R Observatory: Metrics for concatipede version 1.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

concatipede

1.0.1Package record

Easy Concatenation of Fasta Sequences

0packages depend

3Kdownloads / year

68.5%test coverage

13/13flavors OK

Overview

About

Maintained by Matteo VecchiCRAN page ↗GitHub ↗Website ↗Issues ↗

Concatenation of multiple sequence alignments based on a correspondence table that can be edited in Excel doi:10.5281/zenodo.5130603.

Changes in 1.0.1

Fixed some minor issues for CRAN submission.

From NEWS.md in the release

Install

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

install.packages("concatipede", 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("tardipede/concatipede")

Development version from tardipede/concatipede. 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-concatipede

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-concatipede

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-concatipede

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: 1.4 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.1

READMEYes · 107 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 1.0.1Citation fileYes · software entry onlyWebsiteYes · pkgdown

Help pages: 11 (1 internal)
Examples that run: 83%5 run in a plain check · 1 never run
Exported functions with examples: 60%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

Example of package usage HTML

How these are measured

Downloads

3K

CRAN downloads in the past year

Rank #12,577 · ~8/day · ~252/mo

Releases R versions

Daily download trend is not available in this view yet.

28230 days

89690 days

3K1 year

Compare downloads with other packages →

Also on91 r2u3 autocran

How downloads are counted

Repository

tardipede/concatipede ↗Account: tardipede

0Stars

0Forks

1Open issues

0Open PRs

1Releases

246Commits

2Commit identities

246 commits · Last activity 2022-04-12

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: 0

How these are measured

PracticesBeta

9 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/tardipede/concatipede on 2026-10-21.

Continuous integration (3)

GitHub ActionsR CMD check workflowGitLab CI

The R CMD check workflow runs on Linux

Docs source (2)

pkgdown

GitHub Pages site last deployed 2022-04-12

pkgdown site last built 2022-04-12

Coverage (1)

Coverage reporting

Reproducibility and dev environment (1)

Makefile

Show all practicesHide 2 practices

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Installing concatipede adds 32 packages (18 with compiled code, 29 MB of source tarballs). Heaviest: stringi 11 MB, igraph 4.8 MB, readxl 2.1 MB.

Depends (0)

none

Imports (10)

ape dplyr igraph qualV magrittr tibble readxl stringdist stringr writexl

LinkingTo (0)

none

Suggests (5)

DT knitr rmarkdown tidyverse 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 (2)

Matteo Vecchi

Author, Maintainer since 1.0.1 (2021)

Mattieu Bruneaux

Author

Releases (1)

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
1.0.1Latest
record
2021-08-06 · current release
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-08-06
Total releases: 1 / 5 yrs
License: MIT + file LICENSE OSI
Download size: 1.9 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("concatipede")

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

It points to 10.5281/zenodo.5130603.

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 concatipede version 1.0.1 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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