hdf5r

1.3.12

Interface to the 'HDF5' Binary Data Format

21packages depend

276Kdownloads / year

53.5%test coverage

13/13checks pass

Overview

About

Maintained by Holger HoeflingFirst published 2017-10-2517 releasesCRAN page ↗GitHub ↗

'HDF5' is a data model, library and file format for storing and managing large amounts of data. This package provides a nearly feature complete, object oriented wrapper for the 'HDF5' API https://support.hdfgroup.org/documentation/hdf5/latest/_r_m.html using R6 classes. Additionally, functionality is added so that 'HDF5' objects behave very similar to their corresponding R counterparts.

Install

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

install.packages("hdf5r", 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("hhoeflin/hdf5r")

Development version from hhoeflin/hdf5r. 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-hdf5r

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

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-hdf5r

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

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

Health

CRAN checks

13OK

Slowest check: 5.1 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.49

53.5%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 95%
Return-value docs: 94%
References docs: 1%

Downloads

276K

CRAN downloads in the past year

Rank #828 · ~756/day · ~23K/mo

Releases R versions

Daily download trend is not available in this view yet.

20.2K30 days

63.8K90 days

276K1 year

Compare downloads with other packages →

Also on6.5K r2u41.3K conda_forge90 c2d4u

Repository

GitHub ↗ hhoeflin/hdf5r

84Stars

28Forks

90Open issues

4Open PRs

0Releases

247Commits

9Contributors

247 commits · Last activity 2025-01-25 · 0% stars, 30d

Stars over time

2025-05-22 · 822026-07-07 · 84

Repository practices

Upstream repositoryBeta

5 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/hhoeflin/hdf5r on 2026-07-19.

Continuous integration (3)

GitHub ActionsTravis CIAppVeyor

Reproducibility and dev environment (1)

Makefile

CRAN release process (1)

cran-comments.md

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Depends (2)

R >= 3.2.2methods

Imports (3)

R6 bit64utils

LinkingTo (0)

none

Suggests (6)

testthat knitr rmarkdown nycflights13 reshape2 formatR

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

21direct

2indirect

hdf5r.Extra rblt cooltools eyetools iCellR ieegio propagate readNSx rliger spatialGE CytoSimplex Seurat SignacX delarr dynutils dynwrap gedi2 iRfcb misty scCustomize scregclust

Code & Tests

Code Composition

C 157,945 (88%)R 14,640 (8%)Rd 5,319 (3%)Vignettes 627 (0%)Other 1 (0%)

Code characteristics

Object systems

S343R633

Cyclomatic complexity: 2.0 median / 31 max
Test cases: 126 / 0.49 per code line
System requirements: 1 external

Test coverage

Line coverage

54%

Expression

53.6%

Tests / Examples

53.5% / 30% ex

Functions

4492 41 exported

Complexity

3.6 avg / 31 max

Call network

4492 nodes / 13117 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

4492 functions

Function	Cyclo	Coverage
as_hex exp	1	0%
create_empty exp	2	0%
h5garbage_collect exp	2	0%
is.H5R exp	1	0%
is.H5R_DATASET_REGION exp	1	0%
is.H5R_OBJECT exp	1	0%

People & History

People (3)

Maintainer (1)

Holger Hoefling

Author, Maintainer

Authors (2)

Holger Hoefling

Author, Maintainer

Mario Annau

Author

Novartis Institute for BioMedical Research (NIBR)

Package Timeline

17 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
1.3.12Latest
2025-01-20 · current release · diff ↗
1.3.11
2024-07-07 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.3.10
2024-03-02 · diff ↗
1.3.9
2024-01-14 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.3.8
2023-01-21 · diff ↗
1.3.7
2022-10-03 · diff ↗
1.3.6
2022-09-18 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.3.5
2021-11-15 · diff ↗
1.3.4
2021-08-25 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.3.3
2020-08-18 · diff ↗

Show 11 earlier events

R
R 4.0.0 released · 2020-04-24
1.3.2
2020-03-25 · diff ↗
1.3.1
2020-01-10 · diff ↗
1.3.0
2019-10-06 · diff ↗
R
R 3.6.0 released · 2019-04-26
1.2.0
2019-04-20 · diff ↗
1.1.1
2019-03-26 · diff ↗
1.0.1
2018-10-08 · diff ↗
R
R 3.5.0 released · 2018-04-23
1.0.0
2017-10-25
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-10-25
Total releases: 17 / 9 yrs
License: Apache License 2.0 | file LICENSE OSI
Minimum R: ≥ 3.2.2
Download size: 1.8 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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