R Observatory: Metrics for CNVScope version 3.7.7

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

CNVScope

3.7.7Package record

A Versatile Toolkit for Copy Number Variation Relationship Data Analysis and Visualization

0packages depend

4.3Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by James DalgleishCRAN page ↗GitHub ↗Issues ↗

Provides the ability to create interaction maps, discover CNV map domains (edges), gene annotate interactions, and create interactive visualizations of these CNV interaction maps.

Changes in 3.7.7

*Fixed the "Rd files without \usage" NOTE reported by CRAN on

r-devel-linux-x86_64-debian-clang and -gcc. Eight roxygen blocks were

separated from the functions they document by an intervening top-level

globalVariables()/dontCheck() call, so roxygen2 attached the block to that

call and emitted no \usage section. Those calls now precede their roxygen

blocks, and the affected topics (CNVScopeserver, calcCNVKernelProbDist,

downsample_genomic_matrix, formSampleMatrixFromRawGDCData,

getBlockAverageMatrixFromBreakpoints, getInterchromosomalInteractivePlot,

importBreakpointBed, rebinGenomicInteractions) document their usage again.

*Documented the previously undocumented parallel and cnlabel arguments of

formSampleMatrixFromRawGDCData(), which the restored \usage sections revealed.

*Removed stray top-level test code from R/downsample_genomic_matrix.R that ran

Show all changes in 3.7.7Hide the rest of the changes in 3.7.7

at package build time.

From NEWS.md in the release

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("CNVScope", 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("jamesdalg/CNVScope")

Development version from jamesdalg/CNVScope. 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-cnvscope

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

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 10.9 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-09-16
NOTE12 OK, 1 NOTE2026-07-11
OK13 OK2026-07-08
NOTE11 OK, 2 NOTE2026-07-05
ERROR8 OK, 4 NOTE, 1 ERROR2026-06-29

Show 13 earlier changesHide 13 earlier changes

NOTE9 OK, 4 NOTE2026-06-27
ERROR8 OK, 4 NOTE, 1 ERROR2026-06-21
NOTE9 OK, 4 NOTE2026-06-09
ERROR9 OK, 3 NOTE, 1 ERROR2026-06-08
NOTE9 OK, 4 NOTE2026-06-07
ERROR8 OK, 4 NOTE, 1 ERROR2026-06-06
NOTE9 OK, 4 NOTE2026-06-04
ERROR8 OK, 4 NOTE, 1 ERROR2026-05-26
NOTE9 OK, 4 NOTE2026-05-10
ERROR8 OK, 4 NOTE, 1 ERROR2026-05-03
NOTE7 OK, 7 NOTE2026-04-16
ERROR6 OK, 7 NOTE, 1 ERROR2026-04-09
NOTE7 OK, 7 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 3.7.7

READMENoVignettesYes · 4 · dynamicNEWSYes · 33% structured · mentions 3.7.7Citation fileNo

Help pages: 27
Examples that run: 77%20 run in a plain check · 4 never run · 2 hold no code
Exported functions with examples: 100%
Documented parameters: 98%
Return-value docs: 88%
Help pages citing references: 4%

Vignettes (4)

How these are measured

Downloads

4.3K

CRAN downloads in the past year

Rank #5,468 · ~12/day · ~355/mo

Releases R versions

Daily download trend is not available in this view yet.

53730 days

1.5K90 days

4.3K1 year

Compare downloads with other packages →

Also on185 r2u

How downloads are counted

Repository

jamesdalg/cnvscope ↗Account: jamesdalg

8Stars

2Forks

0Open issues

0Open PRs

23Releases

395Commits

4Commit identities

395 commits · Last activity 2026-09-10 · Default branch at 3.7.8, ahead of CRAN 3.7.7 (checked 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

2025-07-29 · 82026-07-07 · 8

How these are measured

PracticesBeta

7 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/jamesdalg/cnvscope 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 (1)

GitHub Pages site last deployed 2026-09-10

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

Show all practicesHide 1 practice

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

46 external dependencies (excludes base and recommended)

Installing CNVScope adds 68 packages (42 with compiled code, 68 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB. 2 more not on CRAN are not measured.

Depends (2)

R >= 4.1.0ggplot2

Imports (16)

tidyr reshape2 magrittr jointseg shiny RCurl foreachMatrixOpenImageR matrixStats plyr data.table dplyr doParallel stringr rtracklayer

LinkingTo (0)

none

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 (4)

James Dalgleish

Author, Maintainer · added in 3.7.5

Alternate contact:

Paul Meltzer

Author, sad

Yonghong Wang

Author

Jack Zhu

Author

Maintainer since 1.9.7 (2018)

Listed in earlier versions (1)

James Dalgeish

no longer listed · 1.9.7 to 3.7.2

Releases (21)

Pick two releases to compare their code metrics.

3.7.7Latest
record
2026-09-10 · current release · diff ↗
3.7.6
record
2026-07-04 · diff ↗
3.7.5
record
2026-07-03 · diff ↗
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
3.7.2
record
2022-03-31 · diff ↗ ·
added 1 export
divisors
3.6.0
record
2021-05-24 · diff ↗
R
R 4.1.0 released · 2021-05-18
3.5.6
record
2021-01-11 · diff ↗
3.3.9
record
2020-12-15 · diff ↗
3.3.7
record
2020-11-29 · diff ↗
3.1.8
record
2020-07-03 · diff ↗
3.0.9
record
2020-04-29 · diff ↗

Show 14 earlier eventsHide 14 earlier events

3.0.8
record
2020-04-28 · diff ↗
3.0.6
record
2020-04-27 · diff ↗
R
R 4.0.0 released · 2020-04-24
3.0.5
record
2020-04-22 · diff ↗
2.9.4
record
2019-12-07 · diff ↗
2.9.2
record
2019-12-05 · diff ↗
2.8.2
record
2019-10-25 · diff ↗
2.8.1
record
2019-10-24 · diff ↗
2.7.7
record
2019-10-14 · diff ↗
2.7.2.5
record
2019-09-22 · diff ↗
2.7.0
record
2019-07-24 · diff ↗ ·
added 1 export
runCNVScopeLocal
R
R 3.6.0 released · 2019-04-26
1.9.7
record
2018-10-20
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-10-20
Total releases: 21 / 8 yrs
License: BSD_3_clause + file LICENSE OSI
Minimum R: ≥ 4.1.0
Bundled data: 2.8 KB / 1 file
Download size: 4.3 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("CNVScope")

Format

Dalgleish, J., Meltzer, P., Wang, Y., & Zhu, J. (2026). CNVScope: A Versatile Toolkit for Copy Number Variation Relationship Data Analysis and Visualization (Version 3.7.7) [Computer software]. https://doi.org/10.32614/CRAN.package.CNVScope

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 CNVScope version 3.7.7 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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