Package: Rarr 1.7.1

Mike Smith

Rarr: Read Zarr Files in R

The Zarr specification defines a format for chunked, compressed, N-dimensional arrays. It's design allows efficient access to subsets of the stored array, and supports both local and cloud storage systems. Rarr aims to implement this specifcation in R with minimal reliance on an external tools or libraries.

Authors:Mike Smith [aut, cre]

Rarr_1.7.1.tar.gz
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Rarr.pdf |Rarr.html✨
Rarr/json (API)
NEWS

# Install 'Rarr' in R:

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

Bug tracker:https://github.com/grimbough/rarr/issues

Uses libs:

c-blosc– High performance meta-compressor optimized for binary data
libzstd– Fast lossless compression algorithm

On BioConductor:Rarr-1.7.1(bioc 3.21)Rarr-1.6.0(bioc 3.20)

dataimport ome-zarr on-disk out-of-memory zarr c-blosc libzstd

6.55 score 34 stars 21 scripts 266 downloads 17 exports 39 dependencies

Last updated 1 months agofrom:8f1c9da389. Checks:OK: 1 NOTE: 1 ERROR: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 26 2024
R-4.5-win-x86_64	ERROR	Dec 04 2024
R-4.5-linux-x86_64	NOTE	Dec 26 2024
R-4.4-win-x86_64	ERROR	Dec 04 2024
R-4.4-mac-x86_64	ERROR	Dec 26 2024
R-4.4-mac-aarch64	ERROR	Dec 26 2024
R-4.3-win-x86_64	ERROR	Dec 04 2024
R-4.3-mac-x86_64	ERROR	Dec 26 2024
R-4.3-mac-aarch64	ERROR	Dec 26 2024

Exports:chunkdim coerce create_empty_zarr_array read_zarr_array type update_zarr_array use_blosc use_bz2 use_gzip use_lz4 use_lzma use_zlib use_zstd write_zarr_array writeZarrArray zarr_overview ZarrArray

Dependencies:abind askpass base64enc BiocGenerics cli crayon curl DelayedArray digest generics glue httr IRanges jsonlite lattice lifecycle magrittr Matrix MatrixGenerics matrixStats mime openssl paws.common paws.storage R.methodsS3 R.oo R.utils R6 Rcpp rlang S4Arrays S4Vectors SparseArray stringi stringr sys vctrs xml2 XVector

Reading Zarr arrays with Rarr

Mike L. Smith

Rendered fromRarr.Rmdusingknitr::rmarkdownon Dec 26 2024.

Last update: 2024-09-06
Started: 2023-01-23

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Compress and write a single chunk	.compress_and_write_chunk
Create a string of the form 'x[idx[[1]], idx[[2]]] <- y' for an array 'x' where the number of dimensions is variable.	.create_replace_call
Decompress a chunk in memory	.decompress_chunk
Format the decompressed chunk as an array of the correct type	.format_chunk
This is a modified version of paws.storge:::get_credentials(). It is included to prevent using the ':::' operator. Look at that function if things stop working.	.get_credentials
Normalize a Zarr array path	.normalize_array_path
Parse the data type encoding string	.parse_datatype
Define compression tool and settings	compressors use_blosc use_bz2 use_gzip use_lz4 use_lzma use_zlib use_zstd
Create an (empty) Zarr array	create_empty_zarr_array
Determine the size of chunk in bytes	get_chunk_size
Determine the size of chunk in bytes after decompression	get_decompressed_chunk_size
Read the .zarray metadata file associated with a Zarr array	read_array_metadata
Read a single Zarr chunk	read_chunk
Read a Zarr array	read_zarr_array
Convert special fill values from strings to numbers	update_fill_value
Update (a subset of) an existing Zarr array	update_zarr_array
Write an R array to Zarr	write_zarr_array
Print a summary of a Zarr array	zarr_overview
ZarrArray constructor	chunkdim,ZarrArraySeed-method coerce coerce,ANY,ZarrMatrix-method coerce,ZarrArray,ZarrMatrix-method coerce,ZarrMatrix,ZarrArray-method matrixClass,ZarrArray-method ZarrArray ZarrArray-class ZarrArray-method ZarrMatrix ZarrMatrix-class
Write arrays to Zarr	chunkdim,ZarrRealizationSink-method coerce,ANY,ZarrArray-method coerce,ANY,ZarrRealizationSink-method coerce,ZarrRealizationSink,DelayedArray-method coerce,ZarrRealizationSink,ZarrArray-method coerce,ZarrRealizationSink,ZarrArraySeed-method coerce,ZarrRealizationSink,ZarrMatrix-method type,ZarrRealizationSink-method writeZarrArray write_block,ZarrRealizationSink-method ZarrRealizationSink ZarrRealizationSink-class