R Observatory: Metrics for bigQF version 1.6

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

bigQF

1.6Package record

Quadratic Forms in Large Matrices

0packages depend

3.5Kdownloads / year

–test coverage

0/13flavors OK

Overview

About

Maintained by Thomas LumleyCRAN page ↗GitHub ↗

A computationally-efficient leading-eigenvalue approximation to tail probabilities and quantiles of large quadratic forms, in particular for the Sequence Kernel Association Test (SKAT) used in genomics doi:10.1002/gepi.22136. Also provides stochastic singular value decomposition for dense or sparse matrices.

Install

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

install.packages("bigQF", 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("tslumley/bigQF")

Development version from tslumley/bigQF. 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-bigqf

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-bigQF

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-bigQF

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

13NOTE

Check messages

NOTERd filesr-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, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64

checkRd: (-1) pQF.Rd:30: Lost braces; missing escapes or markup?
    30 | When \code{M} is not square, a randomised estimator for the trace of \code{crossprod(M)^2} is used. This is the sample size. When \code{M} is of \code{"matrixfree"} and does not include the trace of {crossprod(M)} as a component, this sample size will also be used to compute that. See Hutchinson reference. }
       |                                                                                                                                                                                                        ^

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Thomas Lumley <t.lumley@auckland.ac.nz>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Thomas",
                    family = "Lumley",
                    role = c("aut", "cre"),
                    email = "t.lumley@auckland.ac.nz")
as necessary.

CRAN check page ↗

Slowest check: 4.0 min · r-devel-windows-x86_64

Status changes

NOTE13 NOTE2026-09-08
ERROR12 NOTE, 1 ERROR2026-09-07
NOTE14 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.6

READMENoVignettesYes · 3 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 9includes a package overview page
Examples that run: 100%8 run in a plain check
Exported functions with examples: 100%
Documented parameters: 84%
Return-value docs: 100%
Help pages citing references: 67%

Vignettes (3)

How these are measured

Downloads

3.5K

CRAN downloads in the past year

Rank #7,484 · ~10/day · ~294/mo

Releases R versions

Daily download trend is not available in this view yet.

33030 days

1.2K90 days

3.5K1 year

Compare downloads with other packages →

Also on380 r2u36 autocran

How downloads are counted

Repository

tslumley/bigqf ↗Account: tslumley

6Stars

3Forks

1Open issues

1Open PRs

0Releases

55Commits

1Commit identities

55 commits · Last activity 2021-11-23

Responsiveness

not measured

Stars over time

2021-10-22 · 62026-07-07 · 6

How these are measured

PracticesBeta

Checks run against github.com/tslumley/bigqf on 2026-10-18.

No development-tooling practices detected in the upstream repository.

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

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Installing bigQF adds 4 packages (4 with compiled code, 1.2 MB of source tarballs). Heaviest: coxme 1.0 MB, svd 119 KB, bdsmatrix 47 KB.

Depends (2)

R >= 2.10methods

Imports (5)

svd CompQuadFormMatrixstatscoxme

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown SKAT

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 (from the free-text Author field) (1)

Thomas Lumley

Maintainer since 1.5 (2021)

Releases (2)

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
1.6Latest
record
2021-11-23 · current release · diff ↗
1.5
record
2021-11-08
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-11-08
Total releases: 2 / 5 yrs
License: GPL-2 OSI
Minimum R: ≥ 2.10
Bundled data: 342 KB / 3 files
Download size: 391 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("bigQF")

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 bigQF version 1.6 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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