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Bug in AzimuthReference #219

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zacharyrs opened this issue Apr 5, 2024 · 1 comment
Open

Bug in AzimuthReference #219

zacharyrs opened this issue Apr 5, 2024 · 1 comment

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@zacharyrs
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zacharyrs commented Apr 5, 2024

Hey - I recently started using Azimuth and have had some trouble similar to #155 when building a reference:

Reference must contain an AzimuthData object in the tools slot.

It seems the fix (b1b6895) has a bug in the logic trying to generate the automatically assigned tool name.

The Tool<- method gets the function name that called Tool<-, per https://github.com/satijalab/seurat-object/blob/release/5.0.1/R/seurat.R#L2636.
In this case, the Tool<- call uses the correct "AzimuthReference".

In contrast, the fix uses the outermost function name from sys.calls(), which corresponds with my wrapper function.
It then tries to copy the non-existent value into "AzimuthReference", which deletes the desired entry.

I think this can be fixed by using the innermost (last) function name from sys.calls(), as this is the function that calls Tool<-.

For reference, I am running https://github.com/satijalab/azimuth/tree/release/0.5.0.

@z5ouyang
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z5ouyang commented Apr 17, 2024

That's why I can use "AzimuthReference" in the main function but NOT in a wrapper function. Maybe related to #155

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