sGBJ

0.1.1

Survival Extension of the Generalized Berk-Jones Test

0packages depend

2.7Kdownloads / year

63.8%test coverage

12/13checks pass

Overview

About

Maintained by Laura VillainFirst published 2021-09-152 releasesCRAN page ↗GitHub ↗

Implements an extension of the Generalized Berk-Jones (GBJ) statistic for survival data, sGBJ. It computes the sGBJ statistic and its p-value for testing the association between a gene set and a time-to-event outcome with possible adjustment on additional covariates. Detailed method is available at Villain L, Ferte T, Thiebaut R and Hejblum BP (2021) doi:10.1101/2021.09.07.459329.

Install

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

install.packages("sGBJ", 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("lauravillain/sGBJ")

Development version from lauravillain/sGBJ. 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-sgbj

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

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-sGBJ

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-sGBJ

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

1NOTE12OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 54 s · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.07

63.8%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 147 wordsVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

2.7K

CRAN downloads in the past year

Rank #16,582 · ~7/day · ~226/mo

Releases R versions

Daily download trend is not available in this view yet.

17530 days

64890 days

2.7K1 year

Compare downloads with other packages →

Also on92 r2u

Repository

GitHub ↗ lauravillain/sgbj

1Stars

0Forks

0Open issues

0Open PRs

0Releases

72Commits

4Contributors

License GPL-3.0 · 72 commits · Last activity 2025-04-11

Stars over time

2022-03-15 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/lauravillain/sgbj on 2026-07-31.

Continuous integration (1)

GitHub Actions

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

2 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (3)

GBJstatssurvival

LinkingTo (0)

none

Suggests (1)

testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (4)

Maintainer (1)

Laura Villain

Author, Maintainer

Authors (4)

Author, Maintainer

Author

Author

Author

Package Timeline

2 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.1.1Latest
2025-04-14 · current release · diff ↗
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
0.1.0
2021-09-15
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-09-15
Total releases: 2 / 5 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.5.0
Bundled data: 0.2 KB / 1 file
Download size: 5.8 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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