Package: h5mread 1.4.0

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_1.4.0.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-release.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)

infrastructuredatarepresentationdataimportu24ca289073curlopenssl

9.09 score 3 stars 159 packages 4 scripts 12k downloads 26 exports 18 dependencies

Last updated from:8295c413c9 (on RELEASE_3_23). Checks:5 NOTE, 1 OK, 7 WARNING, 1 FAIL. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE199
linux-devel-arm64NOTE410
linux-devel-x86_64NOTE406
source / vignettesOK384
linux-release-arm64NOTE347
linux-release-x86_64NOTE448
macos-release-arm64WARNING484
macos-release-x86_64WARNING604
macos-oldrel-arm64WARNING321
macos-oldrel-x86_64WARNING654
windows-develWARNING514
windows-releaseWARNING491
windows-oldrelWARNING491
wasm-releaseFAIL169

Exports:close.H5Fileclose.H5FileIDdestroy_H5DSetDescriptordim_as_integerfind_dims_to_collapseget_h5dimnamesget_h5mread_returned_typeh5chunkdimh5dimH5DSetDescriptorh5existsH5FileH5FileIDh5isdataseth5isgrouph5lsh5mreadh5mread_from_reshapedh5readDimnamesh5writeDimnamesopen.H5Fileopen.H5FileIDpathset_h5dimnamesshowvalidate_lengths_of_h5dimnames

Dependencies:abindBiocGenericsbiocmakedir.expiryfilelockgenericsIRangeslatticeMatrixMatrixGenericsmatrixStatsrhdf5rhdf5filtersRhdf5libS4ArraysS4VectorsSparseArrayXVector

The h5mread package

Hervé Pagès

Rendered fromh5mread.Rmdusingknitr::rmarkdownon Jun 13 2026.

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

Readme and manuals

Help Manual

Help pageTopics
Get the dimensions of an HDF5 datasetdim_as_integer h5chunkdim h5dim h5exists h5isdataset h5isgroup
H5File objectscharacter_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 objectsh5ls
An alternative to 'rhdf5::h5read'get_h5mread_returned_type h5mread
Read data from a virtually reshaped HDF5 datasetfind_dims_to_collapse h5mread_from_reshaped
Write/read the dimnames of an HDF5 datasetget_h5dimnames h5readDimnames h5writeDimnames set_h5dimnames validate_lengths_of_h5dimnames