HDF5-API Errors: error #000: H5D.c in H5Dvlen_reclaim(): line 732: invalid argument
rosanababu opened this issue · 4 comments
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
Hi @rosanababu !
Could you post the str.h5mu so the package maintainers can try to replicate the issue?
Robrecht
@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
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? 😄
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?