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

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zipy124 opened this issue Apr 26, 2024 · 3 comments
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@zipy124
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zipy124 commented Apr 26, 2024

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
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zipy124 commented Apr 26, 2024

Just tried with the same versions as the fix landed for #96 that is v1.11.1 with R 4.2.0 and it works, so this is presumably a regression since then.

@lazappi
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lazappi commented Apr 29, 2024

😿 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 lazappi added the bug Something isn't working label Apr 29, 2024
@lazappi lazappi changed the title Conversion Error: Conversion from numpy array type 20 is not supported Conversion Error: Conversion from numpy array type 20 is not supported with reticulate >= 1.36.0 May 27, 2024
@lazappi
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lazappi commented May 27, 2024

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 rstudio/reticulate#1613 but in the meantime a temporary fix would be to downgrade to {reticulate} v1.35.0.

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