R Observatory: Metrics for dbGaPCheckup version 1.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

dbGaPCheckup

1.1.0Package record

dbGaP Checkup

0packages depend

7.5Kdownloads / year

–test coverage

0/13flavors OK

Overview

About

Maintained by Lacey W. HeinsbergCRAN page ↗GitHub ↗Website ↗Issues ↗

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/.

Changes in 1.1.0

added an informative error message when the required VALUES column is missing
adjusted values_check to temporarily create dummy names for blank-named columns beyond VALUES to prevent function from dying if column names after VALUES are blank strings
corrected minmax_check and integer_check bugs that occurred when SUBJECT_ID was a character vector
adjusted misc_format_check to return a WARNING that alerts users if they read in a data set and R automatically fills in column names after VALUES (which is allowed by the package, but not dbGaP itself)
adjusted NA_check to correctly capture NA=N/A VALUES
corrected bug in type_check that was allowing some non-allowable TYPE entries to pass
corrected but in missing_value_check that was flagging some variables even when they had properly encoded NA=N/A VALUES
made complete_check more robust to errors by wrapping functions in tryCatch
used seealso to link utility functions to relevant check functions

From NEWS.md in the release

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. 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-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). 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) value_missing_table.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) value_missing_table.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly

CRAN check page ↗

Slowest check: 3.5 min · r-release-macos-x86_64

Status changes

NOTE13 NOTE2026-06-09
ERROR12 NOTE, 1 ERROR2026-06-08
NOTE13 NOTE2026-05-02
ERROR11 NOTE, 1 ERROR2026-04-25
NOTE14 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.0

READMEYes · 1,399 wordsVignettesYes · 2 · dynamicNEWSYes · 100% structured · mentions 1.1.0Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 99 (1 internal)includes a package overview page
Examples that run: 95%36 run in a plain check · 2 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 88%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (2)

How these are measured

Downloads

7.5K

CRAN downloads in the past year

Rank #6,813 · ~21/day · ~628/mo

Releases R versions

Daily download trend is not available in this view yet.

48230 days

1.3K90 days

7.5K1 year

Compare downloads with other packages →

Also on70 r2u8 autocran

How downloads are counted

Repository

lwheinsberg/dbgapcheckup ↗Account: lwheinsberg

4Stars

2Forks

1Open issues

0Open PRs

4Releases

113Commits

2Commit identities

113 commits · Last activity 2025-05-01 · Default branch at 1.2.0, ahead of CRAN 1.1.0 (checked 2026-10-21)

Responsiveness

How these are sampled

PRs merged (all time): 50%
Median days to close, 50 most recently updated closed issues: 18
Median days to close, 50 most recently updated closed PRs: 4

Stars over time

2024-12-12 · 32026-07-07 · 4

How these are measured

PracticesBeta

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

Checks run against github.com/lwheinsberg/dbgapcheckup on 2026-10-21.

Docs source (3)

README.Rmdpkgdown

GitHub Pages site last deployed 2025-05-01

pkgdown site last built 2025-05-01

CRAN release process (3)

cran-comments.mdrevdep/CRAN-SUBMISSION

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

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Installing dbGaPCheckup adds 96 packages (45 with compiled code, 78 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, bslib 5.6 MB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (3)

Lacey W. Heinsberg

Author, Maintainer since 1.0.0 (2022)

Daniel E. Weeks

Author

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

Releases (4)

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

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("dbGaPCheckup")

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 dbGaPCheckup version 1.1.0 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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