Package: h5mread 0.99.4

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]

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h5mread.pdf |h5mread.html✨
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/hpages/h5mread/issues

Uses libs:
  • openssl– Secure Sockets Layer toolkit
  • curl– Easy-to-use client-side URL transfer library
  • zlib– Compression library

On BioConductor:h5mread-0.99.4(bioc 3.21)

infrastructuredatarepresentationdataimportopensslcurlzlib

6.96 score 1 stars 121 packages 4 scripts 298 downloads 26 exports 16 dependencies

Last updated 30 days agofrom:8aced109b7. Checks:1 OK, 1 NOTE, 6 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 21 2025
R-4.5-win-x86_64WARNINGFeb 21 2025
R-4.5-mac-x86_64WARNINGFeb 21 2025
R-4.5-mac-aarch64WARNINGFeb 21 2025
R-4.5-linux-x86_64NOTEFeb 21 2025
R-4.4-win-x86_64WARNINGFeb 21 2025
R-4.4-mac-x86_64WARNINGFeb 21 2025
R-4.4-mac-aarch64WARNINGFeb 21 2025

Exports:close.H5Fileclose.H5FileIDdestroy_H5DSetDescriptordim_as_integerfind_dims_to_collapseget_h5dimnamesget_h5mread_returned_typeh5chunkdimh5dimH5DSetDescriptorh5existsH5FileH5FileIDh5isdataseth5isgrouph5lsh5mreadh5mread_from_reshapedh5readDimnamesh5writeDimnamesopen.H5Fileopen.H5FileIDpathset_h5dimnamesshowvalidate_lengths_of_h5dimnames

Dependencies:abindBiocGenericscrayongenericsIRangeslatticeMatrixMatrixGenericsmatrixStatsrhdf5rhdf5filtersRhdf5libS4ArraysS4VectorsSparseArrayXVector

The h5mread package

Hervé Pagès

Rendered fromh5mread.Rmdusingknitr::rmarkdownon Feb 21 2025.

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