seqminer

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

v9.9 · Feb 24, 2026 · GPL | file LICENSE

Description

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.

Downloads

CRAN

845

Last 30 days

3901st

2.3K

Last 90 days

11.5K

Last year

Trend: +18.5% (30d vs prior 30d)

r2u CRAN

Last 30 days

146

Last 90 days

521

Last year

Trend: -39.7% (30d vs prior 30d)

CRAN Check Status

2 WARNING

11 OK

Show all 13 flavors

Flavor	Status	Time
r-devel-linux-x86_64-debian-clang	OK	130.5s
r-devel-linux-x86_64-debian-gcc	OK	105.6s
r-devel-linux-x86_64-fedora-clang	OK	187.6s
r-devel-linux-x86_64-fedora-gcc	OK	246.4s
r-devel-windows-x86_64	OK	369s
r-oldrel-macos-arm64	OK	37s
r-oldrel-macos-x86_64	WARNING	172s
r-oldrel-windows-x86_64	OK	392s
r-patched-linux-x86_64	OK	134.8s
r-release-linux-x86_64	OK
r-release-macos-arm64	OK	39s
r-release-macos-x86_64	WARNING	128s
r-release-windows-x86_64	OK	381s

Check details (2 non-OK)

WARNING r-oldrel-macos-x86_64

whether package can be installed

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’

WARNING r-release-macos-x86_64

whether package can be installed

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 Details →

Check History

WARNING 11 OK · 0 NOTE · 2 WARNING · 0 ERROR · 0 FAILURE Jun 9, 2026

WARNING r-release-macos-x86_64

whether package can be installed

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’

WARNING r-oldrel-macos-x86_64

whether package can be installed

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’

ERROR 10 OK · 0 NOTE · 2 WARNING · 1 ERROR · 0 FAILURE Jun 8, 2026

ERROR r-devel-linux-x86_64-debian-gcc

top-level files

Output from running autoreconf:
  autom4te: error: cannot open /tmp/arpEY43a/am4tHBwErK/traces.m4: No space left on device
  aclocal: error: /usr/bin/autom4te failed with exit status: 1
  autoreconf: error: aclocal failed with exit status: 1

WARNING r-release-macos-x86_64

whether package can be installed

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’

WARNING r-oldrel-macos-x86_64

whether package can be installed

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’

WARNING 10 OK · 2 NOTE · 2 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026

WARNING r-release-macos-x86_64

whether package can be installed

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’

NOTE r-oldrel-macos-arm64

installed package size

installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb

WARNING r-oldrel-macos-x86_64

whether package can be installed

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/4.4/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.sdk’

NOTE r-oldrel-windows-x86_64

for GNU extensions in Makefiles

GNU make is a SystemRequirements.

Version History

44 tracked

new 9.9 Mar 10, 2026

updated 9.9 ← 9.7 diff Feb 23, 2026

updated 9.7 ← 9.4 diff Oct 1, 2024

updated 9.4 ← 9.3 diff Feb 2, 2024

updated 9.3 ← 9.1 diff Nov 27, 2023

updated 9.1 ← 8.9 diff Sep 1, 2023

updated 8.9 ← 8.6 diff Apr 6, 2023

updated 8.6 ← 8.5 diff Jan 25, 2023

updated 8.5 ← 8.4 diff Nov 14, 2022

updated 8.4 ← 8.2 diff Feb 6, 2022

updated 8.2 ← 8.0 diff Nov 8, 2021

updated 8.0 ← 7.1 diff Mar 1, 2020

updated 7.1 ← 7.0 diff Jan 7, 2019

updated 7.0 ← 6.7 diff Jan 6, 2019

updated 6.7 ← 6.1 diff Dec 5, 2018