HDF5-API Errors: error #000: H5D.c in H5Dvlen_reclaim(): line 732: invalid argument

[rosanababu]

Hi, I'm trying to convert mudata to Seurat object. I'm getting following error while using ReadH5MU():

seurat <- ReadH5MU("str.h5mu")
Error in self$read_low_level(file_space = self_space_id, mem_space = mem_space_id, :
HDF5-API Errors:
error #000: H5D.c in H5Dvlen_reclaim(): line 732: invalid argument
class: HDF5
major: Invalid arguments to routine
minor: Bad value

Kindly help, thank you

[rcannood]

Hi @rosanababu !

Could you post the str.h5mu so the package maintainers can try to replicate the issue?

Robrecht

[DriesSchaumont]

@ilia-kats @gtca Hi, I encountered this issue and am able to share the data to replicate the issue. Please find the file here:

s3://openpipelines-data/10x_5k_anticmv/5k_human_antiCMV_T_TBNK_connect_mms.h5mu

[gtca]

Thank you, @DriesSchaumont!

As far as I can tell, this happens because one of the modalities has 0 features.

Apart from this, nullable arrays have not been supported by this library yet.

Both things should be addressed in #17.

@DriesSchaumont Can you check that it works? 🙏
@ilia-kats Do these hot-fixes make sense? 😄

[rcannood]

Out of curiosity, I wonder whether rcannood/hdf5r@issue-208-alternative-condition is also a fix to the problem. @DriesSchaumont would you be able to test this?