R Observatory: Metrics for minimalistGODB version 1.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

minimalistGODB

1.1.0Package record

Build a Minimalist Gene Ontology (GO) Database (GODB)

6packages depend

5.7Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Barry ZeebergCRAN page ↗

Normally building a GODB is fairly complicated, involving downloading multiple database files and using these to build e.g. a 'mySQL' database. Accessing this database is also complicated, involving an intimate knowledge of the database in order to construct reliable queries. Here we have a more modest goal, generating GOGOA3, which is a stripped down version of the GODB that was originally restricted to human genes as designated by the HUGO Gene Nomenclature Committee (HGNC) (see https://geneontology.org/). I have now added about two dozen additional species, namely all species represented on the Gene Ontology download page https://current.geneontology.org/products/pages/downloads.html. This covers most of the model organisms that are commonly used in bio-medical and basic research (assuming that anyone still has a grant to do such research). This can be built in a matter of seconds from 2 easily downloaded files (see https://current.geneontology.org/products/pages/downloads.html and https://geneontology.org/docs/download-ontology/), and it can be queried by e.g. w<-which(GOGOA3[,"HGNC"] %in% hgncList) where GOGOA3 is a matrix representing the minimalist GODB and hgncList is a list of gene identifiers. This database will be used in my upcoming package 'GoMiner' which is based on my previous publication (see Zeeberg, B.R., Feng, W., Wang, G. et al. (2003)doi:10.1186/gb-2003-4-4-r28). Relevant .RData files are available from GitHub (https://github.com/barryzee/GO/tree/main/databases).

Install

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

install.packages("minimalistGODB", 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-minimalistgodb

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-minimalistGODB

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-minimalistGODB

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: 1.6 min · r-oldrel-macos-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
WARNING12 OK, 1 WARNING2026-06-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.0

READMENoVignettesYes · 1 · staticNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 11
Examples that run: 100%8 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

minimalistGODB HTML

How these are measured

Downloads

5.7K

CRAN downloads in the past year

Rank #11,945 · ~16/day · ~473/mo

Releases R versions

Daily download trend is not available in this view yet.

30330 days

92290 days

5.7K1 year

Compare downloads with other packages →

Also on101 r2u2 autocran

How downloads are counted

Dependencies

Declared dependencies

3 external dependencies (excludes base and recommended)

Installing minimalistGODB adds no packages beyond those that come with R.

Depends (1)

R >= 4.2.0

Imports (0)

none

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

6direct

0indirect

Imports 6

Depends, Imports or LinkingTo, most downloaded first

HTGM GoMiner HTGM3D HTGM2D HTGM4D randomGODB

How these are counted

Code & Tests

Datasets

People & History

People (1)

Barry Zeeberg

Author, Maintainer since 1.0 (2025)

Releases (2)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.1.0Latest
record
2025-05-04 · current release · diff ↗ ·
added 3 exports
buildGODatabaseDriver, grepList, restrictGOA
R
R 4.5.0 released · 2025-04-11
1.0
record
2025-03-18
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2025-03-18
Total releases: 2 / 1 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 4.2.0
Bundled data: 1.1 MB / 3 files
Download size: 2.1 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("minimalistGODB")

Format

Zeeberg, B. (2025). minimalistGODB: Build a Minimalist Gene Ontology (GO) Database (GODB) (Version 1.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.minimalistGODB

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 minimalistGODB version 1.1.0 [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.

Report a problem with this page →