avidaR

1.2.1

A Computational Biologist’s Toolkit To Get Data From 'avidaDB'

0packages depend

3.5Kdownloads / year

91.5%test coverage

13/13checks pass

Overview

About

Maintained by Raúl OrtegaFirst published 2022-04-085 releasesCRAN page ↗GitLab ↗

Easy-to-use tools for performing complex queries on 'avidaDB', a semantic database that stores genomic and transcriptomic data of self-replicating computer programs (known as digital organisms) that mutate and evolve within a user-defined computational environment.

Install

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

install.packages("avidaR", 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("fortunalab/avidaR")

Development version from fortunalab/avidaR. 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-avidar

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-avidaR

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-avidaR

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

Health

CRAN checks

13OK

Slowest check: 1.8 min · r-oldrel-macos-x86_64

Code health

Yes

Tests · ratio 0.32

91.5%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 589 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 97%
Documented parameters: 100%
Return-value docs: 94%
References docs: 0%

Downloads

3.5K

CRAN downloads in the past year

Rank #12,393 · ~10/day · ~291/mo

Releases R versions

Daily download trend is not available in this view yet.

26830 days

86290 days

3.5K1 year

Compare downloads with other packages →

Also on104 r2u44 autocran

Repository

GitLab ↗ fortunalab/avidar

Repository practices

Upstream repositoryBeta

Repository gitlab.com/fortunalab/avidar is linked, but repository-practices checks have not run for it yet. Checks are GitHub-only for now.

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.6.0

Imports (11)

base64enc xml2 httr dplyr readr tidyr tibble (>= 3.0.6)circlize RColorBrewer R6 curl

LinkingTo (0)

none

Suggests (1)

testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 5,556 (72%)Rd 2,154 (28%)

Code characteristics

Object systems

R61

Cyclomatic complexity: 3.0 median / 25 max
Test cases: 33 / 0.32 per code line

Test coverage

Line coverage

92%

Expression

86.0%

Tests / Examples

91.5% / 70% ex

Functions

59 31 exported

Complexity

4 avg / 25 max

Call network

59 nodes / 190 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

59 functions

Function	Cyclo	Coverage
get_message_from_status_code	5	0%
server_no_response	1	0%
validate_access_options	2	0%
validate_param	2	50%
server_api_get	8	57%
server_api_post	11	60%

People & History

People (2)

Maintainer (1)

Raúl Ortega

Maintainer

Authors (1)

Miguel A. Fortuna

Author

Package Timeline

5 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
1.2.1Latest
2024-06-21 · current release · diff ↗
R
R 4.4.0 released · 2024-04-24
1.2.0
2023-09-14 · diff ↗
unarchivedReturned to CRAN
2023-09-14
archivedRemoved from CRAN
2023-09-11
repeated policy violation On Internet access
R
R 4.3.0 released · 2023-04-21
1.1.3
2022-08-22 · diff ↗
unarchivedReturned to CRAN
2022-08-22
archivedRemoved from CRAN
2022-08-03
policy violation which blocked installation On Internet access, required by top-level code in the package
1.1.2
2022-05-30 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.0.1
2022-04-08
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2022-04-08
Total releases: 5 / 4 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.6.0
Download size: 39 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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