R Observatory: Metrics for lineup version 0.46

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

lineup

0.46Package record

Lining Up Two Sets of Measurements

0packages depend

3.6Kdownloads / year

25.1%test coverage

13/13flavors OK

Overview

About

Maintained by Karl W BromanCRAN page ↗GitHub ↗Issues ↗

Tools for detecting and correcting sample mix-ups between two sets of measurements, such as between gene expression data on two tissues. Broman et al. (2015) doi:10.1534/g3.115.019778.

Changes in 0.46

Added package logo
For parallel computing, use of n.cores=0 argument now results in all but one core (parallel::detectCores()-1) rather than **all** cores.

From NEWS.md in the release

Install

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

install.packages("lineup", 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("kbroman/lineup")

Development version from kbroman/lineup. 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-lineup

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-lineup

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-lineup

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: 2.9 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 0.46

READMEYes · 235 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 0.46Citation fileYes · cites a publication

Help pages: 21 (1 internal)includes a package overview page
Examples that run: 100%20 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

R/lineup user guide HTML

How these are measured

Downloads

3.6K

CRAN downloads in the past year

Rank #7,955 · ~10/day · ~302/mo

Releases R versions

Daily download trend is not available in this view yet.

36630 days

1.1K90 days

3.6K1 year

Compare downloads with other packages →

Also on408 r2u3 autocran71 c2d4u

How downloads are counted

Repository

kbroman/lineup ↗Account: kbroman

4Stars

3Forks

0Open issues

0Open PRs

5Releases

266Commits

1Commit identities

License file reads as GPL-3.0 · 266 commits · Last activity 2026-07-15

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 4
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2022-07-11 · 42026-07-07 · 4

How these are measured

PracticesBeta

4 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/kbroman/lineup 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

Docs source (1)

GitHub Pages site last deployed 2026-07-15

Reproducibility and dev environment (1)

Makefile

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

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Installing lineup adds 1 package (1 with compiled code, 4.2 MB of source tarballs). Heaviest: qtl 4.2 MB.

Depends (1)

R >= 2.10.1

Imports (7)

qtlclassgraphicsgrDevicesutilsstatsparallel

LinkingTo (0)

none

Suggests (5)

roxygen2 knitr rmarkdown devtools 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 (1)

Karl W Broman

Author, Maintainer since 0.34-1 (2012)

Releases (9)

Pick two releases to compare their code metrics.

0.46Latest
record
2026-07-15 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
0.44
record
2024-07-15 · diff ↗
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
0.42
record
2022-07-10 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.40
record
2021-11-03 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.38-3
record
2020-11-17 · diff ↗
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
0.37-11
record
2019-03-06 · diff ↗
R
R 3.5.0 released · 2018-04-23
0.37-10
record
2018-03-23 · diff ↗

Show 8 earlier eventsHide 8 earlier events

R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
0.37-6
record
2015-07-29 · diff ↗
R
R 3.2.0 released · 2015-04-16
R
R 3.1.0 released · 2014-04-10
R
R 3.0.0 released · 2013-04-03
0.34-1
record
2012-10-15
R
R 2.15.0 released · 2012-03-30

Package metadata

First published: 2012-10-15
Total releases: 9 / 14 yrs
License: GPL-3 OSI
Minimum R: ≥ 2.10.1
Bundled data: 1.5 MB / 5 files
Download size: 1.8 MB

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' entry:

citation("lineup")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1534/g3.115.019778.

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 lineup version 0.46 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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