R Observatory: Metrics for tcpl version 3.3.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

tcpl

3.3.1Package record

ToxCast Data Analysis Pipeline

0packages dependsuggested by 3

11.1Kdownloads / year

21.1%test coverage

10/13flavors OK

Overview

About

Maintained by Madison FeshukCRAN page ↗GitHub ↗Website ↗Issues ↗

The ToxCast Data Analysis Pipeline ('tcpl') is an R package that manages, curve-fits, plots, and stores ToxCast data to populate its linked MySQL database, 'invitrodb'. The package was developed for the chemical screening data curated by the US EPA's Toxicity Forecaster (ToxCast) program, but 'tcpl' can be used to support diverse chemical screening efforts.

Changes in 3.3.1

Minor improvements and fixes

Update ctxR and API host server connection for invitrodb v4.2 access (#374)

From NEWS.md in the release

Install

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

install.packages("tcpl", 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("USEPA/CompTox-ToxCast-tcpl")

Development version from USEPA/CompTox-ToxCast-tcpl. 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-tcpl

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-tcpl

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

Health

CRAN checks

1ERROR2NOTE10OK

Check messages

ERRORre-building of vignette outputsr-release-macos-arm64

Error(s) in re-building vignettes:
--- re-building ‘Introduction_Appendices.Rmd’ using rmarkdown
Error: processing vignette 'Introduction_Appendices.Rmd' failed with diagnostics:
pandoc document conversion failed with error 2
--- failed re-building ‘Introduction_Appendices.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction_Appendices.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ...* using check arguments '--no-clean-on-error '

NOTERd contentsr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Rd files without \usage:
  ‘mc5.Rd’
\arguments should not be documented without \usage.

CRAN check page ↗

Slowest check: 9.1 min · r-oldrel-windows-x86_64

Status changes

ERROR10 OK, 2 NOTE, 1 ERRORNow
ERROR11 OK, 1 ERROR2026-04-27
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 3.3.1

READMEYes · 244 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 3.3.1Citation fileNoWebsiteYes

Help pages: 101
Examples that run: 21%6 run in a plain check · 22 never run
Exported functions with examples: 68%
Documented parameters: 98%
Return-value docs: 53%
Help pages citing references: 0%

Vignettes (1)

1. Introduction to tcpl and invitrodb

How these are measured

Downloads

11.1K

CRAN downloads in the past year

Rank #5,501 · ~30/day · ~924/mo

Releases R versions

Daily download trend is not available in this view yet.

55030 days

1.5K90 days

11.1K1 year

Compare downloads with other packages →

Also on90 r2u1.8K conda_forge

How downloads are counted

Repository

usepa/comptox-toxcast-tcpl ↗Organization: USEPA

46Stars

21Forks

30Open issues

1Open PRs

4Releases

1,403Commits

29Commit identities

ordcomptoxcctetoxcastresearch

1,403 commits · Last activity 2025-10-16 · 0% stars, 30d · The default branch showed an older version (3.3.0.9000) than CRAN on 2026-10-11 · Discussions: 5 posts

Responsiveness

How these are sampled

PRs merged (all time): 93%
Median days to close, 50 most recently updated closed issues: 26
Median days to close, 50 most recently updated closed PRs: 2

Stars over time

2025-09-20 · 402026-08-22 · 46

How these are measured

PracticesBeta

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

Checks run against github.com/usepa/comptox-toxcast-tcpl on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Governance and community (1)

Contributing guide

Docs source (1)

README.Rmd

Coverage (1)

Coverage reporting

Show all practicesHide 2 practices

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

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

Dependencies

Declared dependencies

31 external dependencies (excludes base and recommended)

Installing tcpl adds 97 packages (50 with compiled code, 89 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (1)

R >= 4.1.0

Imports (22)

data.table DBI RMariaDB numDeriv RColorBrewerutilsstatsmethodsgraphicsgrDevicessqldf dplyr tidyr plotly tcplfit2 ggplot2 gridExtra stringr rlang ctxR viridis gt

LinkingTo (0)

none

Suggests (14)

roxygen2 knitr prettydoc rmarkdown htmlTable testthat reshape2 kableExtra colorspace magrittr vdiffr httptest rmdformats gtable

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Suggested by 3

Suggests, most downloaded first

tcplfit2 toxEval Rcurvep

How these are counted

Code & Tests

Datasets

People & History

People (18)

Madison Feshuk

Maintainer since 3.2.1 (2025) · added in 3.0.0

Dayne L Filer

Author

Jason Brown

Contributor · added in 2.0.0

Kelly Carstens

Contributor · added in 3.2.0

Sarah E Davidson-Fritz

Contributor · added in 3.0.0

Kurt Dunham

Contributor · added in 3.1.0

Elizabeth Gilson

Contributor · added in 3.3.0

Richard S Judson

Contributor, Thesis advisor

Lindsay Knupp

Contributor · added in 3.3.0

Ashley Ko

Contributor · added in 3.1.0

Show 8 more contributorsHide 8 contributors

Lori Kolaczkowski

Contributor · added in 3.0.0

Parth Kothiya

Contributor

Matthew T Martin

Contributor, Thesis advisor

Katie Paul Friedman

Contributor · added in 2.0.2

Woodrow R Setzer

Contributor

Carter Thunes

Contributor · added in 3.1.0

Zhihui Zhao

Contributor · added in 3.3.0

Todd Zurlinden

Contributor · added in 2.0.2

Previously maintained by Jason Brown (3.0.0 to 3.2.0) and Richard S Judson (2.0.0 to 2.1.0).

Releases (14)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
3.3.1Latest
record
2025-10-17 · current release · diff ↗
3.3.0
record
2025-05-05 · diff ↗
R
R 4.5.0 released · 2025-04-11
3.2.1
record
2025-04-09 · diff ↗
3.2.0
record
2024-10-09 · diff ↗ ·
removed 2 exports
tcplConfExample, tcplLoadClib

added 5 exports
tcplLoadChemList, tcplLoadConcUnit, tcplLoadUnit, tcplPlotLoadData, tcplQueryAPI
R
R 4.4.0 released · 2024-04-24
3.1.0
record
2023-10-06 · diff ↗ ·
added 1 export
tcplDefine
R
R 4.3.0 released · 2023-04-21
3.0.1
record
2022-11-08 · diff ↗
3.0.0
record
2022-08-31 · diff ↗
R
R 4.2.0 released · 2022-04-22
2.1.0
record
2022-03-03 · diff ↗ ·
added 1 export
tcplPlot
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
2.0.2
record
2019-07-26 · diff ↗

Show 9 earlier eventsHide 9 earlier events

R
R 3.6.0 released · 2019-04-26
2.0.1
record
2018-11-16 · diff ↗
2.0.0
record
2018-11-10 · diff ↗ ·
added 7 exports
tcplConfExample, tcplGetAeid, tcplLvlCount, tcplMakeAeidMultiPlts, tcplMakeChidMultiPlts, tcplMultiplot, tcpldbStats
1.4.3
record
2018-05-20 · diff ↗
1.2.2
record
2018-05-10 · diff ↗
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
1.2
record
2016-05-07
R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2016-05-07
Total releases: 14 / 10 yrs
License: MIT + file LICENSE OSI · relicensed from GPL-2 in 3.0.0
Minimum R: ≥ 4.1.0
Bundled data: 131 KB / 10 files
Download size: 2.6 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("tcpl")

Format

Feshuk, M., Brown, J., Carstens, K., Davidson-Fritz, S. E., Dunham, K., Filer, D. L., Gilson, E., Judson, R. S., Knupp, L., Ko, A., Kolaczkowski, L., Kothiya, P., Martin, M. T., Paul Friedman, K., Setzer, W. R., Thunes, C., Zhao, Z., & Zurlinden, T. (2025). tcpl: ToxCast Data Analysis Pipeline (Version 3.3.1) [Computer software]. https://doi.org/10.32614/CRAN.package.tcpl

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 tcpl version 3.3.1 [Data set]. HJJB, LLC. Data release v2026-10-19. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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