R Observatory: Metrics for chem.databases version 1.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

chem.databases

1.0.0Package record

Collection of 3 Chemical Databases from Public Sources

0packages depend

2.8Kdownloads / year

–test coverage

0/13flavors OK

Overview

About

Maintained by Irucka EmbryCRAN page ↗GitLab ↗Issues ↗

Contains the Multi-Species Acute Toxicity Database (CAS & SMILES columns only) [United States (US) Department of Health and Human Services (DHHS) National Institutes of Health (NIH) National Cancer Institute (NCI), "Multi-Species Acute Toxicity Database", https://cactus.nci.nih.gov/download/acute-toxicity-db/] combined with the Toxic Substances Control Act (TSCA) Inventory [United States Environmental Protection Agency (US EPA), "Toxic Substances Control Act (TSCA) Chemical Substance Inventory", <https://www.epa.gov/tsca-inventory/how-access-tsca-inventory} and https://cdxapps.epa.gov/oms-substance-registry-services/substance-list-details/169] and the Agency for Toxic Substances and Disease Registry (ATSDR) Database [United States (US) Department of Health and Human Services (DHHS) Centers for Disease Control and Prevention (CDC)/Agency for Toxic Substances and Disease Registry (ATSDR), "Agency for Toxic Substances and Disease Registry (ATSDR) Database", https://cdxapps.epa.gov/oms-substance-registry-services/substance-list-details/105] in 2 data sets. One data set has a focus on the latter 2 databases and one data set focuses on the former database. Also contains the collection of chemical data from Wikipedia compiled in the US EPA CompTox Chemicals Dashboard [United States Environmental Protection Agency (US EPA) / Wikimedia Foundation, Inc. "CompTox Chemicals Dashboard v2.2.1", https://comptox.epa.gov/dashboard/chemical-lists/WIKIPEDIA].

Changes in 1.0.0

Initial release

From NEWS.md in the release

Install

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

install.packages("chem.databases", 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("iembry/chem.databases")

Development version from iembry/chem.databases. 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-chem.databases

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-chem.databases

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-chem.databases

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) atsdr_tsca_ld50_a.Rd:10: Lost braces
    10 | item{CAS}{Chemical Abstracts Service (CAS) Registry Number}
       |     ^
checkRd: (-1) atsdr_tsca_ld50_a.Rd:10: Lost braces
    10 | item{CAS}{Chemical Abstracts Service (CAS) Registry Number}
       |          ^
checkRd: (-1) atsdr_tsca_ld50_a.Rd:11: Lost braces
    11 | item{Substance Name}{Preferred Chemical Substance Name}
       |     ^
checkRd: (-1) atsdr_tsca_ld50_a.Rd:11: Lost braces
    11 | item{Substance Name}{Preferred Chemical Substance Name}
       |                     ^
checkRd: (-1) atsdr_tsca_ld50_a.Rd:12: Lost braces
    12 | item{Registry Name}{Registry Chemical Name}
       |     ^
checkRd: (-1) atsdr_tsca_ld50_a.Rd:12: Lost braces
    12 | item{Registry Name}{Registry Chemical Name}
       |                    ^
checkRd: (-1) atsdr_tsca_ld50_a.Rd:13: Lost braces
    13 | item{SMILES}{Simplified Molecular-Input Line-Entry System (SMILES) Chemical Structural Notation}
       |     ^
checkRd: (-1) atsdr_ts
...[truncated]...
tem{InChI}{International Chemical Identifier (InChI) Chemical Structural Notation}
       |     ^
checkRd: (-1) chem_wiki.Rd:15: Lost braces
    15 | item{InChI}{International Chemical Identifier (InChI) Chemical Structural Notation}
       |            ^
checkRd: (-1) chem_wiki.Rd:16: Lost braces
    16 | item{InChIKey}{Hashed Version of the InChI}
       |     ^
checkRd: (-1) chem_wiki.Rd:16: Lost braces
    16 | item{InChIKey}{Hashed Version of the InChI}
       |               ^
checkRd: (-1) chem_wiki.Rd:17: Lost braces
    17 | item{Average Mass}{Average Chemical Molecular Mass}
       |     ^
checkRd: (-1) chem_wiki.Rd:17: Lost braces
    17 | item{Average Mass}{Average Chemical Molecular Mass}
       |                   ^
checkRd: (-1) chem_wiki.Rd:18: Lost braces
    18 | item{Monoisotopic Mass}{Single Chemical Isotope Mass}
       |     ^
checkRd: (-1) chem_wiki.Rd:18: Lost braces
    18 | item{Monoisotopic Mass}{Single Chemical Isotope Mass}
       |                        ^

CRAN check page ↗

Slowest check: 1.0 min · r-devel-windows-x86_64

Status changes

NOTE13 NOTE2026-07-16
WARNING12 NOTE, 1 WARNING2026-07-15
NOTE14 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.0

READMEYes · 748 wordsVignettesNoNEWSYes · 67% structured · mentions 1.0.0Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 4 (1 internal)includes a package overview page
Examples that run: no examples
Exported functions with examples: not tracked
Documented parameters: not tracked
Return-value docs: not tracked
Help pages citing references: 0%

How these are measured

Downloads

2.8K

CRAN downloads in the past year

Rank #16,881 · ~8/day · ~230/mo

Releases R versions

Daily download trend is not available in this view yet.

25430 days

74590 days

2.8K1 year

Compare downloads with other packages →

Also on143 r2u13 autocran36 c2d4u

How downloads are counted

Repository

gitlab.com/iembry/chem.databases ↗

0Stars

0Forks

0Open issues

0Open PRs

0Releases

6Commits

1Commit identities

datasetchemicals

6 commits · Last activity 2023-09-20

Responsiveness

not measured

How these are measured

PracticesBeta

Repository gitlab.com/iembry/chem.databases is linked, but repository-practices checks have not run for it yet. Checks are GitHub-only for now.

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

Dependencies

Declared dependencies

3 external dependencies (excludes base and recommended)

Installing chem.databases adds no packages beyond those that come with R.

Depends (1)

R >= 3.5.0

Imports (0)

none

LinkingTo (0)

none

Suggests (3)

data.table install.load spelling

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 (1)

Irucka Embry

Author, Maintainer since 1.0.0 (2023)

Releases (1)

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
1.0.0Latest
record
2023-09-21 · current release
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-09-21
Total releases: 1 / 3 yrs
License: CC0
Copyright: This software is in the public domain because it contains mostly materials that originally came from the United States (US) Environmental Protection Agency (US EPA), the United States (US) Department of Health and Human Services (DHHS) Centers for Disease Control and Prevention (CDC)/ Agency for Toxic Substances and Disease Registry (ATSDR), or the United States (US) Department of Health and Human Services (DHHS) National Institutes of Health (NIH) National Cancer Institute (NCI).
Minimum R: ≥ 3.5.0
Bundled data: 2.3 MB / 3 files
Download size: 2.3 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("chem.databases")

Format

Embry, I. (2023). chem.databases: Collection of 3 Chemical Databases from Public Sources (Version 1.0.0) [Computer software]. https://doi.org/10.32614/CRAN.package.chem.databases

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 chem.databases version 1.0.0 [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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