PGRdup

0.3.0

Discover Probable Duplicates in Plant Genetic Resources Collections

0packages depend

5.1Kdownloads / year

–test coverage

9/13checks pass

Overview

About

Maintained by J. AravindFirst published 2015-04-1416 releasesCRAN page ↗GitHub ↗

Provides functions to aid the identification of probable/possible duplicates in Plant Genetic Resources (PGR) collections using 'passport databases' comprising of information records of each constituent sample. These include methods for cleaning the data, creation of a searchable Key Word in Context (KWIC) index of keywords associated with sample records and the identification of nearly identical records with similar information by fuzzy, phonetic and semantic matching of keywords.

Install

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

install.packages("PGRdup", 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("aravind-j/PGRdup")

Development version from aravind-j/PGRdup. 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-pgrdup

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-PGRdup

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-PGRdup

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

Health

CRAN checks

4NOTE9OK

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-gcc
NOTE r-devel-windows-x86_64

Slowest check: 3.8 min · r-oldrel-macos-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-07-16
10 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-30
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 996 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 89%
References docs: 15%

Downloads

5.1K

CRAN downloads in the past year

Rank #6,417 · ~14/day · ~425/mo

Releases R versions

Daily download trend is not available in this view yet.

35030 days

1.6K90 days

5.1K1 year

Compare downloads with other packages →

Also on420 r2u31 autocran68 c2d4u

Repository

GitHub ↗ aravind-j/pgrdup

1Stars

2Forks

0Open issues

1Open PRs

8Releases

163Commits

2Contributors

rnatural-language-processingplant-genetic-resourcesdouble-metaphonerecord-linkagedouble-metaphone-algorithmpgr

163 commits · Last activity 2026-04-29

Stars over time

2018-02-08 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/aravind-j/pgrdup on 2026-07-19.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Research and citation (2)

CITATION.cffcodemeta.json

Show all practices

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (10)

data.table igraph stringdist stringi ggplot2gridgridExtramethodsutilsstats

LinkingTo (0)

none

Suggests (9)

diagram wordcloud microbenchmark XML httr RCurl knitr rmarkdown pander

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (9)

Maintainer (1)

J. Aravind

Author, Maintainer

Authors (5)

Author, Maintainer

Author

Author

Author

Author

Contributors (3)

Kevin Atkinson

Contributor · added in 0.2.3.2

Maurice Aubrey

Contributor · added in 0.2.3.2

Lawrence Philips

Contributor · added in 0.2.3.2

ICAR-NBGPR

Listed in earlier versions (4)

B. Ananda

no longer listed · 0.2 to 0.2.3.3

R. K.

no longer listed · 0.2 to 0.2.3.3

no longer listed · 0.2.3.4 to 0.3.0

Tyagi

no longer listed · 0.2.3.4 to 0.3.0

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
0.3.0Latest
2026-04-22 · current release · diff ↗
0.2.4.0
2025-12-14 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
0.2.3.9
2023-09-01 · diff ↗
0.2.3.8
2023-05-23 · 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
0.2.3.7
2021-02-17 · diff ↗
unarchivedReturned to CRAN
2021-02-17
archivedRemoved from CRAN
2021-01-21
check problems were not corrected in time
0.2.3.6
2020-07-27 · diff ↗
unarchivedReturned to CRAN
2020-07-27
archivedRemoved from CRAN
2020-06-22
check problems were not corrected in time Misuse of CA bundle from 'RCurl': failed on Fedora 30

Show 18 earlier events

R
R 4.0.0 released · 2020-04-24
0.2.3.5
2020-02-10 · diff ↗
0.2.3.4
2019-09-19 · diff ↗
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
0.2.3.3
2018-01-13 · diff ↗
0.2.3.2
2017-08-05 · diff ↗
R
R 3.4.0 released · 2017-04-21
archivedRemoved from CRAN
2017-04-16
memtest errors were not corrected despite reminders
0.2.3.1
2017-03-15 · diff ↗
0.2.3
2017-02-01 · diff ↗
R
R 3.3.0 released · 2016-05-03
0.2.2.1
2016-03-09 · diff ↗
0.2.2
2016-03-05 · diff ↗
0.2.1
2015-07-23 · diff ↗
R
R 3.2.0 released · 2015-04-16
0.2
2015-04-14
R
R 3.1.0 released · 2014-04-10

Package metadata

First published: 2015-04-14
Total releases: 16 / 11 yrs
License: GPL-2 | GPL-3 OSI
Minimum R: ≥ 4.1.0
Bundled data: 15 KB / 1 file
Download size: 468 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Agricultural Science

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