R Observatory: Metrics for ribiosUtils version 1.7.7

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ribiosUtils

1.7.7Package record

Utilities from and Interface to the 'Bioinfo-C' ('BIOS') Library

4packages depend

2.2Kdownloads / year

3.1%test coverage

13/13flavors OK

Overview

About

Maintained by Jitao David ZhangCRAN page ↗GitHub ↗Website ↗Issues ↗

Provides interface to the 'Bioinfo-C' (internal name: 'BIOS') library and utilities. 'ribiosUtils' is a Swiss-knife for computational biology in drug discovery, providing functions and utilities with minimal external dependency and maximal efficiency.

Install

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

install.packages("ribiosUtils", 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("bedapub/ribiosUtils")

Development version from bedapub/ribiosUtils. 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-ribiosutils

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-ribiosUtils

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-ribiosUtils

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: 3.3 min · r-devel-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 1.7.7

READMEYes · 175 wordsVignettesNoNEWSYes · 67% structuredCitation fileNoWebsiteYes · pkgdown

Help pages: 119 (1 internal)includes a package overview page
Examples that run: 95%105 run in a plain check · 3 only when donttest examples are enabled (R CMD check --as-cran) · 2 never run
Exported functions with examples: 95%
Documented parameters: 99%
Return-value docs: 100%
Help pages citing references: 1%

How these are measured

Downloads

2.2K

CRAN downloads in the past year

Rank #20,736 · ~6/day · ~185/mo

Releases R versions

Daily download trend is not available in this view yet.

20330 days

64490 days

2.2K1 year

Compare downloads with other packages →

Also on246 r2u4 autocran

How downloads are counted

Repository

bedapub/ribiosutils ↗Organization: bedapub

1Stars

1Forks

0Open issues

0Open PRs

3Releases

537Commits

4Commit identities

537 commits · Last activity 2026-06-15 · 0% stars, 30d · Default branch at 1.7.10, ahead of CRAN 1.7.7 (checked 2026-10-21)

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 1,395
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2026-01-08 · 12026-07-07 · 1

How these are measured

PracticesBeta

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

Checks run against github.com/bedapub/ribiosutils on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Docs source (3)

pkgdown

GitHub Pages site last deployed 2026-06-15 · The repository has a site deploy workflow

pkgdown site last built 2026-06-15

Reproducibility and dev environment (1)

Makefile

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Show all practicesHide 1 practice

Lint, format, editor (1)

RStudio project

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

AI coding toolsBeta

This repository shows signs of AI coding tools.

Claude Codefirst seen 2026-01-22
Seen in the repository: .claude, .claude/agents, CLAUDE.md
Named in .Rbuildignore: .claude, CLAUDE.md
Commits: at least 9 crediting it in the message

Models named in its commits

Claude Opus 4.59 commits · Jan 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

2 external dependencies (excludes base and recommended)

Installing ribiosUtils adds no packages beyond those that come with R.

Depends (1)

R >= 3.4.0

Imports (3)

methodsstatsutils

LinkingTo (0)

none

Suggests (2)

devtools testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

4direct

0indirect

Depends 1 · Imports 3 · LinkingTo 1

Depends, Imports or LinkingTo, most downloaded first

ribiosIO ribiosPlot ribiosArg ribiosGraph

How these are counted

Code & Tests

People & History

People (7)

Jitao David Zhang

Author, Maintainer since 1.5-6 (2020), Contributor

Clemens Broger

Author, Contributor

F.Hoffmann-La Roche AG

Copyright holder

Richard Durbin

Copyright holder

Junio C Hamano

Copyright holder

Konrad Rudolph

Copyright holder · added in 1.7.7

Jean Thierry-Mieg

Copyright holder

Releases (2)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
unarchivedReturned to CRAN
2026-02-03
1.7.7Latest
record
2026-02-03 · current release · diff ↗ ·
removed 3 exports
closeFileDevice, getDefaultFontFamily, openFileDevice

added 24 exports
applyTopOrIncAndNotExclFilter, bound, boundNorm, cbindByRownames, corByRownames, cutreeIntoOrderedGroups, equateWellLabelWidth, firstUp, invertList, isEven, isOdd, isTopOrIncAndNotExcl, lastChar, overwriteDir, rbindByColnames, removeColumnsByFunc, removeColumnsWithNA, removeRowsByFunc, removeRowsWithNA, replaceZeroPvalue, rrank, rrankInd, shortenRocheCompoundID, wellIndex2position
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
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
archivedRemoved from CRAN
2020-10-02
check issues were not corrected in time
R
R 4.0.0 released · 2020-04-24
1.5-6
record
2020-03-06
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2020-03-06
Total releases: 2 / 6 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.4.0
Download size: 341 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("ribiosUtils")

Format

Zhang, J. D., F.Hoffmann-La Roche AG, Broger, C., Durbin, R., Hamano, J. C., Rudolph, K., & Thierry-Mieg, J. (2026). ribiosUtils: Utilities from and Interface to the 'Bioinfo-C' ('BIOS') Library (Version 1.7.7) [Computer software]. https://doi.org/10.32614/CRAN.package.ribiosUtils

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 ribiosUtils version 1.7.7 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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