R Observatory: Metrics for romic version 1.3.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

romic

1.3.3Package record

R for High-Dimensional Molecular Data

0packages depend

3.1Kdownloads / year

51.5%test coverage

13/13flavors OK

Overview

About

Maintained by Sean HackettCRAN page ↗GitHub ↗Website ↗Issues ↗Declared funder: Calico Life Sciences LLC

Represents high-dimensional data as tables of features, samples and measurements, and a design list for tracking the meaning of individual variables. Using this format, filtering, normalization, and other transformations of a dataset can be carried out in a flexible manner. 'romic' takes advantage of these transformations to create interactive 'shiny' apps for exploratory data analysis such as an interactive heatmap.

Changes in 1.3.3

Minor Improvements and Fixes

Docstring cleanup and wrapping imputation function in dontrun since impute may not be installed from Bioconductor.

From NEWS.md in the release

Install

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

install.packages("romic", 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("shackett/romic")

Development version from shackett/romic. 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-romic

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-romic

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-romic

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: 4.2 min · r-oldrel-macos-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.3.3

READMEYes · 1,197 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 1.3.3Citation fileNoWebsiteYes

Help pages: 72 (1 internal)includes a package overview page
Examples that run: 98%43 run in a plain check (15 of them under a condition) · 1 never run
Exported functions with examples: 73%
Documented parameters: 100%
Return-value docs: 98%
Help pages citing references: 0%

Vignettes (1)

romic

How these are measured

Downloads

3.1K

CRAN downloads in the past year

Rank #12,267 · ~8/day · ~258/mo

Releases R versions

Daily download trend is not available in this view yet.

31230 days

90990 days

3.1K1 year

Compare downloads with other packages →

Also on80 r2u3 autocran

How downloads are counted

Repository

shackett/romic ↗Account: shackett

1Stars

0Forks

1Open issues

1Open PRs

0Releases

186Commits

3Commit identities

186 commits · Last activity 2026-01-31 · 0% stars, 30d · The default branch showed an older version (1.3.2) than CRAN on 2026-10-21

Responsiveness

How these are sampled

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

Stars over time

2025-04-06 · 12026-07-07 · 1

How these are measured

PracticesBeta

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

Checks run against github.com/shackett/romic 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 2026-01-19 · The repository has a site deploy workflow

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (2)

Lint workflowRStudio project

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

Dependencies

Declared dependencies

19 external dependencies (excludes base and recommended)

Installing romic adds 66 packages (39 with compiled code, 54 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, bslib 5.6 MB.

Depends (1)

R >= 4.1

Imports (13)

checkmate cli dplyr ggplot2 glue purrr readr reshape2 rlang shiny stringr tibble tidyr

LinkingTo (0)

none

Suggests (6)

knitr impute lazyeval rmarkdown usethis testthat (>= 3.0.0)

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)

Sean Hackett

Author, Maintainer since 1.0.0 (2021)

Calico Life Sciences LLC

Copyright holder, Funder

Releases (4)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
unarchivedReturned to CRAN
2026-01-31
1.3.3Latest
record
2026-01-31 · current release · diff ↗ ·
added 6 exports
calculate_sample_mahalanobis_distances, check_design, plot_missing_values, reform_tidy_omic, tomic_to_matrix, update_sample_factors
archivedRemoved from CRAN
2025-12-03
email to the maintainer is undeliverable
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.1.3
record
2023-09-21 · diff ↗ ·
added 1 export
get_tomic_table
R
R 4.3.0 released · 2023-04-21
1.1.1
record
2023-02-02 · diff ↗ ·
removed 2 exports
add_pca_loadings, app_scatter

added 3 exports
add_pcs, app_pcs, impute_missing_values
R
R 4.2.0 released · 2022-04-22
1.0.0
record
2021-07-20
removedRemoved from CRAN
2021-05-18
policy violation Detritus in '/tmp' Back on CRAN on 2021-07-20
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-07-20
Total releases: 4 / 5 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1
Bundled data: 118 KB / 3 files
Download size: 660 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("romic")

Format

Hackett, S., & Calico Life Sciences LLC. (2026). romic: R for High-Dimensional Molecular Data (Version 1.3.3) [Computer software]. https://doi.org/10.32614/CRAN.package.romic

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 romic version 1.3.3 [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.

Report a problem with this page →