CompoundDb
Bioc currentCreating and Using (Chemical) Compound Annotation Databases
Release Lineage
Entered 3.15 · Apr 27, 2022
Current · Requires R 4.6
Description
CompoundDb provides functionality to create and use (chemical) compound annotation databases from a variety of different sources such as LipidMaps, HMDB, ChEBI or MassBank. The database format allows to store in addition MS/MS spectra along with compound information. The package provides also a backend for Bioconductor's Spectra package and allows thus to match experimetal MS/MS spectra against MS/MS spectra in the database. Databases can be stored in SQLite format and are thus portable.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
102 30 exported
Complexity
3.1 avg / 16 max
Call network
102 nodes / 106 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
10,570
Files
67
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
30
Internal functions
72
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.60
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
50%
Unsafe pattern score
0
Dep constraint coverage
9.5%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.1
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
9
First release
2022-09-01
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
3
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 12
- Examples that run
- 100%12 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 8%
Repository practices
7 development-tooling and community-health practices detected across 4 families in the upstream repository
Checks run against github.com/rformassspectrometry/compounddb on 2026-10-11.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
GitHub Pages site last deployed 2026-03-19 · The repository has a site deploy workflow
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| adducts | data.frame | 286 × 7 | No other package |
Topics
Depended on by (2)
Bioconductor (1)
CRAN (1)
Suggested by (3)
People
- Johannes Rainer author maintainer
- Prateek Arora contributor
- Josep M. Badia contributor
- Roger Gine author
- Jan Stanstrup author
- Andrea Vicini author
Cite
Cite this package
Run in R for the authors' entry:
citation("CompoundDb")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.3390/metabo12020173.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.