SparseArray
Bioc currentHigh-performance sparse data representation and manipulation in R
Release Lineage
Entered 3.17 · Apr 26, 2023
Current · Requires R 4.6
Description
The SparseArray package provides array-like containers for efficient in-memory representation of multidimensional sparse data in R (arrays and matrices). The package defines the SparseArray virtual class and two concrete subclasses: COO_SparseArray and SVT_SparseArray. Each subclass uses its own internal representation of the nonzero multidimensional data: the "COO layout" and the "SVT layout", respectively. SVT_SparseArray objects mimic as much as possible the behavior of ordinary matrix and array objects in base R. In particular, they suppport most of the "standard matrix and array API" defined in base R and in the matrixStats package from CRAN.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
1069 28 exported
Complexity
2.8 avg / 26 max
Call network
1069 nodes / 1792 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
39,860
Files
196
Compiled share
52.7%
Has compiled src
Yes
Language breakdown
API
Exported functions
44
Internal functions
246
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.77
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
66.7%
Unsafe pattern score
0
Dep constraint coverage
36.4%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.3.0
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
7
First release
2023-08-30
Latest release
2026-09-21
Avg cadence
170 days
Cold removal rate
100%
Dep drift
1
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 38 (4 internal)
- Examples that run
- 86%30 run in a plain check · 5 hold no code
- Exported functions with examples
- 94%
- Documented parameters
- 94%
- Return-value docs
- 94%
- Help pages citing references
- 0%
- SparseArray objects HTML
Repository practices
1 development-tooling and community-health practice detected across 1 family in the upstream repository
Checks run against github.com/bioconductor/sparsearray on 2026-10-11.
GitHub Pages site
Topics
Depended on by (30)
Show all 35 packagesHide all 35 packages
Bioconductor (29)
CRAN (1)
Suggested by (5)
People
- Hervé Pagès author maintainer
- Vince Carey funder
- Rafael A. Irizarry funder
- Jacques Serizay contributor
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("SparseArray")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.
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.