SVAlignR

0.9.2

Recovering Structure of Long Molecules from Structural Variation Data

0packages depend

1.8Kdownloads / year

–test coverage

12/13checks pass

Overview

About

Maintained by Kevin R. CoombesFirst published 2025-09-241 releasesCRAN page ↗

Implements a method to combine multiple levels of multiple sequence alignment to uncover the structure of complex DNA rearrangements.

Install

R (CRAN)Ubuntu (r2u)

install.packages("SVAlignR", 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-svalignr

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

Health

CRAN checks

1NOTE12OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 5.0 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.64

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-07-24
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-07-23
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

1.8K

CRAN downloads in the past year

Rank #19,210 · ~5/day · ~151/mo

Releases R versions

Daily download trend is not available in this view yet.

14130 days

57390 days

1.8K1 year

Compare downloads with other packages →

Also on65 r2u

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.4

Imports (12)

methodsgraphicsgrDevicesoompaBase Biostrings NameNeedle dendextend ape stringr igraph Polychrome colorspace

LinkingTo (0)

none

Suggests (5)

msa viridisLite R.rsp knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

Kevin R. Coombes

Author, Maintainer

Authors (1)

Kevin R. Coombes

Author, Maintainer

Listed in earlier versions (1)

Coombes

no longer listed · 0.9.2

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.9.2Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-09-24
Total releases: 1 / 1 yrs
License: Apache License (== 2.0)
Minimum R: ≥ 4.4
Bundled data: 8.5 KB / 2 files
Download size: 1.8 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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