R Observatory: Metrics for RNeXML version 2.4.11

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

RNeXML

2.4.11Package record

Semantically Rich I/O for the 'NeXML' Format

1packages dependsuggested by 1

81Kdownloads / year

87.8%test coverage

0/13flavors OK

Overview

About

Maintained by Carl BoettigerCRAN page ↗GitHub ↗Website ↗Issues ↗

Provides access to phyloinformatic data in 'NeXML' format. The package should add new functionality to R such as the possibility to manipulate 'NeXML' objects in more various and refined way and compatibility with 'ape' objects.

Changes in 2.4.11

include local copy of XSD files for validation offline

From NEWS.md in the release

Install

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

install.packages("RNeXML", 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("ropensci/RNeXML")

Development version from ropensci/RNeXML. 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-rnexml

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

# 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-RNeXML

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-RNeXML

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13NOTE

Check messages

NOTERd filesr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64

checkRd: (-1) nexml_get.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nexml_get.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nexml_get.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nexml_get.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nexml_get.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nexml_get.Rd:35: Lost braces in \itemize; meant \describe ?

CRAN check page ↗

Slowest check: 3.9 min · r-oldrel-windows-x86_64

Status changes

NOTE13 NOTE2026-09-08
ERROR12 NOTE, 1 ERROR2026-09-07
NOTE13 NOTE2026-06-09
ERROR12 NOTE, 1 ERROR2026-06-08
NOTE14 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.4.11

READMEYes · 338 wordsVignettesYes · 5 · staticNEWSYes · 33% structured · mentions 2.4.11Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 52 (2 internal)
Examples that run: 67%18 run in a plain check · 9 never run
Exported functions with examples: 61%
Documented parameters: 98%
Return-value docs: 78%
Help pages citing references: 0%

Vignettes (5)

How these are measured

Downloads

81K

CRAN downloads in the past year

Rank #1,450 · ~222/day · ~6.8K/mo

Releases R versions

Daily download trend is not available in this view yet.

5.1K30 days

17.8K90 days

81K1 year

Compare downloads with other packages →

Also on1.1K r2u9 autocran4.2K conda_forge678 bioconda198 c2d4u

How downloads are counted

Repository

ropensci/rnexml ↗Organization: ropensci

15Stars

9Forks

12Open issues

1Open PRs

8Releases

1,018Commits

16Commit identities

rrstatsnexmlphylogeneticsr-package

1,018 commits · Last activity 2024-05-06 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 94%
Median days to close, 50 most recently updated closed issues: 26
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2025-09-26 · 152026-07-07 · 15

How these are measured

PracticesBeta

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

Checks run against github.com/ropensci/rnexml on 2026-10-11.

Continuous integration (5)

GitHub ActionsR CMD check workflowTravis CI (config file)AppVeyorCircleCI

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Governance and community (2)

Code of conduct (inherited from ropensci)Contributing guide

Docs source (3)

README.Rmdpkgdown

GitHub Pages site last deployed 2024-05-06

Coverage (1)

Coverage reporting (Codecov)

Show all practicesHide 3 practices

CRAN release process (1)

cran-comments.md

Research and citation (1)

codemeta.json

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

25 external dependencies (excludes base and recommended)

Installing RNeXML adds 35 packages (26 with compiled code, 26 MB of source tarballs). Heaviest: stringi 11 MB, Rcpp 1.8 MB, ape 1.4 MB.

Depends (3)

R >= 3.0.0apemethods

Imports (11)

XML plyr reshape2 httr (>= 0.3)uuid dplyr tidyr stringr stringi xml2 rlang

LinkingTo (0)

none

Suggests (13)

spelling rdflib geiger phytools knitr rfigshare knitcitations testthat rmarkdown xslt covr taxalight progress

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

17indirect

Imports 1

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

phylobase

Suggests, most downloaded first

rotl

How these are counted

Code & Tests

People & History

People (5)

Carl Boettiger

Maintainer since 1.1-0 (2014), Author

Author

Author

Author

Author

Releases (28)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
2.4.11Latest
record
2023-02-01 · current release · diff ↗
2.4.10
record
2023-01-09 · diff ↗
2.4.9
record
2022-12-16 · diff ↗
2.4.8
record
2022-10-20 · diff ↗
2.4.7
record
2022-05-13 · diff ↗
R
R 4.2.0 released · 2022-04-22
2.4.6
record
2022-02-09 · diff ↗
R
R 4.1.0 released · 2021-05-18
2.4.5
record
2020-06-18 · diff ↗
2.4.4
record
2020-05-10 · diff ↗
R
R 4.0.0 released · 2020-04-24
2.4.3
record
2020-03-01 · diff ↗

Show 25 earlier eventsHide 25 earlier events

2.4.2
record
2020-01-29 · diff ↗
2.4.0
record
2019-11-08 · diff ↗
R
R 3.6.0 released · 2019-04-26
2.3.0
record
2019-01-24 · diff ↗ ·
added 24 exports
expand_prefix, get_all_meta, get_meta, get_metadata_values, nexml, nexml.cell, nexml.char, nexml.characters, nexml.edge, nexml.format, nexml.matrix, nexml.member, nexml.node, nexml.otu, nexml.otus, nexml.polymorphic_states, nexml.row, nexml.seq, nexml.state, nexml.states, nexml.tree, nexml.trees, nexml.uncertain_state, nexml.uncertain_states
2.2.0
record
2018-11-01 · diff ↗
2.1.2
record
2018-08-13 · diff ↗
2.1.1
record
2018-05-07 · diff ↗
2.1.0
record
2018-05-05 · diff ↗
R
R 3.5.0 released · 2018-04-23
2.0.8
record
2017-11-17 · diff ↗
R
R 3.4.0 released · 2017-04-21
2.0.7
record
2016-06-28 · diff ↗
R
R 3.3.0 released · 2016-05-03
2.0.6
record
2016-03-07 · diff ↗
2.0.5
record
2015-12-31 · diff ↗ ·
added 1 export
get_level
2.0.4
record
2015-10-14 · diff ↗
2.0.3
record
2015-05-27 · diff ↗
2.0.2
record
2015-05-01 · diff ↗
R
R 3.2.0 released · 2015-04-16
2.0.1
record
2014-12-26 · diff ↗
2.0.0
record
2014-12-06 · diff ↗
1.1.3
record
2014-08-06 · diff ↗
1.1.2
record
2014-07-19 · diff ↗
1.1-0
record
2014-07-18
R
R 3.1.0 released · 2014-04-10

Package metadata

First published: 2014-07-18
Total releases: 28 / 12 yrs
License: BSD_3_clause + file LICENSE OSI
Minimum R: ≥ 3.0.0
Download size: 482 KB

Appears in task views

Phylogenetics

Cite

Cite this package

Run in R for the authors' entry:

citation("RNeXML")

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

It points to 10.1111/2041-210x.12469.

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 RNeXML version 2.4.11 [Data set]. HJJB, LLC. Data release v2026-10-19. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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