Package: rhdf5client 1.35.2

Alexey Sergushichev

rhdf5client: Access HDF5 content from HDF Scalable Data Service

This package provides functionality for reading data from HDF Scalable Data Service from within R. The HSDSArray function bridges from HSDS to the user via the DelayedArray interface. Bioconductor manages an open HSDS instance graciously provided by John Readey of the HDF Group.

Authors:Samuela Pollack [aut], Shweta Gopaulakrishnan [aut], BJ Stubbs [aut], Alexey Sergushichev [aut, cre], Vincent Carey [aut]

# Install 'rhdf5client' in R:

install.packages('rhdf5client', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:rhdf5client-1.35.2(bioc 3.24)rhdf5client-1.34.2(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

dataimport software infrastructure

5.18 score 2 packages 42 scripts 1 mentions 13 exports 23 dependencies

Last updated from:bd1d8e35db. Checks:1 WARNING, 13 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	180
linux-devel-arm64	OK	274
linux-devel-x86_64	OK	270
source / vignettes	OK	224
linux-release-arm64	OK	221
linux-release-x86_64	OK	295
macos-release-arm64	OK	265
macos-release-x86_64	OK	485
macos-oldrel-arm64	OK	169
macos-oldrel-x86_64	OK	487
windows-devel	OK	221
windows-release	OK	192
windows-oldrel	OK	192
wasm-release	OK	220

Exports:check_hsds extractCompoundJSON getData getHSDSFileList HSDSArray HSDSDataset HSDSFile HSDSSource isplit listDatasets listDomains sproc URL_hsds

Dependencies:abind askpass BiocGenerics curl data.table DelayedArray generics httr IRanges jsonlite lattice Matrix MatrixGenerics matrixStats mime openssl R6 rjson S4Arrays S4Vectors SparseArray sys XVector

HSDSArray -- DelayedArray backend for Remote HDF5

Using the DelayedArray infrastructure | Interface to HSDS (HDF Object Store)

Rendered fromdelayed-array.Rmdusingknitr::rmarkdown

Last update: 2023-07-10
Started: 2018-10-02

Help page	Topics
bracket method for 1d request from HSDSDataset	[,HSDSDataset,numeric,ANY,ANY-method
bracket method for 2d request from HSDSDataset	[,HSDSDataset,numeric,numeric,ANY-method
Coercion method from HSDSMatrix to its superclass HSDSArray	as
a test request	check_hsds
Obtain dimensions of an object of type HSDSArraySeed	dim dim,HSDSArraySeed-method
Obtain names of dimensions for an object of type HSDSArraySeed	dimnames dimnames,HSDSArraySeed-method
Access dataset backed by an HSDSArraySeed	extract_array extract_array,HSDSArraySeed-method
compound operation	extractCompoundJSON
extract elements of a one or two-dimensional HSDSDataset	getData getData,HSDSDataset,character,character-method getData,HSDSDataset,character,missing-method getData,HSDSDataset,list,,missing-method getData,HSDSDataset,list,character-method getData,HSDSDataset,list,missing-method
List files on a directory on HSDS-server	getHSDSFileList
A DelayedArray backend for accessing a remote HDF5 server.	HSDSArray HSDSArray-class
HSDSArraySeed for HSDSArray backend to DelayedArray	HSDSArraySeed HSDSArraySeed-class
Construct an object of type HSDSDataset A HSDSDataset is a representation of a dataset in a HDF5 file.	HSDSDataset
An S4 class to represent a dataset in a HDF5 file.	HSDSDataset-class
Construct an object of type HSDSFile	HSDSFile
An S4 class to represent an HDF5 file accessible from a server.	HSDSFile-class
DelayedMatrix subclass for a two-dimensional HSDSArray	HSDSMatrix HSDSMatrix-class
Construct an object of type HSDSSource.	HSDSSource
An S4 class to represent a HDF5 server listening on a port.	HSDSSource-class
This function is deprecated and will be defunct in the next release.	isplit sproc
Search inner file hierarchy for datasets	listDatasets
List files and subdirectories of a domain	listDomains listDomains,HSDSSource,character-method listDomains,HSDSSource,missing-method
rhdf5client: A package for accessing HDFGroup HDF5 servers from R.	rhdf5client-package rhdf5client
Deprecated functions in package 'rhdf5client'	rhdf5client-deprecated
manage hsds URL	URL_hsds

Package: rhdf5client 1.35.2

rhdf5client: Access HDF5 content from HDF Scalable Data Service

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