R Observatory: Metrics for copyseparator version 1.2.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

copyseparator

1.2.0Package record

Assembling Long Gene Copies from Short Read Data

0packages depend

2.9Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Lei YangCRAN page ↗GitHub ↗Issues ↗

Assembles two or more gene copies from short-read Next-Generation Sequencing data. Works best when there are only two gene copies and read length >=250 base pairs. High and relatively even coverage are important.

Changes in 1.2.0

sep_assem can now process multiple input files placed in the working folder one by one.
Added a new parameter "core_number" for sep_assem. It can now run using multiple CPU cores and the run can be much faster.

From NEWS.md in the release

Install

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

install.packages("copyseparator", 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("LeiYang-Fish/copyseparator")

Development version from LeiYang-Fish/copyseparator. 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-copyseparator

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

2NOTE11OK

Check messages

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Lei Yang <leiyangslu@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Lei",
                    family = "Yang",
                    role = c("aut", "cre"),
                    email = "leiyangslu@gmail.com")
as necessary.

CRAN check page ↗

Slowest check: 3.3 min · r-oldrel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTE2026-08-09
ERROR10 OK, 2 NOTE, 1 ERROR2026-08-02
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.2.0

READMENoVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 1.2.0Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 6
Examples that run: 0%6 never run
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

Usage_of_copyseparator HTML

How these are measured

Downloads

2.9K

CRAN downloads in the past year

Rank #14,987 · ~8/day · ~241/mo

Releases R versions

Daily download trend is not available in this view yet.

27130 days

81290 days

2.9K1 year

Compare downloads with other packages →

Also on83 r2u

How downloads are counted

Repository

leiyang-fish/copyseparator ↗Account: LeiYang-Fish

0Stars

0Forks

0Open issues

0Open PRs

0Releases

Last activity 2024-12-23

Responsiveness

not measured

How these are measured

PracticesBeta

3 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/leiyang-fish/copyseparator on 2026-10-21.

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Installing copyseparator adds 27 packages (18 with compiled code, 33 MB of source tarballs). Heaviest: stringi 11 MB, sp 4.3 MB, seqinr 3.4 MB. 2 more not on CRAN are not measured.

Depends (1)

R >= 3.5.0

Imports (11)

ape seqinr stringr kmer DECIPHER beepr BiostringsgrDevicesdoParallel foreachparallel

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (from the free-text Author field) (1)

Lei Yang

Maintainer since 1.0.0 (2022)

Releases (3)

Pick two releases to compare their code metrics.

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
1.2.0Latest
record
2022-11-25 · current release · diff ↗
1.1.0
record
2022-07-06 · diff ↗ ·
added 1 export
sep_assem
1.0.0
record
2022-05-24
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-05-24
Total releases: 3 / 4 yrs
License: GPL-2 OSI
Minimum R: ≥ 3.5.0
Download size: 98 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("copyseparator")

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 copyseparator version 1.2.0 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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