"chunk_size" missing in RunBanksy?

[reyancoskun]

Hello,

Whenever I try to run this code, xenium.obj <- SeuratWrappers::RunBanksy(xenium.obj, lambda = 0.2, k_geom = 15, assay = "Xenium", slot = "data", features = "variable", verbose=T)

I get this error message:

Fetching data from slot data from assay Xenium Subsetting by features Warning in asMethod(object) : sparse->dense coercion: allocating vector of size 1.9 GiB Computing neighbors... Spatial mode is kNN_median Parameters: k_geom=15 Done Error in Banksy:::computeHarmonics(data_own, knn_df, M, center, verbose) : argument "chunk_size" is missing, with no default

How do I specify chunk_size for this command?

[AlbertoFabbri93]

I just run into the same error with the following version of the package:

R> installed_sha <- packageDescription("SeuratWrappers")$RemoteSha
R> 
R> installed_commit_info <- gh::gh(
+     paste0("GET /repos/satijalab/seurat-wrappers/commits/", installed_sha)
+ )
R> 
R> cat("SHA:", installed_commit_info$sha, "\n")
SHA: 9371845c8d4c9bdeef108e74ef8ca16299261513 
R> cat("Date:", installed_commit_info$commit$author$date, "\n")
Date: 2026-01-08T15:43:57Z 

@reyancoskun did you find a workaround?

[jleechung]

Sorry for the (very) late reply!

We had a similar issue raised here

Could you try re-installing the latest version of BANKSY:

remove.packages('Banksy')
# restart R
remotes::install_github('prabhakarlab/Banksy')

Please also feel free to raise issues re BANKSY here for quicker responses
(we do not regularly watch issues in this repo)