R Observatory: Metrics for pepr version 0.6.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

pepr

0.6.1Package record

Reading Portable Encapsulated Projects

0packages depend

3.1Kdownloads / year

84.6%test coverage

13/13flavors OK

Overview

About

Maintained by Nathan SheffieldCRAN page ↗GitHub ↗Issues ↗

A PEP, or Portable Encapsulated Project, is a dataset that subscribes to the PEP structure for organizing metadata. It is written using a simple YAML + CSV format, it is your one-stop solution to metadata management across data analysis environments. This package reads this standardized project configuration structure into R. Described in Sheffield et al. (2021) doi:10.1093/gigascience/giab077.

Changes in 0.6.1

Fixed

Updated pullProject() to match the current PEPhub API response schema (the raw-project keys sample_list/subsample_list were renamed to samples/subsamples), which had caused a fetch error against the live API.
pullProject() now fails with an informative message when a PEP is missing or the API response is malformed, instead of a cryptic internal error.

Changed

Moved the live PEPhub API test into an opt-in integration suite (set PEPR_INTEGRATION_TESTS=true) that never runs on CRAN; the pullProject() example is no longer executed during checks.

From NEWS.md in the release

Install

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

install.packages("pepr", 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("pepkit/pepr")

Development version from pepkit/pepr. 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-pepr

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-pepr

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-pepr

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: 2.1 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-07-16
ERROR12 OK, 1 ERROR2026-07-03
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.6.1

READMEYes · 86 wordsVignettesYes · 7 · evaluation depends on the environmentNEWSYes · 100% structured · mentions 0.6.1Citation fileYes · cites a publication

Help pages: 51 (34 internal)includes a package overview page
Examples that run: 95%18 run in a plain check · 1 never run
Exported functions with examples: 82%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 2%

Vignettes (7)

Amendments in pepr HTML
Getting Started with pepr
Sample modifiers in pepr: append HTML
Sample modifiers in pepr: derive HTML
Sample modifiers in pepr: imply HTML
Sample modifiers in pepr: imply and derive HTML
Subsample table in pepr HTML

How these are measured

Downloads

3.1K

CRAN downloads in the past year

Rank #9,542 · ~8/day · ~257/mo

Releases R versions

Daily download trend is not available in this view yet.

32530 days

1K90 days

3.1K1 year

Compare downloads with other packages →

Also on88 r2u4 autocran

How downloads are counted

Repository

pepkit/pepr ↗Organization: pepkit

3Stars

1Forks

2Open issues

0Open PRs

12Releases

428Commits

4Commit identities

metadatabioinformaticslab-project-pepkit

428 commits · Last activity 2026-07-08

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 20
Median days to close, 50 most recently updated closed PRs: 1

How these are measured

PracticesBeta

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

Checks run against github.com/pepkit/pepr on 2026-10-25.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Docs source (3)

pkgdown

GitHub Pages site last deployed 2026-07-08 · The repository has a site deploy workflow

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Installing pepr adds 19 packages (14 with compiled code, 23 MB of source tarballs). Heaviest: stringi 11 MB, data.table 5.7 MB, openssl 1.1 MB.

Depends (1)

R >= 4.1.0

Imports (6)

yaml stringr data.tablemethodsRCurl httr2

LinkingTo (0)

none

Suggests (4)

knitr testthat rmarkdown curl

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)

Nathan Sheffield

Michal Stolarczyk

Author

Previously maintained by Michal Stolarczyk (0.3.2 to 0.4.0).

Releases (5)

Pick two releases to compare their code metrics.

0.6.1Latest
record
2026-07-08 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
unarchivedReturned to CRAN
2026-03-01
0.6.0
record
2026-03-01 · diff ↗ ·
added 3 exports
pullProject, saveJWT, saveProject
archivedRemoved from CRAN
2026-01-30
requires archived package 'pryr'
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
unarchivedReturned to CRAN
2023-11-21
0.5.0
record
2023-11-21 · diff ↗
archivedRemoved from CRAN
2023-08-19
email to the maintainer is undeliverable
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
0.4.0
record
2020-10-16 · diff ↗
0.3.2
record
2020-06-04
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-06-04
Total releases: 5 / 6 yrs
License: BSD_2_clause + file LICENSE OSI
Minimum R: ≥ 4.1.0
Download size: 85 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("pepr")

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

It points to 10.1093/gigascience/giab077.

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 pepr version 0.6.1 [Data set]. HJJB, LLC. Data release v2026-10-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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