Package: h5mread 1.5.0

Hervé Pagès

h5mread: A fast HDF5 reader

The main function in the h5mread package is h5mread(), which allows reading arbitrary data from an HDF5 dataset into R, similarly to what the h5read() function from the rhdf5 package does. In the case of h5mread(), the implementation has been optimized to make it as fast and memory-efficient as possible.

Authors:Hervé Pagès [aut, cre]

h5mread_1.5.0.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
h5mread/json (API)
NEWS

# Install 'h5mread' in R:

install.packages('h5mread', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bioconductor/h5mread/issues

Uses libs:

curl– Easy-to-use client-side URL transfer library
openssl– Secure Sockets Layer toolkit

On BioConductor:h5mread-1.5.0(bioc 3.24)h5mread-1.4.0(bioc 3.23)

infrastructure datarepresentation dataimport u24ca289073 curl openssl

9.09 score 3 stars 157 packages 4 scripts 12k downloads 26 exports 18 dependencies

Last updated from:2a42d3c56c. Checks:5 NOTE, 1 OK, 7 WARNING, 1 FAIL. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	197
linux-devel-arm64	NOTE	370
linux-devel-x86_64	NOTE	406
source / vignettes	OK	405
linux-release-arm64	NOTE	413
linux-release-x86_64	NOTE	385
macos-release-arm64	WARNING	311
macos-release-x86_64	WARNING	1837
macos-oldrel-arm64	WARNING	332
macos-oldrel-x86_64	WARNING	454
windows-devel	WARNING	493
windows-release	WARNING	538
windows-oldrel	WARNING	496
wasm-release	FAIL	173

Exports:close.H5File close.H5FileID destroy_H5DSetDescriptor dim_as_integer find_dims_to_collapse get_h5dimnames get_h5mread_returned_type h5chunkdim h5dim H5DSetDescriptor h5exists H5File H5FileID h5isdataset h5isgroup h5ls h5mread h5mread_from_reshaped h5readDimnames h5writeDimnames open.H5File open.H5FileID path set_h5dimnames show validate_lengths_of_h5dimnames

Dependencies:abind BiocGenerics biocmake dir.expiry filelock generics IRanges lattice Matrix MatrixGenerics matrixStats rhdf5 rhdf5filters Rhdf5lib S4Arrays S4Vectors SparseArray XVector

The h5mread package

Hervé Pagès

Rendered fromh5mread.Rmdusingknitr::rmarkdownon Jun 06 2026.

Last update: 2025-01-21
Started: 2024-12-02

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Get the dimensions of an HDF5 dataset	dim_as_integer h5chunkdim h5dim h5exists h5isdataset h5isgroup
H5File objects	character_OR_H5File character_OR_H5File-class class:character_OR_H5File class:H5DSetDescriptor class:H5File class:H5FileID close.H5File close.H5FileID coerce,H5File,H5IdComponent-method destroy_H5DSetDescriptor H5DSetDescriptor H5DSetDescriptor-class H5File H5File-class H5FileID H5FileID-class open.H5File open.H5FileID path,H5File-method show,H5DSetDescriptor-method show,H5File-method show,H5FileID-method
A wrapper to rhdf5::h5ls() that works on H5File objects	h5ls
An alternative to 'rhdf5::h5read'	get_h5mread_returned_type h5mread
Read data from a virtually reshaped HDF5 dataset	find_dims_to_collapse h5mread_from_reshaped
Write/read the dimnames of an HDF5 dataset	get_h5dimnames h5readDimnames h5writeDimnames set_h5dimnames validate_lengths_of_h5dimnames