Package: rhdf5 2.57.1

Hugo Gruson

rhdf5: R Interface to HDF5

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.

Authors:Bernd Fischer [aut], Mike Smith [aut], Gregoire Pau [aut], Martin Morgan [ctb], Daniel van Twisk [ctb], Hugo Gruson [cre], German Network for Bioinformatics Infrastructure - de.NBI [fnd]

rhdf5_2.57.1.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
rhdf5/json (API)

# Install 'rhdf5' in R:
install.packages('rhdf5', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/huber-group-embl/rhdf5/issues

Pkgdown/docs site:https://huber-group-embl.github.io

Uses libs:
  • curl– Easy-to-use client-side URL transfer library
  • openssl– Secure Sockets Layer toolkit
  • c++– GNU Standard C++ Library v3

On BioConductor:rhdf5-2.57.1(bioc 3.24)rhdf5-2.56.0(bioc 3.23)

infrastructuredataimporthdf5rhdf5curlopensslcpp

15.12 score 73 stars 230 packages 6.3k scripts 7 mentions 172 exports 5 dependencies

Last updated from:1dd62c41d0. Checks:1 ERROR, 9 OK, 3 WARNING, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR402
linux-devel-arm64OK335
linux-devel-x86_64OK398
source / vignettesOK656
linux-release-arm64OK346
linux-release-x86_64OK394
macos-release-arm64OK149
macos-release-x86_64OK362
macos-oldrel-arm64OK154
macos-oldrel-x86_64OK176
windows-develWARNING277
windows-releaseWARNING209
windows-oldrelWARNING227
wasm-releaseFAIL130

Exports:H5AcloseH5AcreateH5AdeleteH5AexistsH5Aget_nameH5Aget_spaceH5Aget_typeH5AopenH5Aopen_by_idxH5Aopen_by_nameH5AreadH5AwriteH5closeh5closeAllh5consth5constTypeh5createAttributeh5createDataseth5createFileh5createGroupH5Dchunk_dimsH5DcloseH5Dcreateh5defaulth5deleteh5deleteAttributeH5Dget_create_plistH5Dget_num_chunksH5Dget_spaceH5Dget_storage_sizeH5Dget_typeH5Dis_chunkedh5disableFileLockingH5DopenH5DreadH5Dset_extenth5dumpH5Dwriteh5enableFileLockingh5errorHandlingH5FcloseH5FcreateH5FflushH5Fget_access_plistH5Fget_create_plistH5Fget_filesizeH5Fget_intentH5Fget_nameH5Fis_hdf5H5FopenH5garbage_collectH5GcloseH5GcreateH5Gcreate_anonH5get_libversionH5Gget_infoH5Gget_info_by_idxH5Gget_info_by_nameH5GopenH5Iget_nameH5Iget_typeH5Iis_validH5LcopyH5Lcreate_externalH5LdeleteH5LexistsH5Lget_infoh5listIdentifierH5Lmoveh5lsH5OcloseH5OcopyH5Oget_infoH5Oget_num_attrsH5Oget_num_attrs_by_nameH5OlinkH5OopenH5openH5Pall_filters_availH5PcloseH5PcopyH5PcreateH5Pfill_value_definedH5Pget_chunkH5Pget_classH5Pget_create_intermediate_groupH5Pget_fill_timeH5Pget_filterH5Pget_istore_kH5Pget_layoutH5Pget_libver_boundsH5Pget_nfiltersH5Pget_obj_track_timesH5Pget_shared_mesg_indexH5Pget_shared_mesg_nindexesH5Pget_shared_mesg_phase_changeH5Pget_sizesH5Pget_sym_kH5Pget_userblockH5Pget_versionH5Pset_bloscH5Pset_bzip2H5Pset_chunkH5Pset_chunk_cacheH5Pset_create_intermediate_groupH5Pset_deflateH5Pset_fapl_ros3H5Pset_fill_timeH5Pset_fill_valueH5Pset_filterH5Pset_istore_kH5Pset_layoutH5Pset_libver_boundsH5Pset_lzfH5Pset_nbitH5Pset_obj_track_timesH5Pset_shared_mesg_indexH5Pset_shared_mesg_nindexesH5Pset_shared_mesg_phase_changeH5Pset_shuffleH5Pset_sizesH5Pset_sym_kH5Pset_szipH5Pset_userblockH5RcreateH5Rdereferenceh5readh5readAttributesh5readTimestampsH5Rget_nameH5Rget_obj_typeH5Rget_regionh5saveH5ScloseH5Scombine_hyperslabH5Scombine_selectH5ScopyH5ScreateH5Screate_simpleh5set_extentH5Sget_select_npointsH5Sget_simple_extent_dimsH5Sis_simpleH5Sselect_allH5Sselect_hyperslabH5Sselect_indexH5Sselect_noneH5Sselect_validH5Sset_extent_simpleH5SunlimitedH5TcopyH5Tenum_createH5Tenum_inserth5testFileLockingH5Tget_classH5Tget_csetH5Tget_nmembersH5Tget_precisionH5Tget_sizeH5Tget_strpadH5Tis_variable_strH5Tset_csetH5Tset_precisionH5Tset_sizeH5Tset_strpadh5validObjectsh5versionh5writeh5writeAttributeh5writeDatasetH5Zfilter_availshow

Dependencies:biocmakedir.expiryfilelockrhdf5filtersRhdf5lib

Reading HDF5 Files In The Cloud
Public S3 Buckets | Private S3 Buckets | Session Info
Rendered fromrhdf5_cloud_reading.Rmdusingknitr::rmarkdown

Last update: 2026-05-26
Started: 2020-06-04

rhdf5 Practical Tips
Introduction | Reading subsets of data | Using the index argument | Using hyperslab selections | Irregular selections | Using hyperslab selection tools | Slowdown when selecting unions of hyperslabs | Summary | Writing in parallel | Example data | Serial writing of datasets | Parallel writing of datasets | Session info
Rendered frompractical_tips.Rmdusingknitr::rmarkdown

Last update: 2026-02-17
Started: 2019-09-17

rhdf5 - HDF5 interface for R
Introduction | High level R-HDF5 functions | Creating an HDF5 file and group hierarchy | Writing and reading objects | Writing and reading objects with file, group and dataset handles | Saving multiple objects to an HDF5 file (h5save) | List the content of an HDF5 file | Dump the content of an HDF5 file | Reading HDF5 files with external software | Removing content from an HDF5 file | 64-bit integers | Low level HDF5 functions | Creating an HDF5 file and a group hierarchy | Writing data to an HDF5 file | Session Info
Rendered fromrhdf5.Rmdusingknitr::rmarkdown

Last update: 2025-11-05
Started: 2018-01-05

Readme and manuals

Help Manual

Help pageTopics
Create HDF5 fileh5createFile h5_createFile
Create HDF5 grouph5createGroup h5_createGroup
Delete objects within a HDF5 fileh5delete h5_delete
Delete attributeh5deleteAttribute h5_deleteAttribute
Dump the content of an HDF5 file.h5dump h5_dump
Set how HDF5 error messages are displayedh5errorHandling h5_errorHandling
Test and set file locking for HDF5h5disableFileLocking h5enableFileLocking h5testFileLocking h5_FileLocking
Reads and write object in HDF5 filesh5read h5_read
Read all attributes from a given location in an HDF5 fileh5readAttributes h5_readAttributes
Saves a one or more objects to an HDF5 file.h5save h5_save
Set a new dataset extensionh5set_extent h5_set_extent
Write object to an HDF5 file.h5write h5write.default h5writeDataset h5writeDataset.array h5writeDataset.data.frame h5_write
Write an R object as an HDF5 attributeh5writeAttribute h5writeAttribute.array h5_writeAttribute
Close an HDF5 attributeH5Aclose
Create an attribute for an HDF5 objectH5Acreate
Delete an specified attribute of an HDF5 objectH5Adelete
Check whether an specific attribute exists for an HDF5 objectH5Aexists
Get the name of an HDF5 attribute objectH5Aget_name
Get a copy of the attribute dataspaceH5Aget_space
Get a copy of the attribute datatypeH5Aget_type
Open an attribute for an HDF5 objectH5Aopen H5Aopen_by_idx H5Aopen_by_name
Read data from an HDF5 attributeH5Aread
Write data to an HDF5 attributeH5Awrite
Close open HDF5 handlesh5closeAll
HDF5 library constants.h5const h5constants h5constType h5default
Create HDF5 attributeh5createAttribute
Create HDF5 dataseth5createDataset
Additional functions for finding details of dataset chunking.H5Dchunk_dims H5Dis_chunked H5D_extras
Close an open HDF5 datasetH5Dclose
Create a new HDF5 datasetH5Dcreate
Return a copy of the dataset creation property list for a datasetH5Dget_create_plist
Get the number of chunks in a datasetH5Dget_num_chunks
Return a copy of the HDF5 dataspace for a datasetH5Dget_space
Find the amount of storage allocated for a datasetH5Dget_storage_size
Return a copy of the HDF5 datatype for a datasetH5Dget_type
Open an existing HDF5 datasetH5Dopen
Read from an HDF5 datasetH5Dread
Change the dimensions of an HDF5 datasetH5Dset_extent
Write data to datasetH5Dwrite
Close access to an HDF5 fileH5Fclose
Create an HDF5 fileH5Fcreate
Flush all buffers associated with a file to diskH5Fflush
Find the size of an open HDF5 fileH5Fget_filesize
Determine the read only or read/write status of an open file handle.H5Fget_intent
Retrieve the name of the file to which an object belongsH5Fget_name
Get property lists associated with an HDF5 fileH5Fget_access_plist H5Fget_create_plist H5Fget_plist
Determine whether a file is in the HDF5 formatH5Fis_hdf5
Open an existing HDF5 fileH5Fopen
HDF5 General Library FunctionsH5close H5functions H5garbage_collect H5get_libversion H5open
Close a specified groupH5Gclose
Create a new HDF5 group and link it to a location in a fileH5Gcreate
Create a new HDF5 group without linking it into a fileH5Gcreate_anon
Retrieve information about a groupH5Gget_info H5Gget_info_by_idx H5Gget_info_by_name
Open a specified groupH5Gopen
An S4 class representing an H5 object$,H5IdComponent-method $<-,H5IdComponent-method &,H5IdComponent,character-method H5IdComponent-class show,H5IdComponent-method [,H5IdComponent-method [<-,H5IdComponent-method
Retrieve the name of an object from a given identifierH5Iget_name
Find the type of an objectH5Iget_type
Determine whether an identifier is validH5Iis_valid
Copy a link from one location to anotherH5Lcopy
Create a link to an object in a different HDF5 fileH5Lcreate_external
Remove a link from a groupH5Ldelete
Confirm existence of a linkH5Lexists
Find information about a linkH5Lget_info
List all open HDF5 objects.h5listIdentifier h5listObjects h5validObjects
Move a link within an HDF5 fileH5Lmove
List the content of an HDF5 file.h5ls
Close an HDF5 objectH5Oclose
Copies an HDF5 objectH5Ocopy
Retrieves the metadata for an HDF5 object specified by an identifier.H5Oget_info
Find the number of attributes associated with an HDF5 objectH5Oget_num_attrs H5Oget_num_attrs_by_name
Create a hard link to an object in an HDF5 fileH5Olink
Open an object in an HDF5 fileH5Oopen
Get and set the size of the chunks used to store a chunked layout datasetH5Pget_chunk H5Pset_chunk H5P_chunk
Set parameters for the raw data chunk cacheH5Pset_chunk_cache H5P_chunk_cache
Get and set whether to create missing intermediate groupsH5Pget_create_intermediate_group H5Pset_create_intermediate_group H5P_create_intermediate_group
Set the time when fill values are written to a datasetH5Pget_fill_time H5Pset_fill_time H5P_fill_time
Set the fill value for an HDF5 datasetH5Pset_fill_value H5P_fill_value
Get and set the type of storage used to store the raw data for a datasetH5Pget_layout H5Pset_layout H5P_layout
Control the range of HDF5 library versions that will be compatible with a file.H5Pget_libver_bounds H5Pset_libver_bounds H5P_libver_bounds
Query dataset filter properties.H5Pall_filters_avail H5Pget_filter H5Pget_nfilters
Close and release a property listH5Pclose
Copy an existing property list to create a new property listH5Pcopy
Create a new HDF5 property listH5Pcreate
Determine whether a property list has a fill value definedH5Pfill_value_defined
Return the property list class identifier for a property listH5Pget_class
DeprecatedH5Pget_version
Set whether to record timestamps for operations performed on an HDF5 object.H5Pget_obj_track_times H5Pobject_track_times H5Pset_obj_track_times
Add the BLOSC filter to the chunk processing pipeline.H5Pset_blosc
Add the BZIP2 filter to the chunk processing pipeline.H5Pset_bzip2
Add the deflate compression filter to the chunk processing pipeline.H5Pset_deflate
Set the read-only S3 virtual file driverH5Pset_fapl_ros3
Add a filter to the dataset filter pipeline.H5Pset_filter
Get and set the 1/2 rank of an indexed storage B-treeH5Pget_istore_k H5Pset_istore_k
Add the LZF filter to the chunk processing pipeline.H5Pset_lzf
Add the N-Bit filter to the chunk processing pipeline.H5Pset_nbit
Get and set shared object header message index propertiesH5Pget_shared_mesg_index H5Pset_shared_mesg_index
Get and set the number of object header message indexesH5Pget_shared_mesg_nindexes H5Pset_shared_mesg_nindexes
Get and set threshold values for storage of shared object header message indexesH5Pget_shared_mesg_phase_change H5Pset_shared_mesg_phase_change
Add the shuffle filter to the chunk processing pipeline.H5Pset_shuffle
Get and set the sizes of offsets and lengths used in an HDF5 fileH5Pget_sizes H5Pset_sizes
Get and set the size of the symbol table B-tree 1/2 rank and the leaf node 1/2 sizeH5Pget_sym_k H5Pset_sym_k
Add the SZIP compression filter to the chunk processing pipeline.H5Pset_szip
Get and set the user block sizeH5Pget_userblock H5Pset_userblock
H5R - References to objects and regionsH5R
Create a referenceH5Rcreate
Open a reference object.H5Rdereference
Read the time stamps associated with an HDF5 group or dataset.h5readTimestamps
An S4 class representing H5 references.c,H5Ref-method H5Ref-class length,H5Ref-method show,H5Ref-method [,H5Ref-method
Return the name of the object that a reference points toH5Rget_name
Identify the type of object that a reference points toH5Rget_obj_type
Return selection for a reference to dataset regionH5Rget_region
Close and release a dataspaceH5Sclose
Perform operation between an existing selection and an another hyperslab definition.H5Scombine_hyperslab
Combine two selectionsH5Scombine_select
Create a copy of a dataspaceH5Scopy
Create a new dataspace of a specified typeH5Screate
Create a simple dataspaceH5Screate_simple
Find the number of elements in a dataspace selectionH5Sget_select_npoints
Find the size of a dataspaceH5Sget_simple_extent_dims
Determine whether a dataspace is a simple dataspaceH5Sis_simple
Set the selection region of a dataspace to include all elementsH5Sselect_all
Perform operation between an existing selection and an another hyperslab definition.H5Sselect_hyperslab
Select elements of a dataspace using R-style indexingH5Sselect_index
Set the selection region of a dataspace to include no elementsH5Sselect_none
Check that a selection is validH5Sselect_valid
Set the size of a dataspaceH5Sset_extent_simple
Retrieve value for 'H5S_UNLIMITED' constantH5Sunlimited
Retrieve or set the character set to be used in a string datatype.H5Tget_cset H5Tset_cset H5T_cset
Create or modify an HDF5 enum datatypeH5Tenum_create H5Tenum_insert H5T_enum
Get details of HDF5 data typesH5Tget_class H5Tget_nmembers H5T_ops
Retrieve or set the precision of an HDF5 datatypeH5Tget_precision H5Tset_precision H5T_precision
Retrieve or set the type of padding used by string datatypeH5Tget_size H5Tset_size H5T_size
Retrieve or set the type of padding used by string datatypeH5Tget_strpad H5Tset_strpad H5T_strpad
Copy an existing datatypeH5Tcopy
Determine whether a datatype is a variable length stringH5Tis_variable_str
Print the rhdf5 and libhdf5 version numbersh5version
Determine whether a filter is available on this systemH5Zfilter_avail
rhdf5: An interface between HDF5 and Rrhdf5