R Observatory: Metrics for geneHummus version 1.0.11

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

geneHummus

1.0.11Package record

A Pipeline to Define Gene Families in Legumes and Beyond

0packages depend

2.7Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Jose V. DieCRAN page ↗GitHub ↗Issues ↗

A pipeline with high specificity and sensitivity in extracting proteins from the RefSeq database (National Center for Biotechnology Information). Manual identification of gene families is highly time-consuming and laborious, requiring an iterative process of manual and computational analysis to identify members of a given family. The pipelines implements an automatic approach for the identification of gene families based on the conserved domains that specifically define that family. See Die et al. (2018) doi:10.1101/436659 for more information and examples.

Install

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

install.packages("geneHummus", 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("NCBI-Hackathons/GeneHummus")

Development version from NCBI-Hackathons/GeneHummus. 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-genehummus

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-geneHummus

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-geneHummus

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: 1.5 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-05-11
WARNING12 OK, 1 WARNING2026-05-10
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.11

READMEYes · 150 wordsVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 20includes a package overview page
Examples that run: 71%5 run in a plain check · 1 only when donttest examples are enabled (R CMD check --as-cran) · 1 never run
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

2.7K

CRAN downloads in the past year

Rank #16,721 · ~7/day · ~223/mo

Releases R versions

Daily download trend is not available in this view yet.

29130 days

75990 days

2.7K1 year

Compare downloads with other packages →

Also on70 r2u1 autocran

How downloads are counted

Repository

ncbi-hackathons/genehummus ↗Organization: NCBI-Hackathons

8Stars

2Forks

0Open issues

0Open PRs

3Releases

197Commits

5Commit identities

197 commits · Last activity 2020-09-02

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 4
Median days to close, 50 most recently updated closed PRs: not measured

Stars over time

2025-03-11 · 82026-07-07 · 8

How these are measured

PracticesBeta

Checks run against github.com/ncbi-hackathons/genehummus on 2026-10-21.

No development-tooling practices detected in the upstream repository.

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

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Installing geneHummus adds 26 packages (17 with compiled code, 20 MB of source tarballs). Heaviest: stringi 11 MB, openssl 1.1 MB, jsonlite 1.0 MB.

Depends (1)

R >= 3.4.0

Imports (6)

rentrez stringr dplyr httrutilscurl

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

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 (6)

Jose V. Die

Author, Maintainer since 1.0.0 (2019)

Author

Contributor

Contributor

Contributor

Contributor

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
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
1.0.11Latest
record
2019-04-05 · current release · diff ↗
unarchivedReturned to CRAN
2019-03-26
1.0.1
record
2019-03-26 · diff ↗
archivedRemoved from CRAN
2019-03-25
policy violation Internet access is not guarded
1.0.0
record
2019-03-25
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2019-03-25
Total releases: 3 / 7 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.4.0
Bundled data: 25 KB / 2 files
Download size: 60 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("geneHummus")

Format

Die, J. V., Awe, O. I., Busby, B., Dillman, A., Elmassry, M. M., & LeBlanc, K. H. (2019). geneHummus: A Pipeline to Define Gene Families in Legumes and Beyond (Version 1.0.11) [Computer software]. https://doi.org/10.32614/CRAN.package.geneHummus

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 geneHummus version 1.0.11 [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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