Conversion Error: Conversion from numpy array type 20 is not supported with reticulate >= 1.36.0

theislab / zellkonverter

Conversion between scRNA-seq objects

https://theislab.github.io/zellkonverter/

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Conversion Error: Conversion from numpy array type 20 is not supported with reticulate >= 1.36.0 #116

Closed zipy124 closed 2 months ago

zipy124 commented 4 months ago

When using the same dataset as in #96 , I get an error that numpy array type 20 is not supported for the uns item of rank_genes_groups and its related data.

lupus <- readH5AD("E:\martha\GSE174188_CLUES1_adjusted.h5ad")

When excluding these uns items I still cannot read the file, but have opened a separate issue for that.

zipy124 commented 4 months ago

Just tried with the same versions as the fix landed for https://github.com/theislab/zellkonverter/issues/96 that is v1.11.1 with R 4.2.0 and it works, so this is presumably a regression since then.

lazappi commented 4 months ago

😿 I thought had fixed this but maybe later changes broke it again. Can you please:

Tell me which version of R, {zellkonverter} and {reticulate} doesn't work
Which version of {reticulate} you have installed when it works
Try running it with the failing version, but set readH5AD(..., version = "0.8.0")

lazappi commented 3 months ago

I have been getting errors/warnings about this now and looking in to it, it seems like something changed in {reticulate} v1.36.0 that broke the previous fix. I have opened an issue about it https://github.com/rstudio/reticulate/issues/1613 but in the meantime a temporary fix would be to downgrade to {reticulate} v1.35.0.

lazappi commented 2 months ago

Closing this as {reticulate} v1.38.0 is now available on CRAN.