R Observatory: Metrics for bold version 1.3.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2024-08-26. Its history is shown below.

Reason: repeated policy violation. On Internet access

Details below reflect version 1.3.0, its last release before removal.

bold

1.3.0

Interface to Bold Systems API

0packages depend

–downloads / year

–test coverage

–checks pass

Overview

About

Maintained by Salix Dubois16 releasesCRAN page ↗GitHub ↗

A programmatic interface to the Web Service methods provided by Bold Systems (http://www.boldsystems.org/) for genetic 'barcode' data. Functions include methods for searching by sequences by taxonomic names, ids, collectors, and institutions; as well as a function for searching for specimens, and downloading trace files.

Install

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

url <- "https://cran.r-project.org/src/contrib/Archive/bold/bold_1.3.0.tar.gz"
pkgFile <- "bold_1.3.0.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 (1.3.0) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("ropensci/bold")

Development version from ropensci/bold. 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-bold

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-bold

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

Health

CRAN checks

CRAN check results are not tracked yet.

Code health

Yes

Tests · ratio 18.48

not tracked

Coverage

100%

Documentation · exports

6

Dependencies · direct

Documentation

READMEYes · 512 wordsVignettesNopkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo

Examples that run: 15%
Documented parameters: 92%
Return-value docs: 69%
References docs: 53%

Downloads

Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on113 r2u25 autocran2.4K conda_forge68 c2d4u

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.10

Imports (6)

xml2 crul stringi jsonlite data.tablemethods

LinkingTo (0)

none

Suggests (4)

sangerseqR testthat vcr tibble

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code & Tests

People & History

People (2)

Maintainer (1)

Salix Dubois

Author, Maintainer · added in 1.3.0

Authors (2)

Salix Dubois

Author, Maintainer · added in 1.3.0

Scott Chamberlain

Author

Package Timeline

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

R
R 4.5.0 released · 2025-04-11
archivedRemoved from CRAN
2024-08-26
repeated policy violation On Internet access
R
R 4.4.0 released · 2024-04-24
1.3.0
2023-05-02 · 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
1.2.0
2021-05-11 · diff ↗
1.1.0
2020-06-17 · diff ↗
1.0.0
2020-05-01 · diff ↗
R
R 4.0.0 released · 2020-04-24
0.9.0
2019-06-27 · diff ↗
R
R 3.6.0 released · 2019-04-26
0.8.6
2018-12-14 · diff ↗
0.8.0
2018-10-26 · diff ↗
R
R 3.5.0 released · 2018-04-23

Show 13 earlier events

0.5.0
2017-07-21 · diff ↗
R
R 3.4.0 released · 2017-04-21
0.4.0
2017-01-06 · diff ↗
R
R 3.3.0 released · 2016-05-03
0.3.5
2016-03-29 · diff ↗
0.3.4
2016-03-23 · diff ↗
0.3.0
2015-09-16 · diff ↗
0.2.6
2015-04-17 · diff ↗
R
R 3.2.0 released · 2015-04-16
0.2.0
2014-08-20 · diff ↗
0.1.2
2014-07-24 · diff ↗
0.1.0
2014-05-28
R
R 3.1.0 released · 2014-04-10

Package metadata

Total releases: 16
License: MIT + file LICENSE OSI
Minimum R: ≥ 2.10
Bundled data: 0.6 KB / 1 file
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("bold")

Format

Dubois, S., & Chamberlain, S. (n.d.). bold: Interface to Bold Systems API (Version 1.3.0) [Computer software]. Retrieved August 15, 2026, from https://CRAN.R-project.org/package=bold

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 bold version 1.3.0 [Data set]. HJJB, LLC. Data release v2026-08-15. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-15, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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