl/ips on 2026-08-23.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (2)

cran-comments.mdrevdep/

Docs source (1)

README.Rmd

Show all practices

Research and citation (1)

codemeta.json

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Depends (2)

R >= 3.5.0ape

Imports (7)

data.table dplyr phangorn plyr rlang tibble XML

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (4)

Maintainer (1)

Martin R. Smith

Contributor, Maintainer · added in 0.0.13

Authors (3)

Natalie Cusimano

Author · added in 0.0.11

Christoph Heibl

Author

Franz-Sebastian Krah

Author · added in 0.0.11

Contributors (1)

Martin R. Smith

Contributor, Maintainer · added in 0.0.13

Package Timeline

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

0.1.1Latest
2026-07-08 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
0.0.13
2026-02-23 · diff ↗
unarchivedReturned to CRAN
2026-02-23
archivedRemoved from CRAN
2025-11-28
issues were not corrected despite reminders
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
0.0.12
2024-04-23 · diff ↗
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
R
R 4.0.0 released · 2020-04-24
0.0.11
2019-07-04 · diff ↗
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21

Show 4 earlier events

R
R 3.3.0 released · 2016-05-03
R
R 3.2.0 released · 2015-04-16
0.0-7
2014-11-10
R
R 3.1.0 released · 2014-04-10

Package metadata

First published: 2014-11-10
Total releases: 5 / 12 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 12 KB / 6 files
Download size: 120 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Phylogenetics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("ips")

Format

Smith, M. R., Cusimano, N., Heibl, C., & Krah, F. (2026). ips: Interfaces to Phylogenetic Software in R (Version 0.1.1) [Computer software]. https://doi.org/10.32614/CRAN.package.ips

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 ips version 0.1.1 [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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