R Observatory: Metrics for seqminer version 9.9

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

seqminer

9.9Package record

Efficiently Read Sequence Data (VCF Format, BCF Format, METAL Format and BGEN Format) into R

0packages depend

10.6Kdownloads / year

40.5%test coverage

11/13flavors OK

Overview

About

Maintained by Xiaowei ZhanCRAN page ↗GitHub ↗Website ↗Issues ↗

Integrate sequencing data (Variant call format, e.g. VCF or BCF) or meta-analysis results in R. This package can help you (1) read VCF/BCF/BGEN files by chromosomal ranges (e.g. 1:100-200); (2) read 'RareMETAL' summary statistics files; (3) read tables from a 'tabix'-indexed files; (4) annotate VCF/BCF files; (5) create customized workflow based on Makefile.

Install

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

install.packages("seqminer", 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("zhanxw/seqminer")

Development version from zhanxw/seqminer. 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-seqminer

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-seqminer

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-seqminer

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

2WARNING11OK

Check messages

WARNINGwhether package can be installedr-oldrel-macos-x86_64, r-release-macos-x86_64

r-oldrel-macos-x86_64

Found the following significant warnings:
  SingleChromosomeVCFIndex.cpp:109:51: warning: format specifies type 'long' but the argument has type 'int64_t' (aka 'long long') [-Wformat]
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.5/seqminer.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
* used C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
* used SDK: ‘NA’

r-release-macos-x86_64

Found the following significant warnings:
  SingleChromosomeVCFIndex.cpp:109:51: warning: format specifies type 'long' but the argument has type 'int64_t' (aka 'long long') [-Wformat]
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.6/seqminer.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
* used C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
* used SDK: ‘MacOSX11.3.1.sdk’

Additional issues

rchk

CRAN check page ↗

Slowest check: 7.5 min · r-devel-windows-x86_64

Status changes

WARNING11 OK, 2 WARNING2026-06-09
ERROR10 OK, 2 WARNING, 1 ERROR2026-06-08
WARNING10 OK, 2 NOTE, 2 WARNING2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 9.9

READMEYes · 346 wordsVignettesNoNEWSNoCitation fileYes · cites a publicationWebsiteYes

Help pages: 48 (2 internal)includes a package overview page
Examples that run: 97%38 run in a plain check · 1 never run
Exported functions with examples: 93%
Documented parameters: 100%
Return-value docs: 80%
Help pages citing references: 0%

Also includes 3 demo scripts (run with demo())

How these are measured

Downloads

10.6K

CRAN downloads in the past year

Rank #3,693 · ~29/day · ~882/mo

Releases R versions

Daily download trend is not available in this view yet.

99830 days

2.7K90 days

10.6K1 year

Compare downloads with other packages →

Also on427 r2u3 autocran6.4K conda_forge744 bioconda

How downloads are counted

Repository

zhanxw/seqminer ↗Account: zhanxw

34Stars

12Forks

18Open issues

0Open PRs

1Releases

224Commits

9Commit identities

sequencingannotationnext-generation-sequencingmeta-analysisvcfbcftabixbgen

224 commits · Last activity 2026-02-23 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 3
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2025-10-25 · 322026-08-20 · 34

How these are measured

PracticesBeta

4 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/zhanxw/seqminer 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

Docs source (1)

GitHub Pages site last deployed 2026-02-23

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

Dependencies

Declared dependencies

2 external dependencies (excludes base and recommended)

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

Depends (0)

none

Imports (0)

none

LinkingTo (0)

none

Suggests (2)

testthat SKAT

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (7)

Xiaowei Zhan

Author, Maintainer since 0.1 (2013)

Dajiang Liu

Author

Attractive Chaos

Copyright holder · added in 5.3

We have used the following software and made minimal necessary changes: Tabix, Heng Li (MIT license). We removed…

Broad Institute / Massachusetts Institute of Technology

Copyright holder · added in 5.3

D. Richard Hipp

Copyright holder · added in 8.4

Facebook, Inc

Copyright holder · added in 6.7

Genome Research Ltd (GRL)

Copyright holder · added in 5.3

Listed in earlier versions (6)

Show 6 peopleHide 6 people

Heng Li .

no longer listed · 0.1 to 3.1

Mark Adler

no longer listed · 0.1 to 3.1

with contributions of Jean-loup Gailly

no longer listed · 0.1 to 3.1

Julian Seward

no longer listed · 0.1 to 3.1

with contributions of Heng Li .

no longer listed · 3.4 to 3.7

with contributions from Heng Li .

no longer listed · 3.9 to 5.2

Releases (43)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
unarchivedReturned to CRAN
2026-02-24
9.9Latest
record
2026-02-24 · current release · diff ↗
archivedRemoved from CRAN
2026-01-29
issues were not corrected in time
R
R 4.5.0 released · 2025-04-11
9.7
record
2024-10-02 · diff ↗
R
R 4.4.0 released · 2024-04-24
9.4
record
2024-02-03 · diff ↗
9.3
record
2023-11-28 · diff ↗
9.1
record
2023-09-02 · diff ↗
R
R 4.3.0 released · 2023-04-21
8.9
record
2023-04-07 · diff ↗
8.6
record
2023-01-26 · diff ↗
8.5
record
2022-11-15 · diff ↗
R
R 4.2.0 released · 2022-04-22
8.4
record
2022-02-07 · diff ↗

Show 44 earlier eventsHide 44 earlier events

8.2
record
2021-11-09 · diff ↗
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
8.0
record
2020-03-02 · diff ↗ ·
added 4 exports
createSingleChromosomeBCFIndex, createSingleChromosomeVCFIndex, readSingleChromosomeBCFToMatrixByRange, readSingleChromosomeVCFToMatrixByRange
R
R 3.6.0 released · 2019-04-26
7.1
record
2019-01-08 · diff ↗ ·
added 1 export
openPlink
7.0
record
2019-01-07 · diff ↗ ·
added 1 export
readPlinkToMatrixByIndex
6.7
record
2018-12-06 · diff ↗ ·
added 4 exports
readBGENToListByGene, readBGENToListByRange, readBGENToMatrixByGene, readBGENToMatrixByRange
6.1
record
2018-08-02 · diff ↗
R
R 3.5.0 released · 2018-04-23
6.0
record
2017-05-05 · diff ↗
R
R 3.4.0 released · 2017-04-21
5.9
record
2017-04-18 · diff ↗
5.7
record
2017-01-13 · diff ↗
5.3
record
2016-05-07 · diff ↗
5.2
record
2016-05-03 · diff ↗
R
R 3.3.0 released · 2016-05-03
5.0
record
2015-10-22 · diff ↗
4.9
record
2015-09-16 · diff ↗ ·
added 5 exports
addJob, isTabixRange, newJob, newWorkflow, writeWorkflow
4.7
record
2015-08-19 · diff ↗
4.5
record
2015-06-29 · diff ↗ ·
added 1 export
download.annotation.resource
4.2
record
2015-06-10 · diff ↗
3.9
record
2015-05-21 · diff ↗
3.7
record
2015-05-16 · diff ↗
R
R 3.2.0 released · 2015-04-16
3.4
record
2014-12-08 · diff ↗
3.1
record
2014-05-07 · diff ↗
3.0
record
2014-04-19 · diff ↗ ·
added 1 export
isInRange
2.7
record
2014-04-14 · diff ↗ ·
added 6 exports
annotateGene, annotatePlain, annotateVcf, getRefBase, makeAnnotationParameter, validateAnnotationParameter
R
R 3.1.0 released · 2014-04-10
2.2
record
2014-01-27 · diff ↗ ·
removed 1 export
tabix

added 6 exports
rvmeta.writeCovData, rvmeta.writeScoreData, tabix.createIndex, tabix.createIndex.meta, tabix.createIndex.vcf, tabix.read
2.0
record
2013-11-20 · diff ↗
1.9.1
record
2013-11-15 · diff ↗
1.9
record
2013-11-11 · diff ↗ ·
added 3 exports
rvmeta.readSkewByRange, tabix.read.header, tabix.read.table
1.4
record
2013-09-29 · diff ↗
1.3
record
2013-09-26 · diff ↗ ·
added 1 export
rvmeta.readNullModel
1.0
record
2013-09-04 · diff ↗
0.7
record
2013-07-29 · diff ↗
0.5
record
2013-05-28 · diff ↗
0.3
record
2013-04-13 · diff ↗ ·
removed 1 export
pattern:^[^\\.]

added 9 exports
readVCFToListByGene, readVCFToListByRange, readVCFToMatrixByGene, readVCFToMatrixByRange, rvmeta.readCovByRange, rvmeta.readDataByGene, rvmeta.readDataByRange, rvmeta.readScoreByRange, tabix
R
R 3.0.0 released · 2013-04-03
0.2
record
2013-04-01 · diff ↗ ·
added 1 export
pattern:^[^\\.]
0.1
record
2013-03-20
R
R 2.15.0 released · 2012-03-30

Package metadata

First published: 2013-03-20
Total releases: 43 / 13 yrs
License: GPL | file LICENSE
Copyright: We have used the following software and made minimal necessary changes: tabix, Heng Li <lh3@live.co.uk> (MIT license), SQLite (Public Domain), Zstandard (BSD license). For tabix, we removed standard IO related functions, e.g. printf, fprintf ; also changed its un-safe pointer arithmetics. For zstandard, we removed compiler (clang, MSVC) specific preprocessing flags.
Download size: 4.4 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("seqminer")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

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 seqminer version 9.9 [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.

Report a problem with this page →