R Observatory: Metrics for vcfR version 1.16.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

vcfR

1.16.0Package record

Manipulate and Visualize VCF Data

23packages dependsuggested by 10

99.7Kdownloads / year

68.2%test coverage

8/13flavors OK

Overview

About

Maintained by Brian J. KnausCRAN page ↗GitHub ↗Website ↗

Facilitates easy manipulation of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data is read into R a parser function extracts matrices of data. This information can then be used for quality control or other purposes. Additional functions provide visualization of genomic data. Once processing is complete data may be written to a VCF file (*.vcf.gz). It also may be converted into other popular R objects (e.g., genlight, DNAbin). VcfR provides a link between VCF data and familiar R software.

Install

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

install.packages("vcfR", 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("knausb/vcfR")

Development version from knausb/vcfR. 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-vcfr

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-vcfR

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

Health

CRAN checks

5NOTE8OK

Check messages

NOTER code for possible problemsr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64

Found calls to structure() using deprecated special names:
  vcfR/tests/testthat/test_genetic_diff.R (.Dim: 2, .Dimnames: 2, .Label: 1)
  vcfR/tests/testthat/test_genotype_matrix_functions.R (.Dim: 1, .Dimnames: 1)
'.Dim' should be changed to 'dim'.
'.Dimnames' should be changed to 'dimnames'.
'.Label' should be changed to 'levels'.

CRAN check page ↗

Slowest check: 7.8 min · r-oldrel-windows-x86_64

Status changes

NOTE8 OK, 5 NOTENow
NOTE11 OK, 2 NOTE2026-07-16
OK12 OK2026-04-25
NOTE12 OK, 2 NOTE2026-04-22
ERROR11 OK, 2 NOTE, 1 ERROR2026-04-18
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.16.0

READMEYes · 677 wordsVignettesYes · 4 · dynamicNEWS· In the repository, left out of the releaseCitation fileYes · cites a publicationWebsiteYes

Help pages: 47 (2 internal)includes a package overview page
Examples that run: 93%27 run in a plain check · 2 never run
Exported functions with examples: 66%
Documented parameters: 100%
Return-value docs: 49%
Help pages citing references: 2%

Vignettes (4)

How these are measured

Downloads

99.7K

CRAN downloads in the past year

Rank #1,371 · ~273/day · ~8.3K/mo

Releases R versions

Daily download trend is not available in this view yet.

5K30 days

20.5K90 days

99.7K1 year

Compare downloads with other packages →

Also on1.5K r2u473.4K conda_forge548 bioconda133 c2d4u

How downloads are counted

Repository

knausb/vcfr ↗Account: knausb

270Stars

53Forks

21Open issues

0Open PRs

16Releases

1,478Commits

14Commit identities

vcf-datarstatsgenomicsvisualizationrcpppopulation-geneticspopulation-genomics

1,478 commits · Last activity 2026-06-08 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 71%
Median days to close, 50 most recently updated closed issues: 12
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-10-26 · 2632026-09-11 · 270

How these are measured

PracticesBeta

6 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/knausb/vcfr on 2026-10-25.

Continuous integration (3)

GitHub ActionsR CMD check workflowAppVeyor

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

CRAN release process (2)

cran-comments.mdrevdep/

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

20 external dependencies (excludes base and recommended)

Installing vcfR adds 25 packages (15 with compiled code, 26 MB of source tarballs). Heaviest: stringi 11 MB, pinfsc50 3.3 MB, Rcpp 1.8 MB.

Depends (1)

R >= 3.0.1

Imports (15)

ape dplyrgraphicsgrDevicesmagrittr memusemethodspinfsc50 Rcppstatsstringr tibbleutilsvegan viridisLite

LinkingTo (1)

Rcpp

Suggests (9)

adegenet ggplot2 knitr poppr reshape2 rmarkdown scales testthat tidyr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

23direct

0indirect

Imports 23

Suggested by 10

Show all 33 packagesHide all 33 packages

Depends, Imports or LinkingTo, most downloaded first

Suggests, most downloaded first

dartR statgenGWAS dartR.base rehh pcadapt sequoia tidypopgen BIGpopA MoBPS corridoR

How these are counted

Code & Tests

Datasets

People & History

People (6)

Brian J. Knaus

Maintainer since 1.0.0 (2016), Author

Author

Contributor

Contributor

Contributor

Contributor

Listed in earlier versions (6)

Show 6 peopleHide 6 people

Brian J.

no longer listed · 1.0.0 to 1.16.0

Niklaus J.

no longer listed · 1.0.0 to 1.16.0

Eric C.

no longer listed · 1.1.0 to 1.16.0

David J.

no longer listed · 1.1.0 to 1.16.0

Zhian N.

no longer listed · 1.3.0 to 1.16.0

Javier F.

no longer listed · 1.6.0 to 1.16.0

Releases (17)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.16.0Latest
record
2026-02-23 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.15.0
record
2023-12-08 · diff ↗ ·
removed 20 exports
.CM_to_NM, .NM2winNM, .elementNumber, .extract_GT_to_CM, .extract_haps, .grepa, .gt_to_popsum, .rank_variants, .read_body_gz, .read_meta_gz, .seq_to_rects, .shankaR, .vcf_stats_gz, .window_init, .windowize_NM, .windowize_annotations, .windowize_fasta, .windowize_variants, .write_fasta, .write_vcf_body
R
R 4.3.0 released · 2023-04-21
1.14.0
record
2023-02-10 · diff ↗
1.13.0
record
2022-07-16 · diff ↗ ·
added 1 export
vcfR2hapmap
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
unarchivedReturned to CRAN
2020-09-01
1.12.0
record
2020-09-01 · diff ↗
archivedRemoved from CRAN
2020-07-05
check issues were not corrected in time
1.11.0
record
2020-06-05 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.10.0
record
2020-02-06 · diff ↗

Show 15 earlier eventsHide 15 earlier events

1.9.0
record
2020-01-10 · diff ↗ ·
added 1 export
is.indel
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
1.8.0
record
2018-04-17 · diff ↗ ·
added 1 export
check_keys
1.7.0
record
2018-02-08 · diff ↗
1.6.0
record
2017-12-08 · diff ↗ ·
added 25 exports
.CM_to_NM, .NM2winNM, .elementNumber, .extract_GT_to_CM, .extract_haps, .grepa, .gt_to_popsum, .rank_variants, .read_body_gz, .read_meta_gz, .seq_to_rects, .shankaR, .vcf_stats_gz, .window_init, .windowize_NM, .windowize_annotations, .windowize_fasta, .windowize_variants, .write_fasta, .write_vcf_body, freq_peak_plot, pairwise_genetic_diff, peak_to_ploid, rePOS, vcfR2migrate
1.5.0
record
2017-05-18 · diff ↗ ·
added 1 export
genetic_diff
R
R 3.4.0 released · 2017-04-21
1.4.0
record
2017-01-07 · diff ↗
1.3.0
record
2016-12-08 · diff ↗ ·
added 11 exports
INFO2df, freq_peak, getALT, getFILTER, getID, getINFO, getREF, masplit, metaINFO2df, ordisample, queryMETA
1.2.0
record
2016-12-05 · diff ↗ ·
added 1 export
is_het
1.1.0
record
2016-05-26 · diff ↗ ·
removed 1 export
windowize

added 9 exports
%>%, AD_frequency, addID, extract_gt_tidy, extract_info_tidy, is.het, maf, vcfR2tidy, vcf_field_names
R
R 3.3.0 released · 2016-05-03
1.0.0
record
2016-02-22
R
R 3.2.0 released · 2015-04-16

Package metadata

First published: 2016-02-22
Total releases: 17 / 10 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.0.1
Bundled data: 651 KB / 4 files
Download size: 1.5 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("vcfR")

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

It points to 10.1111/1755-0998.12549, 10.1101/041277.

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 vcfR version 1.16.0 [Data set]. HJJB, LLC. Data release v2026-10-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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