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grimbough committed Nov 25, 2024
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Expand Up @@ -12,11 +12,12 @@ Mike L. Smith
- [Writing to a Zarr array](#writing-to-a-zarr-array)
- [Current Status](#current-status)
- [Reading and Writing](#reading-and-writing)
- [Required system libraries](#required-system-libraries)

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Expand Down Expand Up @@ -98,7 +99,7 @@ zarr_overview(zarr_example)
```

## Type: Array
## Path: /tmp/RtmpF5o9TP/temp_libpath14ca86d0ed64a/Rarr/extdata/zarr_examples/column-first/int32.zarr
## Path: /mnt/data/R-lib/4.5-bioc_3.21/Rarr/extdata/zarr_examples/column-first/int32.zarr
## Shape: 30 x 20 x 10
## Chunk Shape: 10 x 10 x 5
## No. of Chunks: 12 (3 x 2 x 2)
Expand Down Expand Up @@ -255,38 +256,38 @@ requiring conversion from the Zarr datatype. The table below summarises
the current status of datatype support. It will be updated as progress
is made.

| Zarr Data Type | Status<br/>(reading / writing) | Notes |
|-----------------------|:------------------------------:|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| `boolean` | ✔ / ❌ | |
| `int8` | ✔ / ❌ | |
| `uint8` | ✔ / ❌ | |
| `int16` | ✔ / ❌ | |
| `uint16` | ✔ / ❌ | |
| `int32` | ✔ / ✔ | |
| `uint32` | ✔ / ❌ | Values outside the range of `int32` are converted to `NA`. Future plan is to allow conversion to `double` or use the [bit64](https://cran.r-project.org/package=bit64) package. |
| `int64` | ✔ / ❌ | Values outside the range of `int32` are converted to `NA`. Future plan is to allow conversion to `double` or use the [bit64](https://cran.r-project.org/package=bit64) package. |
| `uint64` | ✔ / ❌ | Values outside the range of `int32` are converted to `NA`. Future plan is to allow conversion to `double` or use the [bit64](https://cran.r-project.org/package=bit64) package. |
| `half` / `float16` | ✔ / ❌ | Converted to `double` in R. No effort is made to assess loss of precision due to conversion. |
| `single` / `float32` | ✔ / ❌ | Converted to `double` in R. No effort is made to assess loss of precision due to conversion. |
| `double` / `float64` | ✔ / ✔ | |
| `complex` | ❌ / ❌ | |
| `timedelta` | ❌ / ❌ | |
| `datetime` | ❌ / ❌ | |
| `string` | ✔ / ✔ | |
| `Unicode` | ✔ / ✔ | |
| `void *` | ❌ / ❌ | |
| Structured data types | ❌ / ❌ | |
| Zarr Data Type | Status<br/>(reading / writing) | Notes |
|----|:--:|----|
| `boolean` | ✔ / ❌ | |
| `int8` | ✔ / ❌ | |
| `uint8` | ✔ / ❌ | |
| `int16` | ✔ / ❌ | |
| `uint16` | ✔ / ❌ | |
| `int32` | ✔ / ✔ | |
| `uint32` | ✔ / ❌ | Values outside the range of `int32` are converted to `NA`. Future plan is to allow conversion to `double` or use the [bit64](https://cran.r-project.org/package=bit64) package. |
| `int64` | ✔ / ❌ | Values outside the range of `int32` are converted to `NA`. Future plan is to allow conversion to `double` or use the [bit64](https://cran.r-project.org/package=bit64) package. |
| `uint64` | ✔ / ❌ | Values outside the range of `int32` are converted to `NA`. Future plan is to allow conversion to `double` or use the [bit64](https://cran.r-project.org/package=bit64) package. |
| `half` / `float16` | ✔ / ❌ | Converted to `double` in R. No effort is made to assess loss of precision due to conversion. |
| `single` / `float32` | ✔ / ❌ | Converted to `double` in R. No effort is made to assess loss of precision due to conversion. |
| `double` / `float64` | ✔ / ✔ | |
| `complex` | ❌ / ❌ | |
| `timedelta` | ❌ / ❌ | |
| `datetime` | ❌ / ❌ | |
| `string` | ✔ / ✔ | |
| `Unicode` | ✔ / ✔ | |
| `void *` | ❌ / ❌ | |
| Structured data types | ❌ / ❌ | |

### Compression Tools

| Data Type | Status<br/>(reading / writing) | Notes |
|---------------|:------------------------------:|-------------------------------------------------------------------------------------------------------|
| `zlib / gzip` | ✔ / ✔ | Only system default compression level (normally 6) is enabled for writing. |
| `bzip2` | ✔ / ✔ | Only compression level 9 is enabled for writing. |
| `blosc` | ✔ / ✔ | Only `lz4` compression level 5 is enabled for writing. |
| `LZMA` | ✔ / ✔ | |
| `LZ4` | ✔ / ✔ | |
| `Zstd` | ❌ / ❌ | Algorithm is available via blosc for writing, but can’t currently be accessed through the R interface |
| Data Type | Status<br/>(reading / writing) | Notes |
|----|:--:|----|
| `zlib / gzip` | ✔ / ✔ | Only system default compression level (normally 6) is enabled for writing. |
| `bzip2` | ✔ / ✔ | Only compression level 9 is enabled for writing. |
| `blosc` | ✔ / ✔ | Only `lz4` compression level 5 is enabled for writing. |
| `LZMA` | ✔ / ✔ | |
| `LZ4` | ✔ / ✔ | |
| `Zstd` | ✔ / ✔ | |

Please open an [issue](https://github.com/grimbough/Rarr/issues) if
support for a required compression tool is missing.
Expand All @@ -297,6 +298,20 @@ The is currently no support for additional filters. Please open an
[issue](https://github.com/grimbough/Rarr/issues) if you require filter
support.

# Required system libraries

To provide support for BLOSC and zstd compression tools Rarr links
against libraries providing these tools. If you have them installed on
your system Rarr will attempt to use those versions. If they are not
detected then Rarr will compile and use versions that are distributed
with the package. Either way the functionality will available, however
if you are using the system libraries and then later remove them Rarr
may fail to work correctly.

This only concerns users installing the package from source. If you are
using the pre-built binaries for Windows or Mac OSX distributed by
Bioconductor then this should not be an issue for you.

[^1]: you only need to do the installation step once

[^2]: This is essentially reading and formatting the array metadata that
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