(sfe_cosmx <- readCosMX(dir_use, add_molecules = TRUE))
>>> Constructing cell polygons

Warning message in .df2sf_check(df, spatialCoordsNames, gt, group_col, id_col, subid_col):
“Removed 6 items that have fewer than the minimum of 3 vertices for geometry type POLYGON”
>>> ..removing 7 empty polygons

>>> Checking polygon validity

>>> Reading transcript coordinates

>>> Converting transcript spots to geometry

>>> Writing reformatted transcript spots to disk

Error: Capacity error: array cannot contain more than 2147483646 bytes, have 2148149336
Traceback:

1. readCosMX(dir_use, add_molecules = TRUE)
2. addTxTech(sfe, data_dir, sample_id, tech = "CosMX", z = z, file_out = file_out, 
 .     BPPARAM = BPPARAM, split_cell_comps = split_cell_comps, z_option = z_option)
3. addTxSpots(sfe, file = fn, sample_id = sample_id, spatialCoordsNames = spatialCoordsNames, 
 .     gene_col = gene_col, z = z, phred_col = "qv", min_phred = min_phred, 
 .     split_col = split_col, z_option = z_option, flip = flip, 
 .     file_out = file_out, BPPARAM = BPPARAM)
4. formatTxSpots(file, dest = dest, spatialCoordsNames = spatialCoordsNames, 
 .     gene_col = gene_col, z = z, phred_col = phred_col, min_phred = min_phred, 
 .     split_col = split_col, flip = flip, z_option = z_option, 
 .     file_out = file_out, BPPARAM = BPPARAM, return = TRUE)
5. suppressWarnings(sfarrow::st_write_parquet(mols, file_out))
6. withCallingHandlers(expr, warning = function(w) if (inherits(w, 
 .     classes)) tryInvokeRestart("muffleWarning"))
7. sfarrow::st_write_parquet(mols, file_out)
8. arrow::Table$create(df)
9. Table__from_dots(dots, schema, option_use_threads())