`scDblFinder()` error with R 4.3.1 and Seurat v5: `the 'as_cholmod_sparse' function does not exist in the 'Matrix' package`

yerkes-gencore / bulk_template

Template for ENPRC Genomics Core bulk RNAseq projects

1 stars 0 forks source link

`scDblFinder()` error with R 4.3.1 and Seurat v5: `the 'as_cholmod_sparse' function does not exist in the 'Matrix' package` #14

Open micahpf opened 1 month ago

micahpf commented 1 month ago

See https://github.com/plger/scDblFinder/issues/91#issuecomment-1825482069

Clear your environment, restart R, then run this:

remotes::install_version("Matrix", version = "1.6-4") # see 
renv::install("irlba", rebuild = TRUE, prompt = FALSE)
renv::install("Seurat", rebuild = TRUE, prompt = FALSE)
renv::install("SeuratObject", rebuild = TRUE, prompt = FALSE)

Restart R again (?) and scDblFinder should run smoothly.

This will likely be fixed when we upgrade our R version to 4.4.

micahpf commented 1 month ago

When running merge() I get this error as well:

Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' length

Which is apparently fixed by downgrading to Seurat 5.0.3 and SeuratObject 5.0.1 ☹️

See https://github.com/satijalab/seurat/issues/8916#issuecomment-2164844005