R Observatory: Metrics for varitas version 0.0.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

varitas

0.0.2

Variant Calling in Targeted Analysis Sequencing Data

0packages depend

2.4Kdownloads / year

0.6%test coverage

0/13checks pass

Overview

About

Maintained by Adam MillsFirst published 2020-02-212 releasesCRAN page ↗

Multi-caller variant analysis pipeline for targeted analysis sequencing (TAS) data. Features a modular, automated workflow that can start with raw reads and produces a user-friendly PDF summary and a spreadsheet containing consensus variant information.

Install

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

install.packages("varitas", 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-varitas

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

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-varitas

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-varitas

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13NOTE

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc
NOTE r-devel-windows-x86_64
NOTE r-oldrel-macos-arm64
NOTE r-oldrel-macos-x86_64
NOTE r-oldrel-windows-x86_64
NOTE r-patched-linux-x86_64
NOTE r-release-linux-x86_64
NOTE r-release-macos-arm64
NOTE r-release-macos-x86_64
NOTE r-release-windows-x86_64

Slowest check: 1.9 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.02

0.6%

Coverage · measured lines

100%

Documentation · exports

12

Dependencies · direct

Check history

NOTE2026-06-09
0 OK · 13 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
0 OK · 12 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo

Examples that run: 83%
Documented parameters: 99%
Return-value docs: 100%
References docs: 3%

Downloads

2.4K

CRAN downloads in the past year

Rank #15,885 · ~7/day · ~203/mo

Releases R versions

Daily download trend is not available in this view yet.

15730 days

66490 days

2.4K1 year

Compare downloads with other packages →

Also on99 r2u30 autocran

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (12)

stringr dplyr yaml openxlsx VennDiagram assertthat magrittrtoolsutilstidyr doParallel foreach

LinkingTo (0)

none

Suggests (4)

testthat knitr rmarkdown futile.logger

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (4)

Maintainer (1)

Adam Mills

Author, Maintainer

Authors (4)

Author, Maintainer

Author

Author

Author

Package Timeline

2 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
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
0.0.2Latest
2020-11-14 · current release · diff ↗
unarchivedReturned to CRAN
2020-11-14
archivedRemoved from CRAN
2020-06-02
check problems were not corrected despite reminders
R
R 4.0.0 released · 2020-04-24
0.0.1
2020-02-21
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2020-02-21
Total releases: 2 / 6 yrs
License: GPL-2 OSI
Download size: 148 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("varitas")

Format

Mills, A., Cutts, R., Haider, S., & Holgersen, E. (2020). varitas: Variant Calling in Targeted Analysis Sequencing Data (Version 0.0.2) [Computer software]. https://doi.org/10.32614/CRAN.package.varitas

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 varitas version 0.0.2 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, 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 →