"StackOverflowError" happened in "normalize_object" #7
Description
Hello CellScopes team,
There was an issue when I ran the "normalize_object" function. The test data I used is an imaging-based spatial transcriptomic data downloaded from GEO (GSE227044). I'm running Julia v1.10 on MacBook. Here is the code:
genes = count_df.gene
cells = string.(names(count_df)[2:end])
count_df = count_df[!, 2:end]
count_df = convert(SparseMatrixCSC{Int64, Int64},Matrix(count_df))
raw_count = cs.RawCountObject(count_df, cells, genes)
count_molecules.cell = string.(count_molecules.cell)
count_cells.cell = string.(count_cells.cell)
sham = cs.CartanaObject(count_molecules, count_cells, raw_count; prefix = "sham", min_gene = 0, min_cell = 3)
sham = cs.normalize_object(sham)
Here is the traceback:
julia> sham = cs.normalize_object(sham)
ERROR: StackOverflowError:
Stacktrace:
[1] promote_type(::Type, ::Type, ::Type, ::Type, ::Vararg{Type}) (repeats 7394 times)
@ Base ./promotion.jl:299
[2] hcat(::SparseVector{…}, ::SparseVector{…}, ::SparseVector{…}, ::Vararg{…})
@ SparseArrays /Applications/Julia1.10.app/Contents/Resources/julia/share/julia/stdlib/v1.10/SparseArrays/src/sparsevector.jl:1109
[3] #normalize_object#57
@ ~/.julia/packages/CellScopes/oYdMu/src/scrna/processing.jl:5 [inlined]
[4] normalize_object(ct_obj::CellScopes.RawCountObject; scale_factor::Int64, norm_method::String, pseudocount::Int64)
@ CellScopes ~/.julia/packages/CellScopes/oYdMu/src/scrna/processing.jl:10
[5] normalize_object
@ ~/.julia/packages/CellScopes/oYdMu/src/scrna/processing.jl:9 [inlined]
[6] normalize_object(sc_obj::CellScopes.CartanaObject; scale_factor::Int64, norm_method::String, pseudocount::Int64)
@ CellScopes ~/.julia/packages/CellScopes/oYdMu/src/scrna/processing.jl:16
[7] normalize_object(sc_obj::CellScopes.CartanaObject)
@ CellScopes ~/.julia/packages/CellScopes/oYdMu/src/scrna/processing.jl:15
[8] eval
@ ./boot.jl:385 [inlined]
[9] include_string(mapexpr::typeof(REPL.softscope), mod::Module, code::String, filename::String)
@ Base ./loading.jl:2076
[10] invokelatest(::Any, ::Any, ::Vararg{Any}; kwargs::@Kwargs{})
@ Base ./essentials.jl:892
[11] invokelatest(::Any, ::Any, ::Vararg{Any})
@ Base ./essentials.jl:889
[12] inlineeval(m::Module, code::String, code_line::Int64, code_column::Int64, file::String; softscope::Bool)
@ VSCodeServer ~/.vscode/extensions/julialang.language-julia-1.75.2/scripts/packages/VSCodeServer/src/eval.jl:263
[13] (::VSCodeServer.var"#67#72"{…})()
@ VSCodeServer ~/.vscode/extensions/julialang.language-julia-1.75.2/scripts/packages/VSCodeServer/src/eval.jl:181
[14] withpath(f::VSCodeServer.var"#67#72"{…}, path::String)
@ VSCodeServer ~/.vscode/extensions/julialang.language-julia-1.75.2/scripts/packages/VSCodeServer/src/repl.jl:274
[15] (::VSCodeServer.var"#66#71"{…})()
@ VSCodeServer ~/.vscode/extensions/julialang.language-julia-1.75.2/scripts/packages/VSCodeServer/src/eval.jl:179
[16] hideprompt(f::VSCodeServer.var"#66#71"{…})
@ VSCodeServer ~/.vscode/extensions/julialang.language-julia-1.75.2/scripts/packages/VSCodeServer/src/repl.jl:38
[17] (::VSCodeServer.var"#65#70"{…})()
@ VSCodeServer ~/.vscode/extensions/julialang.language-julia-1.75.2/scripts/packages/VSCodeServer/src/eval.jl:150
[18] with_logstate(f::Function, logstate::Any)
@ Base.CoreLogging ./logging.jl:515
[19] with_logger
@ ./logging.jl:627 [inlined]
[20] (::VSCodeServer.var"#64#69"{VSCodeServer.ReplRunCodeRequestParams})()
@ VSCodeServer ~/.vscode/extensions/julialang.language-julia-1.75.2/scripts/packages/VSCodeServer/src/eval.jl:255
[21] #invokelatest#2
@ ./essentials.jl:892 [inlined]
[22] invokelatest(::Any)
@ Base ./essentials.jl:889
[23] (::VSCodeServer.var"#62#63")()
@ VSCodeServer ~/.vscode/extensions/julialang.language-julia-1.75.2/scripts/packages/VSCodeServer/src/eval.jl:34
Some type information was truncated. Use show(err) to see complete types.
I'm a fresh man to Julia and I've tried my best to solve the error which didn't work. Hope you can give me some help.
Best,
Pedro