pizzarr

A Zarr implementation for R.

Installation

pizzarr ships in two tiers — same version, different builds. The CRAN build is pure R and needs nothing beyond base R dependencies. The r-universe build links in the zarrs Rust crate via extendr, adding parallel decompression and additional codec support.

CRAN (pure R)

install.packages("pizzarr")

r-universe (zarrs backend)

install.packages("pizzarr",
                 repos = c("https://zarr-developers.r-universe.dev",
                            "https://cloud.r-project.org"))

Both sources serve the same release version. The r-universe build distributes pre-compiled binaries for Windows and macOS — no Rust toolchain needed.

The r-universe binaries compile the zarrs backend with local filesystem I/O, synchronous HTTP reads, gzip/zstd/blosc codecs, sharding, and S3/GCS cloud store support via object_store. Any build that compiles Rust enables these features by default. To compile with a different feature set, set PIZZARR_FEATURES explicitly (see below).

pizzarr_compiled_features() lists what the zarrs backend provides, and pizzarr_upgrade() prints the install command when zarrs is not compiled in. pizzarr_config() controls concurrency settings (thread pool size, codec concurrency, HTTP range request batching). See vignette("zarrs-backend") for details.

Building from source (zarrs backend)

If you need to compile the zarrs backend yourself — either because no binary is available for your platform, or because you are developing the Rust side — you need rustc >= 1.91. On Windows, add the GNU target:

rustup target add x86_64-pc-windows-gnu

The build system uses two environment variables to control compilation:

• DEBUG — set to any non-empty value for a debug build. This enables Cargo’s incremental compilation, so subsequent rebuilds are fast (seconds instead of minutes). The resulting library is slower at runtime because it skips link-time optimization and does not strip symbols. Use this during active development on the Rust code.
• PIZZARR_FEATURES — a comma-separated list of extra Cargo features. When unset, the build defaults to s3,gcs (S3 and GCS cloud store support via object_store and tokio, which also pulls in blosc and sharding). Set this explicitly to override — e.g., PIZZARR_FEATURES=none for Cargo’s default features only, or PIZZARR_FEATURES=s3 for S3 without GCS.

A release build (no DEBUG) uses LTO, single codegen unit, and symbol stripping — fast at runtime but takes several minutes to compile from scratch.

# Development: fast rebuilds, slower runtime, S3/GCS included
DEBUG=1 R CMD INSTALL .

# Production: slow first build, fast runtime, S3/GCS included
R CMD INSTALL .

# Production with Cargo default features only (no cloud stores)
PIZZARR_FEATURES=none R CMD INSTALL .

NOT_CRAN=true opts builds out of the offline-vendored-crates path used for CRAN; it’s set automatically when DEBUG is present and only matters when src/rust/vendor.tar.xz is also present.

Development happens on the develop branch. See CONTRIBUTING.md for the branching and release model.

Usage

library(pizzarr)

# Open a sample BCSD climate dataset (Zarr V3)
v3_root <- pizzarr_sample("bcsd_v3")
v3 <- zarr_open(v3_root)

# Print the group summary
v3
#> <ZarrGroup> /
#>   Store type  : DirectoryStore
#>   Zarr format : 3
#>   Read-only   : FALSE
#>   No. members : 5

# View the hierarchy
v3$tree()
#> / 
#> ├── latitude (33) <f4
#> ├── longitude (81) <f4
#> ├── pr (12, 33, 81) <f4
#> ├── tas (12, 33, 81) <f4
#> └── time (12) <f8

# Inspect an array
v3$get_item("pr")
#> <ZarrArray> /pr
#>   Shape       : (12, 33, 81)
#>   Chunks      : (12, 33, 81)
#>   Data type   : <f4
#>   Fill value  : 1.00000002004088e+20
#>   Order       : C
#>   Read-only   : FALSE
#>   Compressor  : ZstdCodec
#>   Store type  : DirectoryStore
#>   Zarr format : 3

# Read a slice: first 3 time steps, first 3 latitudes, first longitude
v3$get_item("pr")$get_item(list(slice(1, 3), slice(1, 3), 1))$data
#> , , 1
#> 
#>        [,1]   [,2]   [,3]
#> [1,] 133.97 144.51 149.92
#> [2,]  75.40  72.38  68.62
#> [3,]  93.14  91.24  89.37

Create an array from scratch:

a <- array(data = 1:20, dim = c(2, 10))
z <- zarr_create(shape = dim(a), dtype = "<f4", fill_value = NA)
z$set_item("...", a)

z
#> <ZarrArray> /
#>   Shape       : (2, 10)
#>   Chunks      : (2, 10)
#>   Data type   : <f4
#>   Fill value  : 0
#>   Order       : F
#>   Read-only   : FALSE
#>   Compressor  : ZstdCodec
#>   Store type  : MemoryStore
#>   Zarr format : 2
z$get_item(list(slice(1, 2), slice(1, 5)))$data
#>      [,1] [,2] [,3] [,4] [,5]
#> [1,]    1    3    5    7    9
#> [2,]    2    4    6    8   10

Remote and cloud data

Zarr stores served over HTTPS need no configuration, and this route works on both install tiers:

# USGS gridMET on an Open Storage Network pod
store <- HttpStore$new("https://usgs.osn.mghpcc.org/mdmf/gdp/gridMET.zarr")
g <- zarr_open(store)
store$listdir()

The same bucket over the S3 API, which needs the r-universe build:

Sys.setenv(AWS_ENDPOINT = "https://usgs.osn.mghpcc.org")

zarrs_get_subset("s3://mdmf/gdp/gridMET.zarr", "lat", list(c(0L, 5L)), NULL)

Coming from xarray or fsspec, the settings you would pass in storage_options — endpoint_url, key, secret, anon — are environment variables here: AWS_ENDPOINT, AWS_ACCESS_KEY_ID, AWS_SECRET_ACCESS_KEY, and unsigned-by-default when no credentials are set. Alternate endpoints (MinIO, Ceph, Wasabi, R2) work the same way. See vignette("remote-stores") for the full mapping, credentials, and the current limits — cloud stores are read-only.

Features

• Zarr V2 and V3 read and write (format auto-detected on open)
• Stores: MemoryStore, DirectoryStore (read/write); HttpStore (read-only); S3Store, GcsStore (r-universe tier, via object_store)
• Data types: boolean, int8–int64, uint8–uint64, float16/32/64, string, Unicode, VLenUTF8
• Compression: zlib/gzip, bzip2, blosc, LZMA, LZ4, Zstd
• Blosc requires the optional blosc package (install.packages("blosc"))

How It Works

pizzarr uses R6 classes mirroring the zarr-python object model:

• Store — backend storage (DirectoryStore for local files, MemoryStore for in-memory, HttpStore for remote read-only, S3Store and GcsStore for cloud buckets on the r-universe tier)
• ZarrGroup — hierarchical container holding arrays and sub-groups (like a directory)
• ZarrArray — chunked, compressed N-dimensional array (like a file)
• Codec — compression/decompression (zlib, zstd, blosc, lz4, etc.)
• Dtype — data-type mapping between R and Zarr

Data flows through the stack: a Store holds raw chunk bytes, a Codec pipeline compresses and decompresses them, and ZarrArray presents typed N-dimensional data to R. Groups and arrays are addressed by path within a store, just like files in a directory tree.

See vignette("pizzarr") for a full walkthrough.

Ecosystem

pizzarr implements the Zarr specification (V2 and V3) for R. Related projects:

• zarr-python — the reference Python implementation
• zarr.js — JavaScript implementation
• zarr — native R V3 implementation (CRAN)
• Rarr — Bioconductor package for reading and writing individual Zarr arrays (V2, limited write support)
• zarr-conformance-tests — cross-implementation validation

Validation with zarr-python

A standalone integration test cross-validates that pizzarr and zarr-python produce equivalent Zarr stores. Both implementations write the same arrays (V2 and V3 formats, multiple dtypes, codecs, chunk layouts, and groups with attributes), then each reads the other’s output and verifies the data matches.

Prerequisites: Python 3.10+ with zarr>=3 and numpy installed.

Rscript inst/extdata/cross-validate.R

The script skips gracefully (exit 0) if Python is not available. On success all checks pass and exit code is 0; any mismatch is reported and exits 1.

Zarr Conformance Tests

pizzarr participates in the zarr-conformance-tests framework, which validates that Zarr implementations can correctly read standard test arrays (V2 and V3 formats, multiple dtypes). These tests run automatically in CI on every push and pull request to main.

Performance

The zarrs backend (r-universe install only) handles chunk I/O and codec execution in Rust, bypassing R’s single-threaded chunk loop entirely. For compressed data — the common case with real Zarr stores — this translates to 6–8x throughput over pure-R.

The table below compares pizzarr’s two tiers against zarr-python/xarray on a 500x500x100 float64 array (~200 MB uncompressed) with 100x100x50 chunks. All numbers are best-of-three throughput in MB/s, measured on Windows (pizzarr 0.2.0-dev, zarr-python 3.1.5, April 2026).

xarray leads on bulk operations because numpy can transpose array memory layout via stride views (zero copy) — R’s array() always copies. The gap narrows with compression since decompression dominates, and zarrs wins on cross-chunk subset reads (200 vs 138 MB/s gzip) because it decodes only the chunks that overlap the selection.

Reproduce with Rscript inst/extdata/benchmark-zarrs-vs-xarray.R (requires Python with zarr>=3 and xarray for the xarray column).

Contributing

See CONTRIBUTING.md for development setup, testing, and documentation build instructions.