blosc compression with rhdf5
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@hoganajjunkbioc-23639
Last seen 17 months ago

I have an R package that uses rhdf5 to read hdf5 files. However, I'm getting the following error when trying to read an hdf5 file written in python:

Unable to read dataset. Not all required filters available.
Missing filters: blosc

I see this related question on zlib: https://github.com/grimbough/Rhdf5lib/issues/15#issuecomment-470847820

But it's not clear to me how to do this build, or how or where to apply the patch linked in the answer. That is, I have blosc installed locally, but how do I include it in my conda recipe so that when others install my R package, it knows where to find /their/ local blosc library at runtime?

rhdf5 • 235 views
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Mike Smith ★ 5.2k
@mike-smith
Last seen 45 minutes ago
EMBL Heidelberg / de.NBI

Unlike zlib, which is linked to when libhdf5 is compiled, BLOSC is used as an external plugin and loaded dynamically at runtime, so I'm not sure the strategy in that issue will work. You also don't just need BLOSC installed, but the HDF5 plugin that interfaces with it.

I've been working on the rhdf5filters package which distributes a BLOSC filter within an R package and will make it available to rhdf5. The integration isn't complete yet, but I'm working on that over the next few days and it should be in the developmental branch soon. I'll update here when there's a version you can test.

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