R Observatory: Metrics for biocompute version 1.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

biocompute

1.1.1Package record

Create and Manipulate BioCompute Objects

0packages depend

3.4Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Soner KocCRAN page ↗GitHub ↗Website ↗Issues ↗Declared funder: Seven Bridges Genomics

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.

Changes in 1.1.1

Improvements

Update package maintainer.

From NEWS.md in the release

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. 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-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). 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: 1.6 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.1

READMEYes · 122 wordsVignettesYes · 2 · dynamicNEWSYes · 100% structured · mentions 1.1.1Citation fileNoWebsiteYes · pkgdown

Help pages: 29 (2 internal)includes a package overview page
Examples that run: 85%23 run in a plain check · 4 never run
Exported functions with examples: 96%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (2)

How these are measured

Downloads

3.4K

CRAN downloads in the past year

Rank #11,682 · ~9/day · ~281/mo

Releases R versions

Daily download trend is not available in this view yet.

30630 days

93490 days

3.4K1 year

Compare downloads with other packages →

Also on126 r2u24 autocran

How downloads are counted

Repository

sbg/biocompute ↗Organization: sbg

3Stars

3Forks

1Open issues

0Open PRs

10Releases

101Commits

5Commit identities

bioinformaticsstandardizationworkflowscience-communicationsevenbridgesbiocomputebiocompute-objects

101 commits · Last activity 2024-06-06

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: 0

How these are measured

PracticesBeta

5 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/sbg/biocompute on 2026-10-22.

Continuous integration (1)

Travis CI (config file)

Docs source (2)

pkgdown

GitHub Pages site last deployed 2024-06-06

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Installing biocompute adds 40 packages (25 with compiled code, 35 MB of source tarballs). Heaviest: stringi 11 MB, bslib 5.6 MB, sass 2.9 MB.

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.

How these are counted

Code & Tests

People & History

People (5)

Soner Koc

Author, Maintainer since 1.1.1 (2022)

Dennis Dean

Author

Jeffrey Grover

Author · added in 1.0.6

Nan Xiao

Author

Seven Bridges Genomics

Copyright holder, Funder

Previously maintained by Jeffrey Grover (1.0.6 to 1.1.0) and Soner Koc (1.0.4).

Releases (5)

Pick two releases to compare their code metrics.

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
record
2022-05-03 · current release · diff ↗
R
R 4.2.0 released · 2022-04-22
1.1.0
record
2021-10-21 · diff ↗ ·
removed 14 exports
compose_description_v1.3.0, compose_error_v1.3.0, compose_execution_v1.3.0, compose_extension_v1.3.0, compose_fhir_v1.3.0, compose_io_v1.3.0, compose_parametric_v1.3.0, compose_provenance_v1.3.0, compose_scm_v1.3.0, compose_tlf_v1.3.0, compose_usability_v1.3.0, compose_v1.3.0, validate_checksum_v1.3.0, validate_schema_v1.3.0

added 15 exports
compose_description_v1.4.2, compose_error_v1.4.2, compose_execution_v1.4.2, compose_extension_v1.4.2, compose_fhir_v1.4.2, compose_io_v1.4.2, compose_parametric_v1.4.2, compose_provenance_v1.4.2, compose_scm_v1.4.2, compose_tlf_v1.4.2, compose_usability_v1.4.2, compose_v1.4.2, read_bco, validate_checksum_v1.4.2, validate_schema_v1.4.2
1.0.6
record
2021-09-29 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.0.4
record
2020-10-16 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.0.3
record
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

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 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 biocompute version 1.1.1 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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