R Observatory: Metrics for dbGaPCheckup version 1.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

dbGaPCheckup

1.1.0

dbGaP Checkup

0packages depend

7.9Kdownloads / year

–test coverage

0/13checks pass

Overview

About

Maintained by Lacey W. HeinsbergFirst published 2022-11-144 releasesCRAN page ↗GitHub ↗

Contains functions that check for formatting of the Subject Phenotype data set and data dictionary as specified by the National Center for Biotechnology Information (NCBI) Database of Genotypes and Phenotypes (dbGaP) https://www.ncbi.nlm.nih.gov/gap/docs/submissionguide/.

Install

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

install.packages("dbGaPCheckup", 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("lwheinsberg/dbGaPCheckup")

Development version from lwheinsberg/dbGaPCheckup. 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-dbgapcheckup

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-dbGaPCheckup

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-dbGaPCheckup

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

Health

CRAN checks

13NOTE

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc
NOTE r-devel-windows-x86_64
NOTE r-oldrel-macos-arm64
NOTE r-oldrel-macos-x86_64
NOTE r-oldrel-windows-x86_64
NOTE r-patched-linux-x86_64
NOTE r-release-linux-x86_64
NOTE r-release-macos-arm64
NOTE r-release-macos-x86_64
NOTE r-release-windows-x86_64

Slowest check: 3.6 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

17

Dependencies · direct

Check history

NOTE2026-06-09
0 OK · 13 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
0 OK · 12 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-05-02
0 OK · 13 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-25
0 OK · 11 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 1,399 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 95%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

7.9K

CRAN downloads in the past year

Rank #5,201 · ~22/day · ~660/mo

Releases R versions

Daily download trend is not available in this view yet.

20130 days

1.5K90 days

7.9K1 year

Compare downloads with other packages →

Also on100 r2u21 autocran

Repository

GitHub ↗ lwheinsberg/dbgapcheckup

4Stars

2Forks

1Open issues

0Open PRs

4Releases

113Commits

2Contributors

113 commits · Last activity 2025-05-01

Stars over time

2024-12-12 · 32026-07-07 · 4

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/lwheinsberg/dbgapcheckup on 2026-08-09.

CRAN release process (3)

cran-comments.mdrevdep/CRAN-SUBMISSION

Docs source (1)

README.Rmd

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

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (17)

readxl tidyr dplyr formatR ggplot2 pander magrittr rmarkdown purrr questionr tibble rlang labelledstatsutilsgraphicsnaniar

LinkingTo (0)

none

Suggests (2)

testthat knitr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (3)

Maintainer (1)

Lacey W. Heinsberg

Author, Maintainer

Authors (2)

Lacey W. Heinsberg

Author, Maintainer

Daniel E. Weeks

Author

Copyright holders (1)

University of Pittsburgh

Copyright holder

Listed in earlier versions (2)

Daniel E.

no longer listed · 1.0.0 to 1.1.0

Lacey W.

no longer listed · 1.0.0 to 1.1.0

Package Timeline

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

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
1.1.0Latest
2023-09-27 · current release · diff ↗
R
R 4.3.0 released · 2023-04-21
1.0.2
2023-02-22 · diff ↗
1.0.1
2022-12-22 · diff ↗
1.0.0
2022-11-14
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-11-14
Total releases: 4 / 4 yrs
License: GPL-2 OSI
Minimum R: ≥ 3.5.0
Bundled data: 133 KB / 19 files
Download size: 581 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("dbGaPCheckup")

Format

Heinsberg, L. W., University of Pittsburgh, , & Weeks, D. E. (2023). dbGaPCheckup: dbGaP Checkup (Version 1.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.dbGaPCheckup

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 dbGaPCheckup version 1.1.0 [Data set]. HJJB, LLC. Data release v2026-08-15. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-15, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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