Package: Rarr 1.7.0
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:
Rarr_1.7.0.tar.gz
Rarr_1.7.0.zip(r-4.5)Rarr_1.7.0.zip(r-4.4)Rarr_1.7.0.zip(r-4.3)
Rarr_1.7.0.tgz(r-4.4-x86_64)Rarr_1.7.0.tgz(r-4.4-arm64)Rarr_1.7.0.tgz(r-4.3-x86_64)Rarr_1.7.0.tgz(r-4.3-arm64)
Rarr_1.7.0.tar.gz(r-4.5-noble)Rarr_1.7.0.tar.gz(r-4.4-noble)
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
On BioConductor:Rarr-1.7.0(bioc 3.21)Rarr-1.6.0(bioc 3.20)
dataimportome-zarron-diskout-of-memoryzarr
Last updated 23 days agofrom:b1dbcfa9eb. Checks:OK: 1 NOTE: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 19 2024 |
| R-4.5-win-x86_64 | NOTE | Nov 19 2024 |
| R-4.5-linux-x86_64 | NOTE | Nov 19 2024 |
| R-4.4-win-x86_64 | NOTE | Nov 19 2024 |
| R-4.4-mac-x86_64 | NOTE | Nov 19 2024 |
| R-4.4-mac-aarch64 | NOTE | Nov 19 2024 |
| R-4.3-win-x86_64 | NOTE | Nov 19 2024 |
| R-4.3-mac-x86_64 | NOTE | Nov 19 2024 |
| R-4.3-mac-aarch64 | NOTE | Nov 19 2024 |
Exports:chunkdimcoercecreate_empty_zarr_arrayread_zarr_arraytypeupdate_zarr_arrayuse_bloscuse_bz2use_gzipuse_lz4use_lzmause_zlibuse_zstdwrite_zarr_arraywriteZarrArrayzarr_overviewZarrArray
Dependencies:abindaskpassbase64encBiocGenericsclicrayoncurlDelayedArraydigestgenericsgluehttrIRangesjsonlitelatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslpaws.commonpaws.storageR.methodsS3R.ooR.utilsR6RcpprlangS4ArraysS4VectorsSparseArraystringistringrsysvctrsxml2XVectorzlibbioc
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 |
