R Observatory: Metrics for Capsule version 0.2.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

Capsule

0.2.0

Comprehensive Reproducibility Framework for R and Bioinformatics Analysis

0packages depend

1.7Kdownloads / year

71.1%test coverage

13/13checks pass

Overview

About

Maintained by Abu SAADATFirst published 2025-11-111 releasesCRAN page ↗GitHub ↗

A comprehensive reproducibility framework designed for R and bioinformatics workflows. Automatically captures the entire analysis environment including R session info, package versions, external tool versions ('Samtools', 'STAR', 'BWA', etc.), 'conda' environments, reference genomes, data provenance with smart checksumming for large files, parameter choices, random seeds, and hardware specifications. Generates executable scripts with 'Docker', 'Singularity', and 'renv' configurations. Integrates with workflow managers ('Nextflow', 'Snakemake', 'WDL', 'CWL') to ensure complete reproducibility of computational research workflows.

Install

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

install.packages("Capsule", 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("SAADAT-Abu/Capsule")

Development version from SAADAT-Abu/Capsule. 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-capsule

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-Capsule

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-Capsule

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

Health

CRAN checks

13OK

Slowest check: 6.5 min · r-oldrel-macos-x86_64

Code health

Yes

Tests · ratio 0.27

71.1%

Coverage · measured lines

100%

Documentation · exports

6

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 454 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 3%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

1.7K

CRAN downloads in the past year

Rank #21,047 · ~5/day · ~138/mo

Releases R versions

Daily download trend is not available in this view yet.

15230 days

52590 days

1.7K1 year

Compare downloads with other packages →

Also on78 r2u12 autocran

Repository

GitHub ↗ saadat-abu/capsule

8Stars

2Forks

0Open issues

0Open PRs

0Releases

16Commits

2Contributors

License MIT · 16 commits · Last activity 2025-12-28 · 0% stars, 30d

Stars over time

2025-11-20 · 32026-07-07 · 8

Repository practices

Upstream repositoryBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/saadat-abu/capsule on 2026-08-09.

Continuous integration (1)

GitHub Actions

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

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.0.0

Imports (6)

renv jsonlite digest yaml cliutils

LinkingTo (0)

none

Suggests (1)

testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Maintainer (1)

Abu SAADAT

Author, Maintainer

Authors (1)

Abu SAADAT

Author, Maintainer

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.2.0Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-11-11
Total releases: 1 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.0.0
Download size: 53 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("Capsule")

Format

SAADAT, A. (2025). Capsule: Comprehensive Reproducibility Framework for R and Bioinformatics Analysis (Version 0.2.0) [Computer software]. https://doi.org/10.32614/CRAN.package.Capsule

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 Capsule version 0.2.0 [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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