R Observatory: Metrics for biocompute version 1.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

biocompute

1.1.1

Create and Manipulate BioCompute Objects

0packages depend

3.3Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Soner KocFirst published 2019-11-285 releasesCRAN page ↗GitHub ↗

Tools to create, validate, and export BioCompute Objects described in King et al. (2019) doi:10.17605/osf.io/h59uh. Users can encode information in data frames, and compose BioCompute Objects from the domains defined by the standard. A checksum validator and a JSON schema validator are provided. This package also supports exporting BioCompute Objects as JSON, PDF, HTML, or 'Word' documents, and exporting to cloud-based platforms.

Install

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

install.packages("biocompute", 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("sbg/biocompute")

Development version from sbg/biocompute. 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-biocompute

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-biocompute

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-biocompute

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

Health

CRAN checks

13OK

Slowest check: 1.6 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

98%

Documentation · exports

13

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 · 122 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 85%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

3.3K

CRAN downloads in the past year

Rank #11,565 · ~9/day · ~278/mo

Releases R versions

Daily download trend is not available in this view yet.

23830 days

84890 days

3.3K1 year

Compare downloads with other packages →

Also on156 r2u25 autocran

Repository

GitHub ↗ sbg/biocompute

3Stars

3Forks

1Open issues

0Open PRs

10Releases

101Commits

5Contributors

bioinformaticsstandardizationworkflowscience-communicationsevenbridgesbiocomputebiocompute-objects

101 commits · Last activity 2024-06-06

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/sbg/biocompute on 2026-08-16.

Continuous integration (1)

Travis CI

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (13)

methodsjsonlite yaml digest uuid jsonvalidate httr curl crayon cli stringr magrittr rmarkdown

LinkingTo (0)

none

Suggests (1)

knitr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (5)

Maintainer (1)

Soner Koc

Author, Maintainer

Authors (4)

Soner Koc

Author, Maintainer

Dennis Dean

Author

Jeffrey Grover

Author · added in 1.0.6

Nan Xiao

Author

Copyright holders (1)

Seven Bridges Genomics

Copyright holder, Funder

Funders (1)

Seven Bridges Genomics

Copyright holder, Funder

Package Timeline

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

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
1.1.1Latest
2022-05-03 · current release · diff ↗
R
R 4.2.0 released · 2022-04-22
1.1.0
2021-10-21 · diff ↗
1.0.6
2021-09-29 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.0.4
2020-10-16 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.0.3
2019-11-28
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-11-28
Total releases: 5 / 7 yrs
License: AGPL-3 OSI
Download size: 496 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("biocompute")

Format

Koc, S., Seven Bridges Genomics, Dean, D., Grover, J., & Xiao, N. (2022). biocompute: Create and Manipulate BioCompute Objects (Version 1.1.1) [Computer software]. https://doi.org/10.32614/CRAN.package.biocompute

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 biocompute version 1.1.1 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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