R Observatory: Metrics for Umpire version 2.0.12

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

Umpire

2.0.12Package record

Simulating Realistic Gene Expression and Clinical Data

0packages dependsuggested by 1

3.1Kdownloads / year

73.9%test coverage

13/13flavors OK

Overview

About

Maintained by Kevin R. CoombesCRAN page ↗Website ↗

The Ultimate Microrray Prediction, Reality and Inference Engine (UMPIRE) is a package to facilitate the simulation of realistic microarray data sets with links to associated outcomes. See Zhang and Coombes (2012) doi:10.1186/1471-2105-13-S13-S1. Version 2.0 adds the ability to simulate realistic mixed-typed clinical data.

Install

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

install.packages("Umpire", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

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-umpire

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-Umpire

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-Umpire

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-oldrel-windows-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09

Show 2 earlier changesHide 2 earlier changes

ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.0.12

READMENoVignettesYes · 3 · dynamicNEWSNoCitation fileNoWebsiteYes

Help pages: 20
Examples that run: 100%15 run in a plain check
Exported functions with examples: 94%
Documented parameters: 92%
Return-value docs: 56%
Help pages citing references: 30%

Vignettes (3)

How these are measured

Downloads

3.1K

CRAN downloads in the past year

Rank #11,786 · ~9/day · ~261/mo

Releases R versions

Daily download trend is not available in this view yet.

48930 days

92390 days

3.1K1 year

Compare downloads with other packages →

Also on80 r2u3 autocran

How downloads are counted

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Installing Umpire adds 22 packages (9 with compiled code, 20 MB of source tarballs). Heaviest: ggplot2 6.0 MB, mclust 2.7 MB, mc2d 2.1 MB.

Depends (1)

R >= 3.0

Imports (4)

methodsstatsmc2d BimodalIndex

LinkingTo (0)

none

Suggests (4)

mclustsurvivalknitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Suggested by 1

Suggests, most downloaded first

SillyPutty

How these are counted

Code & Tests

People & History

People (3)

Kevin R. Coombes

Author, Maintainer since 1.3.4 (2017)

Caitlin E. Coombes

Author · added in 2.0.0

Jiexin Zhang

Author

Releases (13)

Pick two releases to compare their code metrics.

2.0.12Latest
record
2026-09-24 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
2.0.11
record
2025-02-05 · diff ↗
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
2.0.10
record
2020-11-10 · diff ↗
2.0.9
record
2020-08-02 · diff ↗ ·
removed 1 export
setDataTypes

added 3 exports
makeDataTypes, getDataTypes, getDaisyTypes
2.0.3
record
2020-06-01 · diff ↗
2.0.1
record
2020-04-27 · diff ↗
R
R 4.0.0 released · 2020-04-24
2.0.0
record
2020-04-14 · diff ↗ ·
added 4 exports
setDataTypes, ClinicalNoiseModel, ClinicalEngine, MixedTypeEngine
1.3.9
record
2020-02-03 · diff ↗
1.3.8
record
2020-01-08 · diff ↗

Show 7 earlier eventsHide 7 earlier events

1.3.7
record
2019-05-06 · diff ↗
R
R 3.6.0 released · 2019-04-26
1.3.6
record
2019-04-23 · diff ↗
1.3.5
record
2018-05-18 · diff ↗
R
R 3.5.0 released · 2018-04-23
1.3.4
record
2017-07-11
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-07-11
Total releases: 13 / 9 yrs
License: Apache License (== 2.0)
Minimum R: ≥ 3.0
Download size: 341 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("Umpire")

Format

Coombes, K. R., Coombes, C. E., & Zhang, J. (2026). Umpire: Simulating Realistic Gene Expression and Clinical Data (Version 2.0.12) [Computer software]. https://doi.org/10.32614/CRAN.package.Umpire

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 Umpire version 2.0.12 [Data set]. HJJB, LLC. Data release v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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