rhdf5
Bioc currentR Interface to HDF5
Release Lineage
Entered 1.0 · Jan 5, 2001
Current · Requires R 4.6
Description
This package provides an interface between HDF5 and R. HDF5's main features are the ability to store and access very large and/or complex datasets and a wide variety of metadata on mass storage (disk) through a completely portable file format. The rhdf5 package is thus suited for the exchange of large and/or complex datasets between R and other software package, and for letting R applications work on datasets that are larger than the available RAM.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
467 171 exported
Complexity
2.9 avg / 19 max
Call network
467 nodes / 801 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
26,987
Files
314
Compiled share
32.8%
Has compiled src
Yes
Language breakdown
API
Exported functions
171
Internal functions
67
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.56
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
66.7%
Secret pattern count
1
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.0.0
System requirements
1 externalGNU make
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
46
First release
2002-05-02
Latest release
2026-08-10
Avg cadence
184 days
Cold removal rate
100%
Dep drift
8
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 139 (1 internal)
- Examples that run
- 95%39 run in a plain check · 2 never run
- Exported functions with examples
- 30%
- Documented parameters
- 95%
- Return-value docs
- 45%
- Help pages citing references
- 3%
New feature
- NULL pointers in variable length string datasets are now read as
NA_character_rather than an empty string. This allows rhdf5 2.56.1 to readNA_character_from string data written with rhdf5 2.57.10 or later.
From inst/NEWS.Rd in the release
Repository practices
12 development-tooling and community-health practices detected across 5 families in the upstream repository
Checks run against github.com/huber-group-embl/rhdf5 on 2026-10-18.
The R CMD check workflow runs on Linux
GitHub Pages site last deployed 2026-10-06 · The repository has a site deploy workflow
pkgdown site last built 2026-10-06
Show all practicesHide 1 practice
Topics
Depended on by (87)
Show 67 packagesHide 67 packages
Bioconductor (80)
Suggested by (36)
People
- Hugo Gruson maintainer
- German Network for Bioinformatics Infrastructure - de.NBI funder
- Bernd Fischer author
- Martin Morgan contributor
- Gregoire Pau author
-
Mike Smith
author
Maintainer from 2017 to 2025
- Daniel van Twisk contributor
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("rhdf5")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 v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.