R Observatory: Metrics for scimo version 0.0.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

scimo

0.0.3Package record

Extra Recipes Steps for Dealing with Omics Data

0packages depend

2.3Kdownloads / year

80.0%test coverage

13/13flavors OK

Overview

About

Maintained by Antoine BICHATCRAN page ↗GitHub ↗Issues ↗

Omics data (e.g. transcriptomics, proteomics, metagenomics...) offer a detailed and multi-dimensional perspective on the molecular components and interactions within complex biological (eco)systems. Analyzing these data requires adapted procedures, which are implemented as steps according to the 'recipes' package.

Changes in 0.0.3

Add a dependency on **recipes** >= 1.1 to avoid stack overflow errors with long formulas, as this issue has been resolved in this version (#2).
Small improvements in documentation (#6, CRAN notes).

From NEWS.md in the release

Install

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

install.packages("scimo", 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("abichat/scimo")

Development version from abichat/scimo. 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-scimo

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-scimo

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-scimo

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: 5.9 min · r-release-macos-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.0.3

READMEYes · 247 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 0.0.3Citation fileNo

Help pages: 15 (5 internal)includes a package overview page
Examples that run: 100%12 run in a plain check (1 of them under a condition)
Exported functions with examples: 89%
Documented parameters: 97%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

Pediatric cancers HTML

How these are measured

Downloads

2.3K

CRAN downloads in the past year

Rank #18,678 · ~6/day · ~195/mo

Releases R versions

Daily download trend is not available in this view yet.

28130 days

69390 days

2.3K1 year

Compare downloads with other packages →

Also on102 r2u7 autocran

How downloads are counted

Repository

abichat/scimo ↗Account: abichat

5Stars

1Forks

1Open issues

0Open PRs

3Releases

73Commits

2Commit identities

License file reads as GPL-3.0 · 73 commits · Last activity 2025-07-24 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 366
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-10-18 · 52026-07-07 · 5

How these are measured

PracticesBeta

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

Checks run against github.com/abichat/scimo on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Governance and community (1)

PR template

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2025-07-24 · The repository has a site deploy workflow

Reproducibility and dev environment (1)

data-raw/

Show all practicesHide 1 practice

Lint, format, editor (3)

AirVS CodeRStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Installing scimo adds 54 packages (27 with compiled code, 44 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (2)

R >= 2.10recipes

Imports (7)

dplyr generics magrittr rlangstatstibble tidyr

LinkingTo (0)

none

Suggests (4)

ggplot2 knitr rmarkdown testthat

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)

Antoine BICHAT

Author, Maintainer since 0.0.1 (2024)

Julie AUBERT

Contributor

Releases (3)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.0.3Latest
record
2025-07-24 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
0.0.2
record
2024-06-07 · diff ↗ ·
removed 2 exports
cv, var_to_keep

added 1 export
step_taxonomy
R
R 4.4.0 released · 2024-04-24
0.0.1
record
2024-04-03
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2024-04-03
Total releases: 3 / 2 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 2.10
Bundled data: 4.2 MB / 4 files
Download size: 4.3 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("scimo")

Format

BICHAT, A., & AUBERT, J. (2025). scimo: Extra Recipes Steps for Dealing with Omics Data (Version 0.0.3) [Computer software]. https://doi.org/10.32614/CRAN.package.scimo

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 scimo version 0.0.3 [Data set]. HJJB, LLC. Data release v2026-10-20. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-20, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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