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kharchenkolab / Baysor

Bayesian Segmentation of Spatial Transcriptomics Data
MIT License
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SparseArray recursion issue with baysor preview #78

Closed bhhlee closed 11 months ago

bhhlee commented 1 year ago

Hi Baysor team,

First of all thank you for building this great tool. I am having an issue running baysor preview as it seems to get stuck during "estimating local colors." Please see code below.

baysor preview -x X_COL -y Y_COL -g GENE_COL -m 100 MOLECULES.csv

Error:

[07:57:40] Info: # CLI params: -x X_COL -y Y_COL -g GENE_COL -m 100 MOLECULES.csv [07:57:41] Info: (2023-05-15) Run Baysor v0.6.0 [07:57:41] Info: Loading data... [07:57:43] Info: Loaded 1460151 transcripts [07:57:44] Info: Estimating noise level [07:58:11] Info: Done [07:58:11] Info: Estimating local colors Internal error: stack overflow in type inference of _is_fixed(SparseArrays.SparseVector{Float32, Int64}, SparseArrays.SparseVector{Float32, Int64}, SparseArrays.SparseVector{Float32, Int64}, SparseArrays.SparseVector{Float32, Int64} ... ... SparseArrays.SparseVector{Float32, Int64} This might be caused by recursion over very long tuples or argument lists.

Any help would be greatly appreciated!

Thank you.

VPetukhov commented 1 year ago

Hi @bhhlee , could you please provide the installation method you used, and if it's manual installation, your julia version? It looks like a bug in Julia 1.9, which I also encountered. The quickest solution would be to downgrade to Julia 1.8.5

VPetukhov commented 12 months ago

This should be fixed in the dev branch (https://github.com/kharchenkolab/Baysor/commit/4da641c0b7dc905de816f8a8a256bc93d2e3d9cb) and will be a part of the next release.

VPetukhov commented 11 months ago

The release is out there now!

bhhlee commented 11 months ago

Awesome thank you!