R Observatory: Metrics for prider version 1.0.6

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

prider

1.0.6Package record

Multiplexed Primer Design by Linear Set Coverage Approximation

0packages depend

2Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Manu TamminenCRAN page ↗GitHub ↗

Implementation of an oligonucleotide primer and probe design algorithm using a linearly scaling approximation of set coverage. A detailed description available at Smolander and Tamminen, 2021; doi:10.1101/2021.09.06.459073.

Install

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

install.packages("prider", 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("tamminenlab/prider")

Development version from tamminenlab/prider. 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-prider

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-prider

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-prider

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

13OK

CRAN check page ↗

Slowest check: 2.8 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK5 OK2026-04-29

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.6

READMEYes · 47 wordsVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 8includes a package overview page
Examples that run: 100%4 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

2K

CRAN downloads in the past year

Rank #13,883 · ~5/day · ~164/mo

Releases R versions

Daily download trend is not available in this view yet.

39130 days

84490 days

2K1 year

Compare downloads with other packages →

Also on315 r2u5 autocran2K conda_forge

How downloads are counted

Repository

tamminenlab/prider ↗Organization: tamminenlab

7Stars

5Forks

2Open issues

0Open PRs

2Releases

77Commits

3Commit identities

77 commits · Last activity 2026-04-22

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 16
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2024-03-01 · 72026-07-07 · 7

How these are measured

PracticesBeta

3 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/tamminenlab/prider on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

CRAN release process (1)

cran-comments.md

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

AI coding toolsBeta

This repository shows signs of AI coding tools.

Claude Codefirst seen 2026-04-21
Named in .Rbuildignore: .claude
Pull request it wrote: opened by a project member
Commits: at least 4 crediting it in the message

Models named in its commits

Claude Opus 4.74 commits · Apr 2026

Counts are commits, not lines of code. Commits by a tool's accounts count once across all of its accounts. Commits crediting it are the largest count among its credit lines, a minimum.How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Installing prider adds 25 packages (16 with compiled code, 24 MB of source tarballs). Heaviest: stringi 11 MB, gplots 4.6 MB, Rcpp 1.8 MB.

Depends (0)

none

Imports (8)

Rcpp dplyr tidyr purrr stringr magrittr tibble gplots

LinkingTo (1)

Rcpp

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (2)

Manu Tamminen

Author, Maintainer since 1.0.2 (2021)

Niina Smolander

Author

Releases (3)

Pick two releases to compare their code metrics.

unarchivedReturned to CRAN
2026-04-28
1.0.6Latest
record
first seen 2026-04-28 · current release · diff ↗
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
archivedRemoved from CRAN
2022-10-10
requires archived package 'blaster'
R
R 4.2.0 released · 2022-04-22
unarchivedReturned to CRAN
2022-03-11
1.0.4
record
2022-03-11 · diff ↗
archivedRemoved from CRAN
2022-02-24
check problems were not corrected in time
1.0.2
record
2021-09-13
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-09-13
Total releases: 3 / 5 yrs
License: BSD_3_clause + file LICENSE OSI
Download size: 28 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("prider")

Format

Tamminen, M., & Smolander, N. (2026). prider: Multiplexed Primer Design by Linear Set Coverage Approximation (Version 1.0.6) [Computer software]. https://doi.org/10.32614/CRAN.package.prider

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 prider version 1.0.6 [Data set]. HJJB, LLC. Data release v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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