R Observatory: Metrics for genio version 1.1.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

genio

1.1.2Package record

Genetics Input/Output Functions

4packages dependsuggested by 1

15.1Kdownloads / year

89.4%test coverage

13/13flavors OK

Overview

About

Maintained by Alejandro OchoaCRAN page ↗GitHub ↗Issues ↗

Implements readers and writers for file formats associated with genetics data. Reading and writing Plink BED/BIM/FAM and GCTA binary GRM formats is fully supported, including a lightning-fast BED reader and writer implementations. Other functions are 'readr' wrappers that are more constrained, user-friendly, and efficient for these particular applications; handles Plink and Eigenstrat tables (FAM, BIM, IND, and SNP files). There are also make functions for FAM and BIM tables with default values to go with simulated genotype data.

Changes in 1.1.2

6th CRAN submission
Fixed an R-devel warning about sprintf usage (see below).
Solution was to replace calls to sprintf, all of which then went to stop, with direct calls to stop. ```
checking compiled code ... WARNING

File ‘genio/libs/genio.so’:

Found ‘sprintf’, possibly from ‘sprintf’ (C)

Objects: ‘read_bed_cpp.o’, ‘write_bed_cpp.o’

Compiled code should not call entry points which might terminate R nor

write to stdout/stderr instead of to the console, nor use Fortran I/O

nor system RNGs nor [v]sprintf.

```

Show all changes in 1.1.2Hide the rest of the changes in 1.1.2

Ran spellcheck, made one correction.
Updated cran-comments.md

From NEWS.md in the release

Install

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

install.packages("genio", 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("OchoaLab/genio")

Development version from OchoaLab/genio. 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-genio

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-genio

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-genio

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: 3.3 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-04-22
ERROR13 OK, 1 ERROR2026-04-18
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.2

READMEYes · 180 wordsVignettesYes · 1 · staticNEWSYes · 67% structured · mentions 1.1.2Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 35includes a package overview page
Examples that run: 100%35 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 97%
Help pages citing references: 0%

Vignettes (1)

Read and write BED files with `genio` HTML

How these are measured

Downloads

15.1K

CRAN downloads in the past year

Rank #3,641 · ~41/day · ~1.3K/mo

Releases R versions

Daily download trend is not available in this view yet.

84830 days

2.7K90 days

15.1K1 year

Compare downloads with other packages →

Also on577 r2u5 autocran2.6K conda_forge

How downloads are counted

Repository

ochoalab/genio ↗Organization: OchoaLab

19Stars

3Forks

3Open issues

1Open PRs

7Releases

104Commits

1Commit identities

License file reads as GPL-3.0 · 104 commits · Last activity 2025-02-20 · 0% stars, 30d · Default branch at 1.1.6.9000, ahead of CRAN 1.1.2 (checked 2026-10-11)

Responsiveness

How these are sampled

PRs merged (all time): 0%
Median days to close, 50 most recently updated closed issues: 1
Median days to close, 50 most recently updated closed PRs: 84

Stars over time

2025-03-01 · 182026-07-07 · 19

How these are measured

PracticesBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/ochoalab/genio on 2026-10-11.

CRAN release process (1)

cran-comments.md

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Installing genio adds 27 packages (15 with compiled code, 9.4 MB of source tarballs). Heaviest: Rcpp 1.8 MB, vctrs 1.0 MB, dplyr 902 KB.

Depends (0)

none

Imports (4)

readr tibble dplyr Rcpp

LinkingTo (1)

Rcpp

Suggests (6)

testthat knitr rmarkdown BEDMatrix snpStats lobstr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

4direct

0indirect

Imports 4

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

smer jackstraw modACDC lit

Suggests, most downloaded first

MoBPS

How these are counted

Code & Tests

Datasets

People & History

People (1)

Alejandro Ochoa

Author, Maintainer since 1.0.9 (2019)

Releases (7)

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
1.1.2Latest
record
2023-01-07 · current release · diff ↗
1.1.1
record
2022-04-27 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.0.25
record
2021-07-27 · diff ↗
1.0.23
record
2021-06-11 · diff ↗ ·
added 13 exports
count_lines, delete_files_grm, delete_files_phen, geno_to_char, read_eigenvec, read_grm, read_matrix, require_files_grm, require_files_phen, tidy_kinship, write_eigenvec, write_grm, write_matrix
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
1.0.12
record
2019-12-18 · diff ↗ ·
added 2 exports
read_phen, write_phen
1.0.10
record
2019-05-28 · diff ↗
1.0.9
record
2019-05-24
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-05-24
Total releases: 7 / 7 yrs
License: GPL-3 OSI
Download size: 570 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("genio")

Format

Ochoa, A. (2023). genio: Genetics Input/Output Functions (Version 1.1.2) [Computer software]. https://doi.org/10.32614/CRAN.package.genio

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 genio version 1.1.2 [Data set]. HJJB, LLC. Data release v2026-10-19. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-19, 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 →